McShan lab @ Georgia Tech
Mechanisms of classical peptide antigen selection and presentation.
Classical major histocompatibility complex class I (MHC-I) and class II (MHC-II) proteins present self and foreign peptide antigens on the surface of cells to cytotoxic T cells to mediate immune responses in pathogen infection, cancer, and autoimmune disease. One thrust of our research group is to identify MHC-I and MHC-II presented peptide antigens critical for disease, and determine function and atomic structures of the resulting peptide/MHC complexes. We currently study Malaria - a neglected tropical disease known to be mitigated by MHC proteins in humans (HLA or Human Leukocyte Antigen). Over 600,000 people die from Malaria annually worldwide. There is an urgent need to better understand the immunology of Malaria infection and to identify immunogenic Malarial antigens to aid in the development of life-saving treatments and vaccines. Malaria is caused by the Plasmodium parasite, which is transmitted through the bite of a mosquito. We are using computational biology and structural biology approaches to understand the structure and function of peptide/HLA complexes in the context of Plasmodium infection.
Mechanisms of lipid antigen selection and presentation.
Pioneering studies have provided the motivation to understand how lipids and other antigen types are selected by CD1 from the cellular ligandome. One aspect of selection can be attributed to the identity of amino acid residues lining the pockets of the antigen binding groove of different CD1 isoforms, which impose chemical and geometric restrictions on lipid recognition. However, other cellular factors are equally important for antigen selection, such as immunological chaperones and lipid transfer proteins (LTPs). Prior to display at the cell surface, CD1 molecules are found in the endoplasmic reticulum (ER), Golgi apparatus, and endocytic compartments. CD1 molecules seem to have the ability to spontaneously bind lipids, although the efficiency of this process is unclear. There is also an open question in the field of whether immunological chaperones, such as the peptide loading complex (PLC) associated tapasin and PLC-independent TAPBPR, stabilize ligand-deficient (empty) CD1 to actively promote its assembly and lipid loading along the egress to the cell surface. Finally, a plethora of LTPs have been implicated in chaperoning and lipid loading on CD1 in various cellular compartments. Some identified LTPs include microsomal triglyceride transfer protein (MTP), GM2 ganglioside activator (GM2A), Niemann-Pick type C2 protein (NPC2), Fatty acid amide hydrolase (FAAH), and the Saposin family of proteins. There is also evidence that CD1e promotes lipid loading and exchange on other CD1 isoforms. However, the precise mechanisms by which these chaperones and LTPs stabilize and promote lipid loading/exchange on CD1 remains unknown. Discovery and structural biology of disease-associated lipid/CD1 complexes.
Hundreds of thousands of unique peptide sequences have been identified to interact with classical MHC-I complexes providing a treasure trove of putative antigens for vaccine and immunotherapy development. In contrast, only hundreds of antigens have been identified to associate with CD1 molecules. Thus, the first sub-aim of this project is to discover novel lipids, lipid-like molecules, lipopeptides, natural products, and small molecule antigens presented by different CD1 isoforms. We will apply complementary approaches for antigen discovery, such as in silico screening of virtual lipid, natural product, and small molecule libraries, in vitro screening of lipid extracts from diseased cells against recombinant CD1 molecules, and in situ screening of lipids eluted directly from CD1 expressing cells using mass spectrometry. Following identification of ligands, we will probe their biological function and usefulness as drug targets by characterizing their T cell activation properties. The identification of new CD1 antigens will contribute to a broader understanding of the antigen repertoire presented CD1 during both steady and disease states of cells, further define the molecular rules for antigen recognition by CD1, and provide new targets for CD1-mediated therapeutics. De novo protein design.
De novo protein design describes the generation of proteins with amino acid sequences unrelated to those in observed nature. We are now able to generate novel proteins by applying fundamental knowledge of first principles of biophysical and biochemical interactions and protein folding. One major thrust of our lab is to design and engineer new proteins with computers, using software like Rosetta and AlphaFold, that fold into desired shapes or have certain activity. We then make these hypothetical proteins in the lab for the first time and characterize whether they have the expected structure and function. We are broadly interested in applying de novo protein design towards developing new classes of inhibitors to target known biomolecular interactions critical for disease.
Andrew McShan, Ph.D. Miriam Simma Ruoqing Jia Zoey Yang Lizzie Corbin Jiemin (Clary) Fu Uri Miles Prashanth Rathakrishnan Klara Choi Claire Tharp Marielle Frooman Aashi Inani Tori Daniels Cara Dougan Morgan Zitsch Avani Nagireddy Shreyas Gupta Scripts, software, and webservers developed by our lab. Here are fun resources we've compiled over the years. A lot of it focuses on how science, math, and art can integrate together to elucidate the beauty of nature. We hope you find something that sparks your interest.
At a minimum the McShan lab pledges to: Educate ourselves about justice and systemic discrimination against marginalized communities. Listen to and uplift voices from these communities even when they challenge our assumptions and make us uncomfortable. Speak out and push for change when we see microaggressions or institutional policies that disadvantage these communities, both within our lab and within the larger Georgia Tech community. Make space and time for trainees to heal, take care of their communities, fight for justice, and provide financial, career, and other support while they do so. Donate whenever possible to organizations that promote the success and well-being of marginalized communities in STEM or in the larger community. Examples include (but are not limited to): Fellowship for the Future by 500 Women Scientists Society for Advancement of Chicanos/Hispanics and Native Americans in Science We are extremely grateful to the following funding institutions and agencies: We love to hear from anyone who is interested in our research. Previous experience in biochemistry is beneficial, but not required. All levels of experience are welcome! The McShan lab is physically located in the Molecular Sciences and Engineering ("MoSE") building on the Georgia Institute of Technology campus in Atlanta, Georgia.Structural Biochemistry, Immunological Antigens, Lipid Transfer Proteins, Protein Design
home.
Welcome to the McShan Lab at Georgia Tech!
Research in our lab has a wide scope and includes:
- Structural Biochemistry: We determine atomic structure and functions of biomolecules with biological relevance and therapeutic potential.
- Immunological antigens: We identify and characterize antigens (peptides, small molecules, lipids) involved in adaptive and innate immune responses. In particular, we focus on antigen presentation by the major histocompatibility complex family of proteins and their biomolecular interaction with cellular receptors, such as T cell receptors. We want to understand how antigens regulate immune responses, and also to harness the intrinsic features of antigens for therapeutics.
- Lipid Transfer Proteins: We study the structure and function of lipid transfer proteins to elucidate their role in lipid trafficking/homeostasis, lipid antigen presentation, and rare lipid storage disorders.
- De novo protein design: We design new proteins that don't exist in nature to interact with specific therapeutic targets or to have interesting activity/structures.
We are not focused on any particular approach or technique, although we are particularly fond of solution nuclear magnetic resonance (NMR) spectroscopy. We strive to solve outstanding biological questions with relevance to immunology, medicine, and pathology. Trainees joining our lab will gain hands on experience in biochemical/biophysical characterization of protein-protein and lipid-protein interactions (surface plasmon resonance, isothermal titration calorimetry, hydrogen/deuterium exchange mass spectroscopy), structural biology (solution NMR, X-ray crystallography, cryo-electron microscopy), computational biology (Rosetta modeling, molecular dynamics simulations), protein design/engineering, chemical biology, and immunological assays.
Illustration by Dr. McShan depicting our mascot Buzz cheering on an NMR spectrometer.
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social media.
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research.
We focus on the CD1 family of major histocompatibility complex class I (MHC-I) related proteins, which present both self and foreign lipids to αβ, γδ, and natural killer T cells. Examples of CD1 complexes involved in the adaptive and innate immune response to human disease include those associated with lipids derived from cancerous cells (Leukemia, Carcinoma, Lymphoma, Melanoma), wasp/bee venom including yellowjackets of the genus Vespula who represent Georgia Tech's mascot Buzz (Hymenoptera venom allergy), bacterial pathogens (Mycobacterium tuberculosis - Tuberculosis, Borrelia burgdorferi - Lyme Disease, Pseudomonas aeruginosa - Pneumonia), viral pathogens (HSV-1 - Herpes, HBV - Hepatitis B), marine sponges, and self cells in autoimmune disease (Dermatitis, Psoriasis, Lysosomal Storage Disease). Recent studies have shown that CD1 can also associate with and present a much broader range of antigens, such as skin oils that lack a discernible hydrophilic head group, lipopeptides, and non-lipid small molecules. Unlike peptide antigen presentation by high polymorphic human MHC-I complexes for which therapeutics must be tailored to a patients genetic background, the non-polymorphic nature of CD1 means that lipid/CD1 molecules are attractive candidates for donor-unrestricted (i.e. universal and patient-haplotype independent) vaccines and immunotherapy treatments. Progress in the development of lipid/CD1 mediated therapies has been hindered by an incomplete understanding in several important features of the CD1 antigen processing and presentation pathway as well as a lack of structural information for clinically relevant lipid/CD1 complexes. We aim to address these knowledge gaps with our research.
Our goals are to i. understand how lipid antigens are selected and loaded onto CD1 molecules in various cellular compartments, ii. solve macromolecular structures of CD1 complexes with different disease-associated lipids antigens, iii. characterize how T cell receptors engage lipid/CD1 molecules towards activation of the immune response, iv. design lipid-based sensors of disease, and v. engineer T cell receptors (TCRs) and chimeric antigen receptors (CARs) with enhanced affinity and specificity for lipid/CD1 complexes to eliminate diseased cells. With structure, function, and design principles in hand, we become uniquely situated to develop novel immunotherapies targeting lipids associated with tumor cells, pathogen infected cells, or autoreactive cells.
The video below is a great introduction into how antigen presentation can be exploited for immunotherapy. While it focuses on classical peptide/MHC-I molecules, the approach directly translates to lipid/CD1 complexes. Credit to Dr. Samir Khleif of the Georgetown Lombardi Comprehensive Cancer Center.
The primary bottleneck to understanding antigen selection and loading on CD1 is the complete lack of structural information for chaperone or LTP interaction with CD1. Thus, the aim of this research project is to decipher the molecular mechanisms by which immunological chaperones and LTPs contribute to lipid antigen selection, loading and exchange on CD1. We will apply our expertise to provide structural and functional insights into these important interactions. Our studies will also expand upon the role of lipid antigens in human health as deficiencies in many LTPs result in lipid storage diseases (MTP - Abetalipoproteinemia, GM2A - GM2-gangliosidosis aka Tay-Sachs and Sandhoff disease, NPC2 - Niemann-Pick disease, FAAH - Fatty acid hydroxylase-associated neurodegeneration, Saposins - Metachromatic leukodystrophy and Gaucher disease).
Discovery of antigens is an essential and important first step. The second sub-aim of this project is to use complementary structural biology techniques, such as cryo-EM, X-ray crystallography, and solution NMR, towards determining macromolecular structures of antigen/CD1 complexes. Our solved structures will allow us to characterize in detail the molecular interactions between antigens and the CD1 groove. Our structures will also illuminate which surface(s) of the antigen are presented to TCRs and natural killer cell immunoglobulin-like receptors (KIRs). The black and white image on the right side of the page is an example structure of the lipid/CD1 antigen binding groove (PDB ID 1UQS), where the bacterial glycolipid is represented as spheres and CD1 is shown as a cartoon.
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team.
Principal Investigator
Assistant Professor
School of Chemistry and Biochemistry
Molecular Sciences and Engineering Building (MoSE)
Georgia Institute of Technology
E-mail: andrew.mcshan@chemistry.gatech.edu
Office location: MoSE G022
Office Phone #: (404) 385-6052
Pronouns: They/them
Andrew is queer, non-binary structural biologist and immunologist. They joined the faculty at Georgia Tech as an Assistant Professor in the School of Chemistry and Biochemistry in Summer 2022. They are featured on 500 queer scientists. Previously, they were a postdoctoral fellow in the lab of Dr. Nikolaos Sgourakis at the Children's Hospital of Philadelphia & The University of Pennsylvania (2020-2022) studying antigen presentation of classical peptide/MHC-I molecules. Before that, they were also with Dr. Sgourakis at the University of California, Santa Cruz (2016-2020). They also worked as a biotechnology intern in the lab of Y. John Wang at Genentech (2015). They obtained their Ph.D. in Molecular, Cellular & Developmental Biology at the University of Kansas in the lab of Dr. Roberto De Guzman (2011-2016) studying bacterial type III section systems. They carried out undergraduate research in epigenetics (also at KU) in the lab of Dr. Justin Blumenstiel.
You may find Dr. McShan at:
Twitter
LinkedIn
Google Scholar
In their spare time they love to partake in spontaneous adventures, make curated Spotify playlists, and create music under the moniker Emo Side Project.
Graduate Students
Pronouns: She/her
Ph.D. student, Chemistry and Biochemistry
I am from Dacula, GA and did my undergraduate degree at Oglethorpe University in Chemistry with research in the Walden lab. My research in the McShan lab involves understanding how proteins associate with lipids towards their role in immunological signaling and rare lipid storage disorders. In my free time I like lifting weights, traveling, going to Hogwarts, and eating good food.
Pronouns: She/her
Ph.D. student, Chemistry and Biochemistry
I completed my undergraduate study in Nutritional Science and Chemistry at Pennsylvania State University and come to continue my education here at the Georgia Institute of Technology. My research in McShan Lab focuses on studying different lipid transfer proteins towards solving their atomic structures and mechanisms of action. Outside the lab, I am a big Disney fan. I have a Little Mermaid tattoo! I have been to all of the Disney parks around the world. So far, I think DisneyWorld is the best.
Pronouns: She/her
Ph.D. student, Bioinformatics
I completed my undergrad in pharmacy at Taipei Medical University in Taiwan and pursued my Master's in computational biology at Carnegie Mellon University. My research in the McShan lab involves developing and applying computational biology methods to understand protein/protein and lipid/protein interactions, and to design new protein therapeutics. Outside of the lab, I enjoy music, surfing, scuba diving, traveling, and playing with cute animals.
Pronouns: She/her
Ph.D. student, Chemistry and Biochemistry
I am from Orlando, FL and completed my Bachelor's in biological sciences at Florida State University. Recently, I completed my Master's in biology here at Georgia Tech. In the McShan lab, I am using structural biology to answer fundamental questions about the adaptive and innate immune systems and towards discovery of novel antigens. Outside of lab, I enjoy sports, Disney World, and adventuring around Georgia.
Pronouns: She/her
Ph.D. student, Material Science and Engineering
I completed my undergraduate study in Polymer Science and Engineering at Sichuan University in China and pursued Master’s in Material Science and Engineering at University of Pennsylvania. Now I am a Ph.D. student in Valeria Milam's lab at Georgia Tech (School of Materials Science and Engineering) where I am co-advised by Dr. McShan. I am engineering carbohydrate-modified nucleic acid aptamers that will serve as therapeutic modulators of biomolecular targets. I am also applying biochemistry, biophysics, and structural biology to characterze aptamer/protein complexes. Outside the lab, I enjoy playing the piano, reading books, watching movies, and traveling.
Pronouns: He/him
Ph.D. student, Chemistry and Biochemistry
I completed my undergraduate study in Chemistry at Ariel University in Israel in the lab of Flavio Grynszpan. Now I am a Ph.D. student in "the one and only" MG Finn's lab at Georgia Tech (School of Chemistry and Biochemistry) where I am co-advised by Dr. McShan. I am using a combination of organic synthesis, biophysical assays, and structural biology to define mechanisms underpinning cancer lipid immunology. Outside the lab, I enjoy rock climbing and listening to ambient music.
Undergraduates
Pronouns: He/him
Undergraduate student, Biology major
I am from Duluth, GA. I am interested in the biology of the immune system at the molecular level. In the McShan lab, my research involves characterizing antigen repertoires of CD1 immunoreceptors using computational biology approaches. Outside of the lab, I love to volunteer at healthcare facilities, explore the city, and listen to music.
Pronouns: She/her
Undergraduate student, Biology major
I am from Alpharetta, GA. In the McShan lab, my research involves characterizing immune responses to Malaria using structural biology methods. Outside of the lab and school, I enjoy reading books, spending time in animal shelters, and volunteering with mobile health clinics.
Pronouns: She/her
Undergraduate student, Biochemistry major
I am from Decatur, GA. In the McShan lab, my research involves examining how certain proteins associate with lipids in relation to their role in immunological signaling. Outside of the lab, I enjoy reading, volunteering in animal shelters, and bingeing TV shows.
Pronouns: She/her
Undergraduate student, Biochemistry major
I am from right here in Atlanta! Before coming to Tech, I performed a yearlong study on the teratogenic effects of chronic gestational caffeine exposure. Now, in the McShan lab, I am using structural biology to better understand immune responses to malaria. Outside of the lab, you’ll usually find me walking around campus shamelessly playing Pokémon go.
Pronouns: She/her
Undergraduate student, Biochemistry major
I am from Suwanee, GA! In the McShan Lab, my research involves protein design and characterization to inhibit microbe pathogens. Outside of lab, I enjoy traveling, going to concerts, and binge-watching TV shows.
Pronouns: She/her
Undergraduate student, Neuroscience major, Chem/Biochem Minor
In the McShan lab, I'm researching proteins involved in epilepsy and their potential as a therapeutic target. In the future, I hope to study the glymphatic system or uterine health while pursuing a career in medicine. Outside of the lab, I volunteer at the Children's Hospital and play in the Yellow Jacket Marching Band. Through music organizations at Tech, I've been able to create events that highlight our musicians and support our students. I created "Jazz Dessert," which promoted our Jazz ensembles, brought back alumni, and fundraised scholarships for our music organizations. Although having leadership in two music organizations takes a lot of my time, I love binging shows, playing games, and being pulled into interesting side quests.
Pronouns: She/her
Undergraduate student, Biochemistry major
I am from Covington, GA. In the McShan Lab, my research involves the characterization of de novo designed proteins. Outside of the lab I enjoy trying new restaurants and going out with friends.
Pronouns: She/her
Undergraduate student, Biochemistry major
I am from Marietta, GA. In the McShan lab, I study the interaction between de novo proteins and their targets. Outside the lab, I enjoy baking, volunteering with medical clinics, and exploring national parks.
Pronouns: She/her
Undergraduate student, Biomedical Engineering major
I'm from Chesterfield, New Jersey. In the lab, I am involved with characterizing the interactions of de novo designed proteins with their molecular target to validate computational binding modes. Outside of the lab, I enjoy reading, travelling, and binge-watching TV shows.
Pronouns: He/him
Undergraduate student, Biology major
I am from Marietta, GA. In the McShan Lab, my research focuses on evaluating the performance of physics-based and machine learning-based docking and structure prediction tools in modeling lipid/protein interactions. In my free time, you’ll likely find me enjoying Taco Bell or cheering on the Atlanta Falcons.
Previous Members / Alumni
Shreyaa Srinivasan, Master's student (Biomedical Engineering), Spring 2023–Spring 2024
Ji Yoon Jung, Master's student (Biomedical Engineering), Spring 2023–Spring 2024
Maya Z. Kahn, Undergraduate Student (Biochemistry major), Fall 2022–Spring 2024
Aubrielle Cunningham, REU Student from Savannah State University (Forensic Science major), Summer 2023
Jenna RisCassi, Undergraduate Student (Chemistry major), Spring 2023
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publications.
See below for a full list of our peer reviewed publications:
McShan Lab Publications @ Google Scholar
‡ These authors contributed equally to this work
* Corresponding author
# Co-corresponding authors
Bold = McShan lab member
Publications while at the Georgia Institute of Technology
33. Zhong W, Olugbami J, Rathakrishnan P, Mohanty I, Moore SG, Garg N, Oyelere AK, Turner T, McShan AC#, Agarwal V#. Discovery and folding dynamics of a fused bicyclic cysteine knot undecapeptide from the marine sponge Halichondria bowerbanki. The Journal of Organic Chemistry, 89, 17, 12748–12752, 2024
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32. Lisanza SL‡, Gershon JM‡, Tipps SWK‡, Sims JN‡, Arnoldt L‡, Hendel SJ, Simma MK, Liu G, Yase M, Wu H, Tharp CD, Li X, Kang A, Brackenbrough E, Bera AK, Gerben S, Wittman BJ, McShan AC, Baker D*. Multistate and functional protein design using RoseTTAFold sequence space diffusion. In press at Nature Biotechnology, 2024
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31. Srinivasan S, Zhu C, McShan AC*. Structure, Function, and Immunomodulation of the CD8 Co-Receptor. Frontiers in Immunology, 15:1412513, 2024
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30. Agarwal V#, McShan AC#. The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins. Nature Chemical Biology, 20, 950–959, 2024
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29. Robang AS, Roy A, Dodd-o J, He D, Le JV, McShan AC, Hu Y, Kumar VA, Paravastu AK*. Structural consequences of introducing bioactive domains to designer β-sheet peptide self-assemblies. Biomacromolecules (Special Issue - Peptide Materials), 25, 3, 1429–1438, 2024
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28. Nguyen NA‡, Vidya FNU‡, Yennawar NH, Wu H, McShan AC#, Agarwal V#. Disordered regions in proteusin peptides guide post-translational modification by a flavin-dependent RiPP brominase. Nature Communications, 15, 1265, 2024
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27. Dodd-o J‡, Roy A‡, Siddiqui Z, Jafari R, Coppola F, Ramasamy S, Kolloli A, Kumar D, Kaundal S, Zhao B, Kumar R, Robang AS, Li J, Azizogli AR, Pai V, Acevedo-Jake A, Heffernan C, Lucas A, McShan AC, Paravastu AK, Prasad BVV, Subbian S, Král P#, Kumar V#. Antiviral fibrils of self-assembled peptides with tunable compositions. Nature Communications, 15(1):1142, 2024
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26. Satalkar V, Degaga GD, Li W, Pang YT, McShan AC, Gumbart JC, Mitchell JC#, Torres MP#. Generative β-Hairpin Design Using a Residue-Based Physicochemical Property Landscape. Biophysical Journal (Special Issue - Machine Learning in Biophysics), S0006-3495(24)00070-5, 2024
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25. Rathakrishnan P, McShan AC*. In silico identification and characterization of small molecule presentation by the CD1d immunoreceptor. Journal of Biomolecular Structure and Dynamics, 2023
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24. McShan AC‡, Flores-Solis D‡, Sun Y, Garfinkle SE, Toor JS, Young MC, Sgourakis NG*. Conformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition. Nature Communications, 14, 8204, 2023
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23. Stewart J‡, Shawon J‡, Ali MA, Williams B, Shahinuzzaman ADA, Rupa SA, Al-Adhami T, Jia R, Bourque C, Faddis R, Stone K, Sufian MA, Islam R, McShan AC, Rahman KM, Halim MA*. Antiviral Peptides Inhibiting the Main Protease of SARS-CoV-2 Investigated by Computational Screening and In-Vitro Protease Assay. Journal of Peptide Science, e3553, 2023
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22. Zhong W‡, Deutsch JM‡, Yi D, Abrahamse NH, Mohanty I, Moore SG, McShan AC, Garg N, Agarwal V*. Discovery and biosynthesis of ureidopeptide natural products macrocyclized via indole N-acylation produced by marine Microbulbifer spp. bacteria. ChemBioChem e202300190, 2023
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21. McShan AC*. Utility of methyl side chain probes for solution NMR studies of large proteins. Journal of Magnetic Resonance Open 14–15, 100087, 2023
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Publications while at the Children's Hospital of Philadelphia / University of Pennsylvania (Sgourakis lab)
20. McShan AC, Devlin CA, Papadaki GF, Sun Y, Green AI, Morozov GI, Burslem GM, Procko E, Sgourakis NG*. TAPBPR employs a ligand-independent docking mechanism to chaperone MR1 molecules. Nature Chemical Biology 18, 859–868, 2022
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19. McShan AC‡, Devlin CA‡, Morozov GI, Overall SA, Moschidi D, Akella N, Procko E#, Sgourakis NG#. TAPBPR Promotes Loading of Cargo on MHC-I Molecules Using a Peptide Trap. Nature Communications 12, 3174, 2021
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18. Nerli S‡, De Paula VS‡, McShan AC, Sgourakis NG*. Backbone-independent NMR resonance assignments of methyl probes in large proteins. Nature Communications 12, 691, 2021
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Publications while at the University of California, Santa Cruz (Sgourakis lab)
17. Koehler Leman J#, Weitzner BD#, Renfrew PD, Lewis, SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, RosettaCommons Consortium (including McShan AC), Bystroff C, Schief W, Gront D, Schueler-Furman O, Baker D, Bradley P, Roland Dunbrack R, Kortemme T, Leaver-Fay A, Strauss CE, Meiler J, Kuhlman B, Gray JJ, and Bonneau R#. Better together: Elements of successful scientific software development in a distributed collaborative community. PLOS Computational Biology 16(5):e1007507, 2020
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16. Wei KY, Moschidi D, Bick MJ, Nerli S, McShan AC, Carter LP, Huang PS, Fletcher DA, Sgourakis NG, Boyken SE, Baker D*. Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. PNAS 117(13):7208-7215, 2020
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15. Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DA, Baker D*. De novo design of a homo-trimeric amantadine-binding protein. eLife 8. pii: e47839, 2019
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14. McShan AC‡, Devlin CA‡, Overall SA, Park J, Toor JS, Moschidi D, Flores-Solis D, Choi H, Tripathi S, Procko E#, Sgourakis NG#. Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection. PNAS 116(51):25602-25613, 2019
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13. Marceau AH‡, Brison C‡, Nerli S‡, Arsenault HE, McShan AC, Chen E, Lee HW, Benanti JA, Sgourakis NG, Rubin SM*. An order-to-disorder structural switch activates the FoxM1 transcription factor. eLife 8. pii: e46131, 2019
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12. Marcos E, Chidyausiku TM, McShan AC, Evangelidis T, Nerli S, Carter L, Nivon LG, Davis A, Oberdorfer G, Tripsianes K, Sgourakis NG, Baker D*. De novo design of a non-local β-sheet protein with high stability and accuracy. Nature Structural and Molecular Biology 25(11):1028-1034, 2018
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11. McShan AC, Natarajan K, Kumirov VK, Flores-Solis D, Jiang J, Badstubner M, Toor JS, Bagshaw CR, Kovrigin EL, Margulies DH, Sgourakis NG*. Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle. Nature Chemical Biology 14(8):811-820, 2018
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10. Natarajan K, Jiang J, May NA, Mage MG, Boyd LF, McShan AC, Sgourakis NG, Bax A, Margulies DH*. The Role of Molecular Flexibility in Antigen Presentation and T Cell Receptor-Mediated Signaling. Frontiers in Immunology 9:1657, 2018
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9. Nerli S, McShan AC, Sgourakis NG*. Chemical shift-based methods in NMR structure determination. Progress in Nuclear Magnetic Resonance Spectroscopy 106-107, 2018
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8. Toor JS, Rao AA, McShan AC, Yarmarkovich M, Nerli S, Yamaguchi K, Madejska AA, Nguyen S, Tripathi S, Maris JM, Salama SR, Haussler D, Sgourakis NG*. A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations. Frontiers in Immunology 9:99, 2018
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7. Natarajan K, McShan AC, Jiang J, Kumirov VK, Wang R, Zhao H, Schuck P, Tilahun ME, Boyd LF, Ying J, Bax A, Margulies DH, Sgourakis NG*. An allosteric site in the T-cell receptor Cβ domain plays a critical signalling role. Nature Communications 16;8:15260, 2017
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Publications while at Genentech (Wang lab)
6. McShan AC, Kei P, Ji JA, Kim DC, Wang YJ*. Hydrolysis of Polysorbate 20 and 80 by a Range of Carboxylester Hydrolases. PDA Journal of Pharmaceutical Science and Technology 70(4):332-45, 2016
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Publications while at the University of Kansas (De Guzman lab)
5. McShan AC, Kaur K, Chatterjee S, Knight KM, De Guzman RN*. NMR Identification of the Binding Surfaces Involved in the Salmonella and Shigella Type III Secretion Tip-Translocon Protein-Protein Interactions. Proteins 84, 1097-1107, 2016
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4. McShan AC, Anbanandam A, Patnaik S, De Guzman RN*. Characterization of the Binding of Hydroxyindole, Indoleacetic acid and Morpholinoaniline to the Salmonella Type III Secretion System Proteins SipD and SipB. ChemMedChem 11, 963-971, 2016
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3. McShan AC, De Guzman RN*. The bacterial type III secretion system as a target for developing new antibiotics. Chemical Biology and Drug Design 85(1):30-42, 2015
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2. Rathinavelan T, Lara-Tejero M, Lefebre M, Chatterjee S, McShan AC, Guo DC, Tang C, Galan JE, De Guzman RN*. NMR model of PrgI-SipD interaction and its implications in the needle-tip assembly of the Salmonella type III secretion system. Journal of Molecular Biology 12;426(16):2958-69, 2014
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1. Chatterjee S, Chaudhury S, McShan AC, Kaur K, De Guzman RN*. Structure and biophysics of type III secretion in bacteria. Biochemistry, 52(15):2508-17, 2013
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structure gallery.
Below is a gallery of structures solved by our lab, either independently or through collaborative efforts with other labs. We love to solve macromolecular structures because they inform scientists of biological function, provide important insights into disease, and open new avenues for drug development.
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De novo designed protein MS3 - PDB ID 8VL4
Collaboration with Baker lab (UW)
Function: De novo designed protein
De novo designed protein MS2 - PDB ID 8VL3
Collaboration with Baker lab (UW)
Function: De novo designed protein
Solution NMR structure of halichondamide A, a fused bicyclic cysteine knot undecapeptide from the marine sponge Halichondria bowerbanki - PDB ID 9BHN
Solved in collaboration with Agarwal lab (GaTech)
Function: Natural products
Solution NMR structure of a RiPP proteusin precursor protein - PDB ID 8TB1
Solved in collaboration with Agarwal lab (GaTech)
Function: Natural products
De novo designed β-hairpin peptides - PDB ID 8TXS
Solved in collaboration with Torres lab (GaTech)
Function: De novo designed peptides
De novo designed β-hairpin peptides - PDB ID 8T61
Solved in collaboration with Torres lab (GaTech)
Function: De novo designed peptides
De novo designed β-hairpin peptides - PDB ID 8T62
Solved in collaboration with Torres lab (GaTech)
Function: De novo designed peptides
De novo designed β-hairpin peptides - PDB ID 8T63
Solved in collaboration with Torres lab (GaTech)
Function: De novo designed peptides
Temporin L in absence of SDS - PDB ID 8TV4
Solved in collaboration with Halim lab (Kennesaw State University)
Function: Candidate SARS-CoV-2 Mpro inhibitor
Ac-6-FP/MR1/TAPBPR structure - PDB ID 7RNO
Solved while in the Sgourakis lab (UPENN/CHOP)
Function: Metabolite antigen presentation
NRASQ61K/HLA-A*01:01 structure - PDB ID 6MPP
Solved in the Sgourakis Lab together with David Flores-Solis (UC Santa Cruz)
Function: Neoepitope antigen presentation in neuroblastoma
De novo designed protein XAA - PDB ID 6O0I
Solved in the Sgourakis lab together with Danai Moschidi and Santrupti Nerli (UC Santa Cruz)
Collaboration with Kathy Wei in the Baker lab (UW)
Function: De novo designed protein
Disulfide linked P18-I10/H2-Dd - PDB ID 6NPR
Solved in the Sgourakis lab together with Joey Toor and Sarvind Tripathi (UC Santa Cruz)
Function: Peptide antigen presentation
FoxM1 transcription factor - PDB ID 6OSW
Solved in the Sgourakis Lab together with Santrupti Nerli (UC Santa Cruz)
Collaboration with Aimee Marceau in the Rubin lab (UC Santa Cruz)
Function: Cancer associated transcription factor
De novo designed double-stranded beta-helix - PDB ID 6E5C
Solved in the Sgourakis Lab together with Santrupti Nerli (UC Santa Cruz)
Collaboration with Enrique Marcos in the Baker lab (UW)
and Thomas Evangelidis in the Tripsianes lab (CEITEC)
Function: De novo designed protein
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resources.
BioDolphin
Biological Database of Lipid-Protein Highly Inclusive Interactions
webserver link
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learn.
Below are resources to learn about macromolecule structures and the experimental techniques commonly used by our lab.
I am also providing other learning resources useful to researchers in STEM fields.
*The CD1 family: serving lipid antigens to T cells since the Mesozoic era introduction to CD1
* 5 challenges we could solve by designing new proteins by David Baker
* AlphaFold: The making of a scientific breakthrough
*iBiology interesting and state-of-the-art science lectures
*Ask a Scientist Gaming hosted by Kenneth Hanson where video games and science collide
*ICMBRS Webinars biomolecular NMR lectures
*Protein Folding and Dynamics Webinars lectures on protein folding and dynamics
*Global NMR Discussion Meetings biomolecular NMR lectures
*Getting Started in Cryo-EM tutorial by Grant Jensen
*Basics of Macromolecular Crystallography by Andrea Thorn
*Learn Rosetta computational biomolecular modeling tutorials
*Walter Bauer nmr spectroscopy meets music
*Frank Delaglio lecture on nmr processing in nmrpipe
*The Science of Mentorship Podcast introduction to inclusive, equity minded mentoring in STEM
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teaching/mentoring.
Dr. McShan's Lectures, Presentations, and Mentoring Material
Dr. McShan's Frequently Asked Questions (FAQs) for Joining a Lab for Master’s and Ph.D. students:
GaTech SoCB FAQs Document
Dr. McShan's ABCs of Amazing Proteins
A children's book about the structure and function of some cool proteins.
Women+ in Chemistry Spring 2023 Retreat Lecture slides:
"Research Based Lessons for Effective Mentor/Mentee Relationships in STEM"
Teaching at Georgia Tech
Fall 2024 - CHEM 8853 - Practical Biomolecular NMR Spectroscopy
Syllabus Fall 2024
Spring 2024 - CHEM 6501 - Biochemistry I
Syllabus Spring 2024
Fall 2023 - CHEM 3521/CHEM 6501 - Biochemistry I
Syllabus Fall 2023
Fall 2022 - CHEM 6501 - Biochemistry I
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outreach.
Molecular Detectives: Is My Honey Pure?
As part of the Atlanta Science Festival, the Georgia Tech NMR center opened up its doors for a public demo of how NMR spectroscopy can be used to detect honey adulteration
Summary and Protocol
Molecular Detectives: Using Magnetic Resonance Imaging for Fruits and Veggies
As part of the Atlanta Science Festival, the Georgia Tech MRI center opened up its doors for a public demo of how MRI can be used in research of fruits and veggies, and beyond
View Poster Presentation
Crystallizing Lysozyme
Queer Science holds a hands on demonstration where Atlanta area high school students learn about protein crystallography, and form their own protein crystals!
Read Protocol
Acid-Base Chemistry: Making a rainbow out of buffers and pH indicators
Queer Science holds a hands on demonstration where Atlanta area high school students learn about acid/base chemistry and learn how to make a rainbow from buffers using pH indicators
Read Protocol
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fun.
numbers:
*3D-XplorMath. open source software for topological surface visualization
virtual math museum gallery of shapes and surfaces made using 3D-XplorMath
*46 billion pixel panorama image of the Milk Way galaxy astronomy
a:
*acapellascience science, music
*Susan Aldworth website science based art, illustration, etching, mixed media
*Rafael Araujo website math based art, illustration, landscapes
*art for science science journal and book illustrations
*The Aquabats! - Doing Science! science, music
b:
*BALLView website biomolecular visualization software
*Michele Banks website science based art, biology, watercolor, collage
*Tom Beddard website math based art, fractals, 3D
*Drew Berry Bjork - Hollow 3d biology animation for a Bjork video
*Luc Benard collaboration with Richard Palais
*Bill Nye The Science Guy - Every Measurement You Take science, music
*Biologic Models science, 3D printing, proteins
*BioBlender open source software for 3D rendering with science applications
*Paul Bourke website math based art, simulations, etc.
*Caroline Bowen website math and physics based art
*Kelsey Brookes website science based art, biochemistry, pop, abstract, psychedelic
*Roger Brown website science based art, paper sculptures
c:
*Santiago Calatrava website science and math based architecture and engineering, ceramics, sculpture, drawings
*Jonathan Callan website using books and paper as a sculptural medium
*Alexander Calder website sculpture, abstract
Calder and abstraction: from avant-garde to iconic
*Joey Camacho website science based art, 3D motion and graphic design
*Camila Sitarama Carlow website science based art, nature, mixed media
*George F. Chambers list of books as pdf vintage astronomy illustrations
*Julie Alice Chappell website science based art
*Chemistry in pictures website science, photography
*William Chyr website science based art, sculpture, balloons
*Andreas Cellarius some of his works vintage astronomy illustrations, cartography
check out Harmonia Macrocosmica
*Chemical Bouillon website science based art, chemical reactions, video, patterns and abstract shapes
*Dale Chihuly website abstract, glass work
*Caleb Charland website abstract
*Anita Chowdry website math based art, paper sculptures, abstract, etching, geometry
*Francesco de Comite website math based art, geometry, 3D printing
flickr
*Jean Constant website math based art, topology
*Justine Cooper website science based art
*Crystal Proteins science, 3D glass etchings, proteins
*Pedro Cruz website science based art, creative coding, generative art
d:
*Erik Demaine website math based art, geometry, origami
*Maja Divjak vimeo science based art, molecular movies, 3D
*DNA: The Secret of Photo 51 science, DNA, documentary
Thomas Dolby - She Blinded Me With Science science, music
*Katharine Dowsen website science based art, sculpture, glass work
*Greg Dunn website science based art, neuroscience, etching, scrolls
e:
*James R. Eads website abstract, illustration
*Maria Clara Eimmart some examples vintage astronomy illustrations
*Francisco Enguita behance science based art, proteins
*Olafur Eliasson website sculpture, light/color
*M.C. Escher website math based art, abstract, multimedia
*Engineering at Cambridge University flickr science based art and photography, check out their photography competitions
*EteRNA RNA folding game, software
f:
*Sarah Featon website scientific illustration, botany
*Fold It! biochemistry and protein folding game, software
*Anatoly Fomenko website math based art, abstract
*Lucio Fontana artsy abstract, painting, graphic design
*R. Buckminster Fuller artsy architecture, geometry, engineering
g:
*Fred Gambino website science fiction, concept design, animation
*Eleanor Gates-Stuart website science based art
*Giant Microbes science based art, plush microbes
*Steve Gildea website science based art, space art, painting, drawing, 3D
*Linden Gledhill website science based art, abstract
*Andy Goldsworthy visual melt science based art, nature, symmetry
*David Goodsell website science based art, biology illustrations, proteins and organisms
*Akinori Goto tumblr media art
*Bathsheba Grossman website science based art, sculpture, laser crystals, glass work
h:
*Ernst Haeckel art forms in nature vintage biology illustrations
*Bradford Hansen-Smith website math based art, sculpture, paper sculpture
*George W. Hart website math based art, sculpture, design
*Stuart Haygarth website math based art, sculpture, abstract
*HEBOCON HEBOCON: The Robot Contest for Dummies engineering
*Patrik Huebner website math based art, creative coding, generative design
*Jonty Hurwitz website science and math based art, abstract, nanosculptures
i:
*Iconographic Encyclopedia of Science, Literature and Art vintage science illustrations
*Illustrated Atom science based art
* The Institute For Figuring website creative engagements with topology, physics, computation and biology
crochet coral reef crochet, marine biology
*Interactions Image Bank website image databank of physics stuff. particle collision images are particularly beautiful.
*Ig Nobel Prize abstract and interesting research
j:
*Wenzel Jamnitzer BibliOdyssey vintage math based art, symmetry, etching
*Christopher Janney website math based art, architecture, sound
*Luke Jerram website science based art, biology, glass work, multimedia
*Brian Johnston views through a mathematical microscope of some 3D oddities
*Janusz Jurek website math based art, illustration, sculpture
behance
k:
*Markos R. Kay website science based art, 3d motion graphics, simulations, prints
check out aDiatomea
*Ikumi Kayama website science based art, illustration
*Alexey Kashpersky website science based art, digital art, 3D, photography
*Dinara Kasko website architectural, geometry, gastronomy
*Melanie Kathryn-King website science based art, illustration, photography
*Charles Knight website vintage biology art, dinosaurs
*Stephen R. Kutcher website science based art, art using insects, painting
*Martin Krzywinski website science based art, data visualization
l:
*Robert J. Lang website origami
*The Left Handed DNA Hall of Fame website science, DNA
*Kenneth Libbrecht website science based art
check out snow crystals
*Emma Lindstrom website painting
*Richard Long website math and science based art, nature, symmetry, sculpture, drawing
*Lorem Ipsum tumblr creative coding, generative art, abstract
*Marcus Lyon website design, photography
*The Lumen Prize website art generated by technology
*Eleanor Lutz website scientific illustration
m:
*Benoit Mandelbrot Mandelbrot set. fractals, geometry, math
*Making Music from Proteins science, proteins, music
*Friedrich Heinrich Wilhelm Martini shell prints vintage science illustration
*Oliver Marsden website math based art, abstract, painting, illustration, prints
*melodysheep Symphony of science science topic based music
check out a glorious dawn a tribute to carl sagan
*Nathalie Miebach website science art, abstract, music, sculpture
*Steve Miller website science based art, sculpture, painting
*Hine Mizushima website science based art, felt
*Anne Mondro website sculpture
* Molecular Nodes open source software for 3D visualization and rendering of proteins and molecules
n:
*NASA science
NASA project apollo archive space photography
astronomy picture of the day large library of space photography
*Neurobureau brain art gallery science based art, neuroscience
*Odra Noel Odra Noel science based art
*Nikon Small World in Motion youtube channel science based art, microscopy, photography
*Paul Nylander website math and physics based art
o:
*Nuala O'Donovan website math based art, sculpture, ceramics, abstract
*Fabian Oefner website science based art, paint, multimedia
*Neri Oxman website science based art, 3d printed fashion, sculpture
p:
*Pacific Northwest National Laboratory flickr check out their science as art section
*Kate Patterson youtube science based art, molecular movies, 3D
*J. C. Park website science fiction, concept, design
*Sui Park website sculpture
*The Particle Zoo website science based art, plush dolls of fundamental particles, particle physics
*PhD Comics website comics, humor for graduate students
*Picture A Scientist website science, film, documentary, gender inequality in STEM
*Princeton University art as science galleries
*Processing open source software for creative coding and generative art
open processing sharing of sketches and code made using Processing
*PyMol open source software for 3D visualization and rendering of proteins and molecules
*Helen Pynor website science based art, sculpture, illustration
q:
r:
*Sabine Reckewell website design, sculpture
*Ribosome dance Protein synthesis: an epic on the cellular level biochemistry
*Jane S. Richardson Biophysical Highlights from 54 Years of Macromolecular Crystallography science illustration, biochemistry (particularly beta-sheet containing proteins)
website
The Anatomy and Taxonomy of Protein Structures
*Michael Rigley website math and science based art, 3D, animation, design
*Bridget Riley gallery of her works math based art, op art
*Anthony Roussel website math based art, jewelry, digital art
s:
*Tomas Saraceno website math and science based art, architecture
*SASJ website creative coding, generative art, geometry, shapes, game design
*Science-Art databank of science based art, mostly nature and medical illustration
*Nina Sellars website science based art, 3D
*James B. Settles some of his works vintage science fiction illustrations
*Alyson Shotz website math based art, architecture, sculpture
*Oleg Soroko behance math based art, architecture, sculpture, abstract
*Susi Sie website science and math based videos, abstract
*JR Bee website science based illustration
*Claudia Stocker website science based art, illustration
*Nils Henrik Sundqvist website science based art, illustration, design, prints
t:
*P. G. Tait check out the 'On Knots' series vintage math illustrations, knot theory
*Jared Tarbell website science and math based art, creative coding, generative art, photography
flickr
*Steve Tobin website math based art, sculpture, abstract, glass work, steel work
*Anais Tondeur website science based art, space art, drawing
*Ray Troll website science based art
u:
*Julijonas Urbonas website engineering, math
*UCSF RBVI Holiday Card Gallery website biochemistry, holiday cards
v:
*Van Cleef & Arpels Midnight Planetarium timepiece astronomy, watch
*Roman Verostko website math based art, illustrations, generative art
*Arie van't Riet website science based art, photography, x-ray images
*Julian Voss-Andreae website sculpture
w:
*Elise Wagner website science based art, painting, wax, abstract
*WeatherStar 4000 simulator website meteorology, simulation
*Wintergatan Marble Machine engineering, music
x:
y:
*Motoi Yamamoto website media art, installation
z:
*Doug Zongker chicken chicken chicken lecture what watching an academic lecture feels like sometimes
what reading an academic paper feels like sometimes
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DEI values.
The McShan lab is committed to maintaining an inclusive research environment, regardless of age, gender, gender identity, sexual orientation, disability, race, religion, nationality, immigration status, or socio-economic background.
The poster and pledge have been derived from images and words by Sammy Katta.
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funding.
President's Undergraduate Research Award (PURA)
Graduate Assistance in Areas of National Need (GAANN)
Shurl and Kay Curci Foundation
Georgia Tech's School of Chemistry and Biochemistry - Start up funds
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join us.
We openly welcome members of the LGBTQAI+ community, women, disabled scientists (including those with invisible disabilities), and scientists of color.
Prospective graduate students should first apply to Georgia Tech's Chemistry and Biochemistry Graduate Program. You can apply here: Graduate Admission @ Georgia Tech's Chemistry and Biochemistry program. Accepted students should feel free to reach out and discuss opportunities in our lab.
Undergraduate students interested in getting hands on experience with research should also reach out to us at andrew.mcshan@chemistry.gatech.edu
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contact.
Please contact us via e-mail at andrew.mcshan@chemistry.gatech.edu
Office location: MoSE G022
Office Phone #: (404) 385-6052
Lab location: MoSE G125
901 Atlantic Drive NW
Atlanta, GA 30332-0400
Send USPS deliveries to:
Dr. Andrew McShan
901 Atlantic Drive NW
School of Chemistry and Biochemistry
Georgia Institute of Technology
Atlanta, GA 30332-0400
Send UPS and FedEx deliveries to:
Dr. Andrew McShan
311 Ferst Drive NW
School of Chemistry and Biochemistry
Georgia Institute of Technology
Atlanta, GA 30332-0400
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Georgia Institute of Technology
School of Chemistry & Biochemistry
Website design by Dr. McShan
