Graduates of the MBTG

Sulyman Barkho

Email: sb1899@gmail.com
Linkedin: https://www.linkedin.com/in/sbarkho/
Program: Chemistry & Biochemistry
Advisor: Patricia Jennings

Publications:

Barkho S, Pierce LC, Li S, Adams JA, Jennings PA (2015) .Theoretical Insights Reveal Novel Motions in Csk's SH3 Domain That Control Kinase Activation.PLoS One. 10(6):e0127724.     PMC4507846

Barkho S, Pierce LC, McGlone ML, Li S, Woods VL Jr, Walker RC, Adams JA, Jennings PA. (2013) Distal loop flexibility of a regulatory domain modulates dynamics and activity of C-terminal SRC kinase (csk). PLoS Comput Biol. 9(9):e1003188. PMC4452171

Hailey KL, Capraro DT, Barkho S, Jennings PA (2013) Allosteric switching of agonist/antagonist activity by a single point mutation in the interluekin-1 receptor antagonist, IL-1Ra.. J Mol Biol. 2013 425(13):2382-92. PMC4059520

Jeffrey Brodin

Email: jbrodin3@gmail.com
Linkedin: https://www.linkedin.com/in/jeffrey-brodin-00703784/
Program: Chemistry & Biochemistry
Advisor: Akif Tezcan

Publications:

Salgado EN, Ambroggio XI, Brodin JD, Lewis RA, Kuhlman B, Tezcan FA. (2010) Metal templated design of protein interfaces.Proc Natl Acad Sci U S A. 107(5):1827-32. PMC2836610

Brodin JD, Medina-Morales A, Ni T, Salgado EN, Ambroggio XI, Tezcan FA.(2010) Evolution of metal selectivity in templated protein interfaces. J Am Chem Soc. 132(25):8610-7. PMC2896502

Salgado EN, Brodin JD, To MM, Tezcan FA. (2011) Templated construction of a Zn-selective protein dimerization motif. Inorg Chem. 2011 Jul 4;50(13):6323-9.

Brodin JD, Ambroggio XI, Tang C, Parent KN, Baker TS, Tezcan FA. (2012) Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays. Nat Chem. 2012 4(5):375-82. PMC3335442

Medina-Morales A, Perez A, Brodin JD, Tezcan FA. (2013) In vitro and cellular self-assembly of a Zn-binding protein cryptand via templated disulfide bonds. J Am Chem Soc. 135(32):12013-22. PMC4289141

Brodin JD, Carr JR, Sontz PA, Tezcan FA. (2014) Exceptionally stable, redox-active supramolecular protein assemblies with emergent properties. Proc Natl Acad Sci U S A. 111(8):2897-902. PMC3939893

Brodin JD, Smith SJ, Carr JR, Tezcan FA. (2015) Designed, Helical Protein Nanotubes with Variable Diameters from a Single Building Block. J Am Chem Soc. 137(33):10468-71.

Churchfield LA, Medina-Morales A, Brodin JD, Perez A, Tezcan FA. (2016) De Novo Design of an Allosteric Metalloprotein Assembly with Strained Disulfide Bonds. J Am Chem Soc. 138(40):13163-13166. PMC5085265

Andrew Caldwell

Email: abcaldwell@ucsd.edu
Linkedin: https://www.linkedin.com/in/andrewbcaldwell/
Program: Chemistry & Biochemistry
Advisor: Alex Hoffman

Publications: 

Shih VF, Tsui R, Caldwell A, Hoffmann A. (2011) A single NFκB system for both canonical and non-canonical signaling. Cell Res. 21(1):86-102. PMC3193412

Caldwell AB, Cheng Z, Vargas JD, Birnbaum HA, Hoffmann A. (2014) Network dynamics determine the autocrine and paracrine signaling functions of TNF. Genes Dev. 28(19):2120-33.     PMC4180974

Eileen Chen

Email: me2youtw11@gmail.com
Linkedin: https://www.linkedin.com/in/eileenchen111/
Program: Chemistry & Biochemistry
Advisor: Simpson Joseph

Publications: 

Chen E, Sharma MR, Shi X, Agrawal RK, Joseph S. (2014) Fragile X mental retardation protein regulates translation by binding directly to the ribosome. Mol Cell. 54(3):407-417. PMC4019695

Chen E, Joseph S. (2015) Fragile X mental retardation protein: A paradigm for translational control by RNA-binding proteins. Biochimie. 114:147-54. PMC4458461

Natalie Shanks

Email:
Linkedin: https://www.linkedin.com/in/natalie-shanks-b7510171/
Program: Chemistry & Biochemistry
Advisor: Terunaga Nakagawa

Publications:

Shanks NF, Maruo T, Farina AN, Ellisman MH, Nakagawa T. (2010) Contribution of the global subunit structure and stargazin on the maturation of AMPA receptors. J Neurosci. 30(7):2728-40. PMC2842908

Shanks NF, Savas JN, Maruo T, Cais O, Hirao A, Oe S, Ghosh A, Noda Y, Greger IH, Yates JR 3rd, Nakagawa T. (2012) Differences in AMPA and kainate receptor interactomes facilitate identification of AMPA receptor auxiliary subunit GSG1L. Cell Rep. 1(6):590-8. PMC3401968

Shanks NF, Cais O, Maruo T, Savas JN, Zaika EI, Azumaya CM, Yates JR 3rd, Greger I, Nakagawa T. (2014) Molecular dissection of the interaction between the AMPA receptor and cornichon homolog-3. J Neurosci. 34(36):12104-20. PMC4152608

Elegheert J, Kakegawa W, Clay JE, Shanks NF, Behiels E, Matsuda K, Kohda K, Miura E, Rossmann M, Mitakidis N, Motohashi J, Chang VT, Siebold C, Greger IH, Nakagawa T, Yuzaki M, Aricescu AR. Structural basis for integration of GluD receptors within synaptic organizer complexes. Science. 353(6296):295-9. PMC5291321

William Sinko

Email: wsinko@gmail.com
Linkedin: https://www.linkedin.com/in/williamsinko/
Program: Chemistry & Biochemistry
Advisor: J. Andrew McCammon

Publications:

Sierecki E, Sinko W, McCammon JA, Newton AC. (2010) Discovery of small molecule inhibitors of the PH domain leucine-rich repeat protein phosphatase (PHLPP) by chemical and virtual screening. J Med Chem. 53(19):6899-911. PMC2951065

Sinko W, de Oliveira C, Williams S, Van Wynsberghe A, Durrant JD, Cao R, Oldfield E, McCammon JA. (2011) Applying molecular dynamics simulations to identify rarely sampled ligand-bound conformational states of undecaprenyl pyrophosphate synthase, an antibacterial target. Chem Biol Drug Des. 77(6):412-20. PMC3095679

Sinko W, Sierecki E, de Oliveira CA, McCammon JA. (2012) Guide to virtual screening: application to the Akt phosphatase PHLPP. Methods Mol Biol. 819:561-73.

Sinko W, de Oliveira CA, Pierce LC, McCammon JA. (2012) Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations. J Chem Theory Comput. 8(1):17-23. PMC3254191

Zhu W, Zhang Y, Sinko W, Hensler ME, Olson J, Molohon KJ, Lindert S, Cao R, Li K, Wang K, Wang Y, Liu YL, Sankovsky A, de Oliveira CA, Mitchell DA, Nizet V, McCammon JA, Oldfield E. (2013) Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A. 110(1):123-8. PMC3538244

Sinko W, Lindert S, McCammon JA. (2013) Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design. Chem Biol Drug Des. 81(1):41-9. PMC3540989

Arrar M, de Oliveira CA, Fajer M, Sinko W, McCammon JA. (2013) w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations. J Chem Theory Comput. 9(1):18-23. PMC3541756

Sinko W, Miao Y, de Oliveira CA, McCammon JA. (2013) Population based reweighting of scaled molecular dynamics. J Phys Chem B. 117(42):12759-68. PMC3808002

Feixas F, Lindert S, Sinko W, McCammon JA. (2014) Exploring the role of receptor flexibility in structure-based drug discovery. Biophys Chem. 2014 Feb;186:31-45. PMC4459653

Sinko W, Wang Y, Zhu W, Zhang Y, Feixas F, Cox CL, Mitchell DA, Oldfield E, McCammon JA. (2014) Undecaprenyl diphosphate synthase inhibitors: antibacterial drug leads. J Med Chem. 57(13):5693-701. PMC4096218

Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA. (2014) Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. J Chem Theory Comput. 10(7):2677-2689. PMC4095935

Kim MO, Feng X, Feixas F, Zhu W, Lindert S, Bogue S, Sinko W, de Oliveira C, Rao G, Oldfield E, McCammon JA. (2015) A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility and Implications for Computer-aided Drug Discovery. Chem Biol Drug Des. 85(6):756-69. PMC4412765

Jeramie Watrous

Email: jeramie.watrous@gmail.com 
Linkedin: https://www.linkedin.com/in/jeramie-watrous-6993b012/
Program: Chemistry & Biochemistry
Advisor: Pieter Dorrestein

Publications: 

Watrous J, Burns K, Liu WT, Patel A, Hook V, Bafna V, Barry CE 3rd, Bark S, Dorrestein PC. (2010) Expansion of the mycobacterial "PUPylome". Mol Biosyst. 6(2):376-85. PMC2846642

Watrous J, Hendricks N, Meehan M, Dorrestein PC. (2010) Capturing bacterial metabolic exchange using thin film desorption electrospray ionization-imaging mass spectrometry. Anal Chem. 82(5):1598-600. PMC4112561

Yang JY, Karr JR, Watrous JD, Dorrestein PC. (2011) Integrating '-omics' and natural product discovery platforms to investigate metabolic exchange in microbiomes. Curr Opin Chem Biol. 15(1):79-87. PMC3174688

Watrous JD, Alexandrov T, Dorrestein PC. (2011) The evolving field of imaging mass spectrometry and its impact on future biological research. J Mass Spectrom. 46(2):209-22. PMC3303182

Watrous JD, Dorrestein PC. (2011) Imaging mass spectrometry in microbiology. Nat Rev Microbiol. 9(9):683-94. PMC3710447

Watrous J, Roach P, Alexandrov T, Heath BS, Yang JY, Kersten RD, van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC. (2012) Mass spectral molecular networking of living microbial colonies. Proc Natl Acad Sci U S A. 109(26):E1743-52. PMC3387089

Guthals A, Watrous JD, Dorrestein PC, Bandeira N. (2012) The spectral networks paradigm in high throughput mass spectrometry. Mol Biosyst.(10):2535-44. PMC3893064

Yang JY, Phelan VV, Simkovsky R, Watrous JD, Trial RM, Fleming TC, Wenter R, Moore BS, Golden SS, Pogliano K, Dorrestein PC. (2012) Primer on agar-based microbial imaging mass spectrometry. J Bacteriol. 194(22):6023-8. PMC3486372

Watrous JD, Phelan VV, Hsu CC, Moree WJ, Duggan BM, Alexandrov T, Dorrestein PC. (2013) Microbial metabolic exchange in 3D. ISME J.7(4):770-80. PMC3603389

Nguyen DD, Wu CH, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C, Ballesteros J, Sanchez J, Watrous JD, Phelan VV, van de Wiel C, Kersten RD, Mehnaz S, De Mot R, Shank EA, Charusanti P, Nagarajan H, Duggan BM, Moore BS, Bandeira N, Palsson BØ, Pogliano K, Gutiérrez M, Dorrestein PC. (2013) MS/MS networking guided analysis of molecule and gene cluster families. Proc Natl Acad Sci U S A.110(28):E2611-20. PMC3710860

Traxler MF, Watrous JD, Alexandrov T, Dorrestein PC, Kolter R. (2014) Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome. MBio. 4(4). pii: e00459-13. PMC3747584

Watrous J, Roach P, Heath B, Alexandrov T, Laskin J, Dorrestein PC. (2013) Metabolic profiling directly from the Petri dish using nanospray desorption electrospray ionization imaging mass spectrometry. Anal Chem. 85(21):10385-91. PMC3913783

Winnikoff JR, Glukhov E, Watrous J, Dorrestein PC, Gerwick WH. (2014) Quantitative molecular networking to profile marine cyanobacterial metabolomes. J Antibiot (Tokyo). 67(1):105-12. PMC5105604

Bleich R, Watrous JD, Dorrestein PC, Bowers AA, Shank EA. (2015) Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis. Proc Natl Acad Sci U S A. 112(10):3086-91. PMC4364203

Michelsen CF, Watrous J, Glaring MA, Kersten R, Koyama N, Dorrestein PC, Stougaard P. (2015) Nonribosomal peptides, key biocontrol components for Pseudomonas fluorescens In5, isolated from a Greenlandic suppressive soil. MBio. 6(2):e00079. PMC4453515

Oetjen J, Veselkov K, Watrous J, McKenzie JS, Becker M, Hauberg-Lotte L, Kobarg JH, Strittmatter N, Mróz AK, Hoffmann F, Trede D, Palmer A, Schiffler S, Steinhorst K, Aichler M, Goldin R, Guntinas-Lichius O, von Eggeling F, Thiele H, Maedler K, Walch A, Maass P, Dorrestein PC, Takats Z, Alexandrov T. Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry. Gigascience. 4:20. PMC4418095

Van Der Voort M, Meijer HJ, Schmidt Y, Watrous J, Dekkers E, Mendes R, Dorrestein PC, Gross H, Raaijmakers JM. (2015) Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds. Front Microbiol. 6:693. PMC4493835

Song C, Mazzola M, Cheng X, Oetjen J, Alexandrov T, Dorrestein P, Watrous J, van der Voort M, Raaijmakers JM. (2015) Molecular and chemical dialogues in bacteria-protozoa interactions. Sci Rep. 5:12837. PMC4542665

de Bruijn I, Cheng X, de Jager V, Expósito RG, Watrous J, Patel N, Postma J, Dorrestein PC, Kobayashi D, Raaijmakers JM. (2015) Comparative genomics and metabolic profiling of the genus Lysobacter. BMC Genomics. 16:991. PMC4657364

Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. (2016) Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 34(8):828-837. PMC5321674

Brandon Razooky

Email: brandon.razooky@rockefeller.edu
Linkedin: https://www.linkedin.com/in/brandon-razooky-46026557/
Program: Chemistry & Biochemistry
Advisor: Leor Weinberger

Publications: 

Singh A, Razooky B, Cox CD, Simpson ML, Weinberger LS. (2010) Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression. Biophys J. 98(8):L32-4. PMC2856162

Razooky BS, Weinberger LS. (2011) Mapping the architecture of the HIV-1 Tat circuit: A decision-making circuit that lacks bistability and exploits stochastic noise. Methods. 53(1):68-77. PMC4096296

Singh A, Razooky BS, Dar RD, Weinberger LS. (2012) Dynamics of protein noise can distinguish between alternate sources of gene-expression variability. Mol Syst Biol. 8:607. PMC3435505

Razooky BS, Gutierrez E, Terry VH, Spina CA, Groisman A, Weinberger LS. (2012) Microwell devices with finger-like channels for long-term imaging of HIV-1 expression kinetics in primary human lymphocytes. Lab Chip. 12(21):4305-12. PMC3589574

Dar RD, Razooky BS, Singh A, Trimeloni TV, McCollum JM, Cox CD, Simpson ML, Weinberger LS. (2012) Transcriptional burst frequency and burst size are equally modulated across the human genome. Proc Natl Acad Sci U S A. 109(43):17454-9. PMC3491463

Rouzine IM, Razooky BS, Weinberger LS. (2014) Stochastic variability in HIV affects viral eradication. Proc Natl Acad Sci U S A. 111(37):13251-2. PMC4169906

Dar RD, Razooky BS, Weinberger LS, Cox CD, Simpson ML. (2015) The Low Noise Limit in Gene Expression. PLoS One. 10(10):e0140969. PMC4619080

Razooky BS, Pai A, Aull K, Rouzine IM, Weinberger LS. (2015) A hardwired HIV latency program. Cell. 160(5):990-1001. PMC4395878

Dar RD, Shaffer SM, Singh A, Razooky BS, Simpson ML, Raj A, Weinberger LS. (2016) Transcriptional Bursting Explains the Noise-Versus-Mean Relationship in mRNA and Protein Levels. PLoS One. 11(7):e0158298. PMC4965078

Razooky BS, Cao Y, Hansen MMK, Perelson AS, Simpson ML, Weinberger LS. (2017) Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean. PLoS Biol. 15(10):e2000841. PMC5646755

Hansen MMK, Wen WY, Ingerman E, Razooky BS, Thompson CE, Dar RD, Chin CW, Simpson ML, Weinberger LS. (2018) A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization. Cell. 173(7):1609-1621.e15. PMC6044448

Nicholas Schafer

Email: 
Linkedin: https://www.linkedin.com/in/npschafer/
Program: Chemistry & Biochemistry
Advisor: 

Publications: 

Davtyan A, Schafer NP, Zheng W, Clementi C, Wolynes PG, Papoian GA.(2012) AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing. J Phys Chem B. 116(29):8494-503. PMC3406225

Zheng W, Schafer NP, Davtyan A, Papoian GA, Wolynes PG. (2012) Predictive energy landscapes for protein-protein association. Proc Natl Acad Sci U S A.109(47):19244-9. PMC3511104

Schafer NP, Hoffman RM, Burger A, Craig PO, Komives EA, Wolynes PG. (2012) Discrete kinetic models from funneled energy landscape simulations. PLoS One. 7(12):e50635. PMC3520928

Zheng W, Schafer NP, Wolynes PG. (2013) Frustration in the energy landscapes of multidomain protein misfolding. Proc Natl Acad Sci U S A. 110(5):1680-5. PMC3562767

Truong HH, Kim BL, Schafer NP, Wolynes PG. (2013) Funneling and frustration in the energy landscapes of some designed and simplified proteins. J Chem Phys. 139(12):121908. PMC3732306

Zheng W, Schafer NP, Wolynes PG. (2013) Free energy landscapes for initiation and branching of protein aggregation. Proc Natl Acad Sci U S A. 110(51):20515-20. PMC3870682

Kim BL, Schafer NP, Wolynes PG. (2014) Predictive energy landscapes for folding α-helical transmembrane proteins. Proc Natl Acad Sci U S A. 111(30):11031-6. PMC4121805

Morcos F, Schafer NP, Cheng RR, Onuchic JN, Wolynes PG. (2014) Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection. Proc Natl Acad Sci U S A. 111(34):12408-13. PMC4151759

Schafer NP, Kim BL, Zheng W, Wolynes PG. (2014) Learning To Fold Proteins Using Energy Landscape Theory. Isr J Chem. 54(8-9):1311-1337. PMC4189132

Sarah Smith

Email: sarah.smith115@gmail.com
Linkedin: https://www.linkedin.com/in/sarah-smith-88a692a5/
Program: 
Advisor: Akif Tezcan

Publications:

Smith SJ, Du K, Radford RJ, Tezcan FA. (2013) Functional, metal-based crosslinkers for α-helix induction in short peptides. Chem Sci. 4(9):3740-3747. PMC3800689

Brodin JD, Smith SJ, Carr JR, Tezcan FA. (2015) Designed, Helical Protein Nanotubes with Variable Diameters from a Single Building Block. J Am Chem Soc. 137(33):10468-71.

Smith SJ, Radford RJ, Subramanian RH, Barnett BR, Figueroa JS, Tezcan FA. (2016) Tunable Helicity, Stability and DNA-Binding Properties of Short Peptides with Hybrid Metal Coordination Motifs. Chem Sci. 2016 7(8):5453-5461. PMC5085262

Subramanian RH, Smith SJ, Alberstein RG, Bailey JB, Zhang L, Cardone G, Suominen L, Chami M, Stahlberg H, Baker TS, Tezcan FA. (2018) Self-Assembly of a Designed Nucleoprotein Architecture through Multimodal Interactions. ACS Cent Sci. 4(11):1578-1586. PMC6276041

Zachary Berndsen

Email: zacharyberndsen@gmail.com 
Linkedin: https://www.linkedin.com/in/zachary-t-berndsen-0ba988b1/
Program: Chem/Biochem
Advisor: Douglas Smith

Publications:

Berndsen ZT, Keller N, Grimes S, Jardine PJ, Smith DE. (2014) Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging. Proc Natl Acad Sci U S A. 111(23):8345-50.     PMC4060647

Berndsen ZT, Keller N, Smith DE. (2015) Continuous allosteric regulation of a viral packaging motor by a sensor that detects the density and conformation of packaged DNA. Biophys J. 108(2):315-24. PMC4302192

Keller N, Berndsen ZT, Jardine PJ, Smith DE. (2017) Experimental comparison of forces resisting viral DNA packaging and driving DNA ejection. Phys Rev E. 95(5-1):052408.

Patrick Blachly

Email: pblachly@gmail.com 
Linkedin: https://www.linkedin.com/in/pblachly/
Program: Chem/Biochem
Advisor: J. Andrew McCammon

Publications:

Williams SL, Blachly PG, McCammon JA. (2011) Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study. Proteins. 79(12):3381-8. PMC3227005

Blachly PG, de Oliveira CA, Williams SL, McCammon JA. (2013) Utilizing a dynamical description of IspH to aid in the development of novel antimicrobial drugs. PLoS Comput Biol. 9(12):e1003395. PMC3868525

Martin DP, Blachly PG, Marts AR, Woodruff TM, de Oliveira CA, McCammon JA, Tierney DL, Cohen SM. (2014) Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site. J Am Chem Soc. 136(14):5400-6. PMC4104174

Martin DP, Blachly PG, McCammon JA, Cohen SM. (2014) Exploring the influence of the protein environment on metal-binding pharmacophores. J Med Chem. 57(16):7126-35. PMC4148168

Kim MO, Blachly PG, Kaus JW, McCammon JA. (2015) Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies. J Phys Chem B. 119(3):861-72. PMC4306499

Blachly PG, Sandala GM, Giammona DA, Liu T, Bashford D, McCammon JA, Noodleman L. (2014) Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition. J Chem Theory Comput. 10(9):3871-3884. PMC4159220

Blachly PG, Sandala GM, Giammona DA, Bashford D, McCammon JA, Noodleman L. (2015) Broken-Symmetry DFT Computations for the Reaction Pathway of IspH, an Iron-Sulfur Enzyme in Pathogenic Bacteria. Inorg Chem. 54(13):6439-61. PMC4568833

Kim MO, Blachly PG, McCammon JA. (2015) Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. PLoS Comput Biol. 11(10):e1004341. PMC4623973

Lindsay Dawson

Email: lindsay.dawson1@gmail.com 
Linkedin: https://www.linkedin.com/in/lindsayadawson/
Program: Chem/Biochem
Advisor: Stanley Opella

Publications: 

Cook GA, Dawson LA, Tian Y, Opella SJ. (2013) Three-dimensional structure and interaction studies of hepatitis C virus p7 in 1,2-dihexanoyl-sn-glycero-3-phosphocholine by solution nuclear magnetic resonance. Biochemistry. 52(31):5295-303. PMC3855088

Lindsey Handley

Email: lindseyhandley@gmail.com 
Linkedin: https://www.linkedin.com/in/lindseydhandley/
Program: Chem/Biochem
Advisor: Elizabeth Komives

Publications:

Cervantes CF, Handley LD, Sue SC, Dyson HJ, Komives EA. (2013) Long-range effects and functional consequences of stabilizing mutations in the ankyrin repeat domain of IκBα. J Mol Biol. 425(5):902-13. PMC3744861

Handley LD, Treuheit NA, Venkatesh VJ, Komives EA. (2015) Thrombomodulin Binding Selects the Catalytically Active Form of Thrombin. Biochemistry. 54(43):6650-8. PMC4697735

Handley LD, Fuglestad B, Stearns K, Tonelli M, Fenwick RB, Markwick PR, Komives EA.(2017) NMR reveals a dynamic allosteric pathway in thrombin. Sci Rep. 7:39575. PMC5216386

Benjamin Madej

Email: bdmadej@gmail.com 
Linkedin: https://www.linkedin.com/in/benjamin-madej-12b3b314/
Program: Chem/Biochem
Advisor: Ross Walker

Publications:

Skjevik ÅA, Madej BD, Walker RC, Teigen K. (2012) LIPID11: a modular framework for lipid simulations using amber. J Phys Chem B. 116(36):11124-36. PMC3771533

Dickson CJ, Madej BD, Skjevik AA, Betz RM, Teigen K, Gould IR, Walker RC. (2014) Lipid14: The Amber Lipid Force Field. J Chem Theory Comput. 10(2):865-879. PMC3985482

Skjevik ÅA, Madej BD, Dickson CJ, Teigen K, Walker RC, Gould IR. (2015) All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields. Chem Commun (Camb). 51(21):4402-5. PMC5084445

Madej BD, Gould IR, Walker RC. (2015) A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field. J Phys Chem B. 119(38):12424-35. PMC5079186

Skjevik ÅA, Madej BD, Dickson CJ, Lin C, Teigen K, Walker RC, Gould IR. (2016) Simulation of lipid bilayer self-assembly using all-atom lipid force fields. Phys Chem Chem Phys. 18(15):10573-84. PMC5091658

Christopher Pierse

Email:
Linkedin: https://www.linkedin.com/in/christopher-pierse/
Program: Physics
Advisor: Olga Dudko

Publications:

Pierse CA, Dudko OK. (2013) Kinetics and energetics of biomolecular folding and binding. Biophys J. 105(9):L19-22.  PMC3824551

Pierse CA, Dudko OK. (2017) Distinguishing Signatures of Multipathway Conformational Transitions. Phys Rev Lett.118(8):088101.

Chelsea Stewart

Email:
Program: BMS
Advisor: Partho Ghosh

Publications:

Stewart CM, Buffalo CZ, Valderrama JA, Henningham A, Cole JN, Nizet V, Ghosh P. (20160 Coiled-coil destabilizing residues in the group A Streptococcus M1 protein are required for functional interaction. Proc Natl Acad Sci U S A. 113(34):9515-20. PMC5003295

Döhrmann S, LaRock CN, Anderson EL, Cole JN, Ryali B, Stewart C, Nonejuie P, Pogliano J, Corriden R, Ghosh P, Nizet V. (2017) Group A Streptococcal M1 Protein Provides Resistance against the Antimicrobial Activity of Histones. sSci Rep. 7:43039. PMC5318940

Zhaleh Amini

Email: zhalehnamini@gmail.com
Linkedin: https://www.linkedin.com/in/zhalehamini/
Program: Chem/Biochem
Advisor: Ulrich Muller 

Publications:

Amini ZN, Müller UF. (2013) Low selection pressure aids the evolution of cooperative ribozyme mutations in cells. J Biol Chem. 288(46):33096-106. PMC3829158

Amini ZN, Olson KE, Müller UF. (2014) Spliceozymes: ribozymes that remove introns from pre-mRNAs in trans. PLoS One. 9(7):e101932. PMC4094466

Amini ZN, Müller UF. (2015) Increased efficiency of evolved group I intron spliceozymes by decreased side product formation. RNA. 21(8):1480-9. PMC4509937

Donald Johnson

Email:
Linkedin: https://www.linkedin.com/in/donald-johnson-phd/
Program: Chem/Biochem
Advisor: Mark Ellisman, Susan Taylor

Publications:

Bushong EA, Johnson DD Jr, Kim KY, Terada M, Hatori M, Peltier ST, Panda S, Merkle A, Ellisman MH. (2015) X-ray microscopy as an approach to increasing accuracy and efficiency of serial block-face imaging for correlated light and electron microscopy of biological specimens. Microsc Microanal. 21(1):231-8.  PMC4415271

Ignacio Lopez

Email:
Linkedin: 
Program: Chem/Biochem
Advisor: Judy Kim

Publications:

Kang G, López-Peña I, Oklejas V, Gary CS, Cao W, Kim JE. (2012) Förster resonance energy transfer as a probe of membrane protein folding. Biochim Biophys Acta. 1818(2):154-61. PMC3253952

López-Peña I, Leigh BS, Schlamadinger DE, Kim JE. (2015) Insights into Protein Structure and Dynamics by Ultraviolet and Visible Resonance Raman Spectroscopy. Biochemistry. 54(31):4770-83.     PMC5092233

Hoang Thien Nguyen

Email: 
Linkedin: 
Program: Chem/Biochem
Advisor: Hector Viadiu

Publications:

Ethayathulla AS, Nguyen HT, Viadiu H. (2013) Crystal structures of the DNA-binding domain tetramer of the p53 tumor suppressor family member p73 bound to different full-site response elements. J Biol Chem. 288(7):4744-54. PMC3576079

Ciribilli Y, Monti P, Bisio A, Nguyen HT, Ethayathulla AS, Ramos A, Foggetti G, Menichini P, Menendez D, Resnick MA, Viadiu H, Fronza G, Inga A. (2013) Transactivation specificity is conserved among p53 family proteins and depends on a response element sequence code. Nucleic Acids Res. 41(18):8637-53. PMC3794606

Mulero MC, Huang DB, Nguyen HT, Wang VY, Li Y, Biswas T, Ghosh G. (2017) DNA-binding affinity and transcriptional activity of the RelA homodimer of nuclear factor κB are not correlated. J Biol Chem. 292(46):18821-18830. PMC5704467

Joseph Kaus

Email: joekaus@gmail.com
Linkedin: https://www.linkedin.com/in/joe-kaus-56323a97/
Program: Chem/Biochem
Advisor: J. Andrew McCammon

Publications:

Kaus JW, Arrar M, McCammon JA. (2014) Accelerated adaptive integration method. J Phys Chem B. 118(19):5109-18. PMC4025579

Kim MO, Blachly PG, Kaus JW, McCammon JA. (2015) Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies. J Phys Chem B. 119(3):861-72. PMC4306499

Kaus JW, McCammon JA. (2015) Enhanced ligand sampling for relative protein-ligand binding free energy calculations. J Phys Chem B. 119(20):6190-7. PMC4442669

Kaus JW, Harder E, Lin T, Abel R, McCammon JA, Wang L. (2015) How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations. J Chem Theory Comput. 11(6):2670-9. PMC4462751

Jessica Peters

Email: jessica.peters@ucsf.edu 
Linkedin: https://www.linkedin.com/in/jessica-peters-biochemist/
Program: Chem/Biochem
Advisor: Navtej Toor

Publications:

Robart AR, Chan RT, Peters JK, Rajashankar KR, Toor N. (2014) Crystal structure of a eukaryotic group II intron lariat. Nature. 514(7521):193-7. PMC4197185

Peters JK, Toor N. (2015) Group II intron lariat: Structural insights into the spliceosome. RNA Biol. 12(9):913-7. PMC4615233

Chan RT, Peters JK, Robart AR, Wiryaman T, Rajashankar KR, Toor N. (2018) Structural basis for the second step of group II intron splicing. Nat Commun. 9(1):4676. PMC6224600

Alan West

Email:
Linkedin: https://www.linkedin.com/in/alan-west-66594a80/
Program: BMS
Advisor: Kevin Corbett

Publications:

West AMV, Komives EA, Corbett KD. (2018) Conformational dynamics of the Hop1 HORMA domain reveal a common mechanism with the spindle checkpoint protein Mad2. Nucleic Acids Res. 46(1):279-292. PMC5758881

West AM, Rosenberg SC, Ur SN, Lehmer MK, Ye Q, Hagemann G, Caballero I, Usón I, MacQueen AJ, Herzog F, Corbett KD. (2019) A conserved filamentous assembly underlies the structure of the meiotic chromosome axis. Elife. 8. pii: e40372. PMC6349405

Clifford Woodford

Email: crwoodford4@gmail.com 
Linkedin: https://www.linkedin.com/in/clifford-woodford-5183567b/
Program: Chem/Biochem
Advisor: Roger Tsien

Publications:

Woodford CR, Frady EP, Smith RS, Morey B, Canzi G, Palida SF, Araneda RC, Kristan WB Jr, Kubiak CP, Miller EW, Tsien RY. (2015) Improved PeT molecules for optically sensing voltage in neurons. J Am Chem Soc.137(5):1817-24. PMC4513930

Lewis Churchfield

Email: lewis.churchfield@gmail.com
Linkedin: https://www.linkedin.com/in/lewis-churchfield/
Program: Chem/Biochem
Advisor: Akif Tezcan

Publications:

Bailey JB, Subramanian RH, Churchfield LA, Tezcan FA. (2016) Metal-Directed Design of Supramolecular Protein Assemblies. Methods Enzymol. 580:223-50. PMC5131729

Churchfield LA, Medina-Morales A, Brodin JD, Perez A, Tezcan FA. (2016) De Novo Design of an Allosteric Metalloprotein Assembly with Strained Disulfide Bonds. J Am Chem Soc. 138(40):13163-13166. PMC5085265

Churchfield LA, Alberstein RG, Williamson LM, Tezcan FA. (2018) Determining the Structural and Energetic Basis of Allostery in a De Novo Designed Metalloprotein Assembly. J Am Chem Soc. 140(31):10043-10053. PMC6085756

Jamie Schiffer

Email: schiff.jamie@gmail.com
Linkedin: https://www.linkedin.com/in/jamie-schiffer-52044b86/
Program: Chem/Biochem
Advisor: Elizabeth Komives

Publications:

Balasubramaniam D, Schiffer J, Parnell J, Mir SP, Amaro RE, Komives EA. (2015) How the ankyrin and SOCS box protein, ASB9, binds to creatine kinase. Biochemistry. 54(8):1673-80. PMC4348336

Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, Komives EA. (2016) Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer. Structure. 24(8):1248-1256. PMC4972691

Schiffer JM, Feher VA, Malmstrom RD, Sida R, Amaro RE. (2016) Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A. Biophys J. 111(8):1631-1640. PMC5071553

Mulero MC, Shahabi S, Ko MS, Schiffer JM, Huang DB, Wang VY, Amaro RE, Huxford T, Ghosh G. (2018) Protein Cofactors Are Essential for High-Affinity DNA Binding by the Nuclear Factor κB RelA Subunit. Biochemistry. 57(20):2943-2957. PMC5993198

Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE. (2019) Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant. Biophys J. 116(2):205-214. PMC6349996

Bryan Stephens

Email: bsstephens3@gmail.com
Linkedin: 
Program: BMS
Advisor: Tracy Handel

Publications:

Stephens B, Handel TM. (2013) Chemokine receptor oligomerization and allostery. Prog Mol Biol Transl Sci. 115:375-420. PMC4072031

Kufareva I, Stephens B, Gilliland CT, Wu B, Fenalti G, Hamel D, Stevens RC, Abagyan R, Handel TM. (2013) A novel approach to quantify G-protein-coupled receptor dimerization equilibrium using bioluminescence resonance energy transfer. Methods Mol Biol. 1013:93-127. PMC4091634

Ziarek JJ, Getschman AE, Butler SJ, Taleski D, Stephens B, Kufareva I, Handel TM, Payne RJ, Volkman BF. (2013) Sulfopeptide probes of the CXCR4/CXCL12 interface reveal oligomer-specific contacts and chemokine allostery. ACS Chem Biol. 8(9):1955-63. PMC3783652

Kawamura T, Stephens B, Qin L, Yin X, Dores MR, Smith TH, Grimsey N, Abagyan R, Trejo J, Kufareva I, Fuster MM, Salanga CL, Handel TM. (2014) A general method for site specific fluorescent labeling of recombinant chemokines. PLoS One. 9(1):e81454. PMC3904831

Kufareva I, Stephens BS, Holden LG, Qin L, Zhao C, Kawamura T, Abagyan R, Handel TM. (2014) Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: molecular modeling and experimental validation. Proc Natl Acad Sci U S A. 111(50):E5363-72. PMC4273337

Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S, Abagyan R, Chance MR, Kufareva I, Handel TM. (2017) Structural basis of ligand interaction with atypical chemokine receptor 3. Nat Commun. 8:14135. PMC5253664

Kufareva I, Gustavsson M, Zheng Y, Stephens BS, Handel TM. (2017) What Do Structures Tell Us About Chemokine Receptor Function and Antagonism? Annu Rev Biophys.46:175-198. PMC5764094

Grimsey NJ, Narala R, Rada CC, Mehta S, Stephens BS, Kufareva I, Lapek J, Gonzalez DJ, Handel TM, Zhang J, Trejo J. (2018) A Tyrosine Switch on NEDD4-2 E3 Ligase Transmits GPCR Inflammatory Signaling. Cell Rep. 24(12):3312-3323.e5. PMC6226018

Nicholas Tiee

Email: n.tiee90@gmail.com
Linkedin: https://www.linkedin.com/in/nicholas-tiee-83a897ba/
Program: Chem/Biochem
Advisor: Patricia A. Jennings

Publications:

Cheng RR, Haglund E, Tiee NS, Morcos F, Levine H, Adams JA, Jennings PA, Onuchic JN. (2018) Designing bacterial signaling interactions with coevolutionary landscapes. PLoS One. 13(8):e0201734. PMC6101370

Bryan Arias

Email:
Linkedin: https://www.linkedin.com/in/bryan-arias-40b22327/
Program: Biology
Advisor: Simpson Joseph

Publications:

Arias-Mireles BH, de Rozieres CM, Ly K, Joseph S. (2018) BRNA Modulates the Interaction between Influenza A Virus NS1 and Human PABP1 Biochemistry 57(26) 3590-3598. PMC6205234

Chris Fisher

Email: fishercjf@gmail.com

Linkedin: https://www.linkedin.com/in/christopher-james-fisher/

Program: Chem/Biochem

Advisor: Kamil Godula

Publications:

Huang ML, Cohen M, Fisher CJ, Schooley RT, Gagneux P, Godula K. (2015) Determination of receptor specificities for whole influenza viruses using multivalent glycan arrays. Chem Commun (Camb). 51(25):5326-9. PMC4359031

Cohen M, Fisher CJ, Huang ML, Lindsay LL, Plancarte M, Boyce WM, Godula K, Gagneux P. (2016) Capture and characterization of influenza A virus from primary samples using glycan bead arrays. Virology. 493:128-35. PMC4860064

Huang ML, Fisher CJ, Godula K. (2016) Glycomaterials for probing host-pathogen interactions and the immune response. Exp Biol Med (Maywood). 241(10):1042-53. PMC4950362

Cohen M, Senaati HP, Fisher CJ, Huang ML, Gagneux P, Godula K. (2016) Synthetic Mucus Nanobarriers for Identification of Glycan-Dependent Primary Influenza A Infection Inhibitors. ACS Cent Sci. 2(10):710-714. PMC5084083

Huang ML, Michalak AL, Fisher CJ, Christy M, Smith RAA, Godula K. (2018) Small Molecule Antagonist of Cell Surface Glycosaminoglycans Restricts Mouse Embryonic Stem Cells in a Pluripotent State. Stem Cells. 36(1):45-54. PMC6237099

Chris Lee

Email: chrislee4123@gmail.com 
Linkedin: 
Program: Chem/Biochem
Advisor: J. Andrew McCammon

Publications:

Malmstrom RD, Lee CT, Van Wart A, Amaro RE. (2014) On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins. J Chem Theory Comput.  10(7):2648-2657. PMC4248791

Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC. (2016) Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J Chem Inf Model. 56(4):721-33. PMC5280572

Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. (2016) Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev. 116(11):6370-90. PMC4901368

Votapka LW, Lee CT, Amaro RE. (2016) Two Relations to Estimate Membrane Permeability Using Milestoning. J Phys Chem B. 120(33):8606-16. PMC5002937

Jagger BR, Lee CT, Amaro RE. (2018) Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. J Phys Chem Lett. 9(17):4941-4948. PMC6443090

Lee CT, Amaro RE. (2018) Exascale Computing: A New Dawn for Computational Biology. Comput Sci Eng. 2018 Sep-Oct;20(5):18-25. PMC6458592

Taylor BC, Lee CT, Amaro RE. (2019) Structural basis for ligand modulation of the CCR2 conformational landscape. Proc Natl Acad Sci U S A. 116(17):8131-8136. PMC6486717

Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ. (20190 The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. ACM Trans Math Softw. 45(3). pii: 28. PMC6716611

Kristen Ramsey

Email: kmramseyphd@gmail.com
Linkedin: https://www.linkedin.com/in/kristen-ramsey-824284a1/
Program: Chem/Biochem
Advisor: Elizabeth Komives, Gourisankar Ghosh

Publications:

Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, Komives EA. (2016) Binding of NFκB Appears to Twist the Ankyrin Repeat Domain of IκBα. Biophys J.110(4):887-95. PMC4776026

Ramsey KM, Dembinski HE, Chen W, Ricci CG, Komives EA. (2017) DNA and IκBα Both Induce Long-Range Conformational Changes in NFκB. J Mol Biol. 429(7):999-1008. PMC5389416

Ramsey KM, Narang D, Komives EA. (2018) Prediction of the presence of a seventh ankyrin repeat in IκBε from homology modeling combined with hydrogen-deuterium exchange mass spectrometry (HDX-MS). Protein Sci.  27(9):1624-1635. PMC6194264

Ramsey KM, Chen W, Marion JD, Bergqvist S, Komives EA. (2019) Exclusivity and Compensation in NFκB Dimer Distributions and IκB Inhibition. Biochemistry. 58(21):2555-2563. PMC6642826

Jeff Wagner

Email: jwagnerjpl@gmail.com
Linkedin: https://www.linkedin.com/in/jeffrey-r-wagner/
Program: Chem/Biochem
Advisor: Rommie Amaro

Publications:

Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. (2016) Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev. 116(11):6370-90. PMC4901368

Wagner JR, Sørensen J, Hensley N, Wong C, Zhu C, Perison T, Amaro RE. POVME 3.0: Software for Mapping Binding Pocket Flexibility. J Chem Theory Comput. 13(9):4584-4592. PMC5751414

Shi K, Demir Ö, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H. (2017) Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. Sci Rep. 7(1):17415. PMC5727031

Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE. (2019) Determinants of Oligonucleotide Selectivity of APOBEC3B. J Chem Inf Model. 59(5):2264-2273. PMC6644697

Wagner JR, Churas CP, Liu S, Swift RV, Chiu M, Shao C, Feher VA, Burley SK, Gilson MK, Amaro RE. (2019) Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. Structure. 27(8):1326-1335.e4. PMC6685748

Charles Lin

Email: midnight2103@gmail.com
Linkedin: https://www.linkedin.com/in/charles-l-a9646bb9/
Program: Chem/Biochem
Advisor: Ross Walker

Publications:

Skjevik ÅA, Madej BD, Dickson CJ, Lin C, Teigen K, Walker RC, Gould IR. (2016) Simulation of lipid bilayer self-assembly using all-atom lipid force fields. Phys Chem Chem Phys. 18(15):10573-84. PMC5091658

Mermelstein DJ, Lin C, Nelson G, Kretsch R, McCammon JA, Walker RC. (2018) Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. J Comput Chem. 39(19):1354-1358.

Lee TS, Cerutti DS, Mermelstein D, Lin C, LeGrand S, Giese TJ, Roitberg A, Case DA, Walker RC, York DM. (2018) GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. J Chem Inf Model. 58(10):2043-2050. PMC6226240

Ben-Shalom IY, Lin C, Kurtzman T, Walker RC, Gilson MK. (2019) Simulating Water Exchange to Buried Binding Sites. J Chem Theory Comput. 15(4):2684-2691. PMC6456390

Sophie Kantonen

Email: skantonen@ucsd.edu
Linkedin:
Program: Chem/Biochem
Advisor: Michael Gilson

Publications:

Kantonen SA, Henriksen NM, Gilson MK. 2017. Evaluation and Minimization of Uncertainty in ITC Binding Measurements: Heat Error, Concentration Error, Saturation, and Stoichiometry. Biochim Biophys Acta Gen Subj. 1861(2):485-498. PMC5195854

Kantonen SA, Henriksen NM, Gilson MK. 2018. Accounting for apparent deviations between calorimetric and van't Hoff enthalpies. Biochim Biophys Acta Gen Subj. 1862(3):692-704. PMC5851798

Kellett K, Kantonen SA, Duggan BM, Gilson MK. Toward expanded diversity of host-guest interactions via synthesis and characterization of cyclodextrin derivatives. J. Sol. Chem. 47: 1597-1608, 2018.

Kantonen SA, Muddanan HS, Schauperl M, Henriksen NM, Wang L-P,Gilson MK. Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters. J Chem Theory Comput 16:1115–1127, 2020.

Ryan Lumpkin

Email: lumpkin@dfci.harvard.edu
Linkedin: https://www.linkedin.com/in/charles-l-a9646bb9/
Program: Chem/Biochem
Advisor: Elizabeth Komives

Publications:

Lumpkin, RJ, Gu, H, Zhu, Y, Leonard, M, Ahmad, AS, Clauser, KR, Meyer, JR, Bennett, EJ, Komives, EA (2017) Site-specific identification and quantitation of endogenous SUMO modifications under native conditions Nat Comm 8(1):1171. PMC5660086

Lumpkin RJ, Komives EA. Mol Cell Proteomics. 2019 DECA, A Comprehensive, Automatic Post-processing Program for HDX-MS Data. 18(12):2516-2523. PMC6885705

Lumpkin RJ, Baker RW, Leschziner AE, Komives EA. 2020. Structure and dynamics of the ASB9 CUL-RING E3 Ligase. Nat Commun. 2020 11(1):2866. PMC7280518

Steve Rees

Email: sdrees@health.ucsd.edu
Linkedin:
Program: BMS
Advisor: Geoffrey Chang

Publications:

Zaramela LS, Martino C, Alisson-Silva F, Rees SD, Diaz SL, Chuzel L, Ganatra MB, Taron CH, Secrest P, Zuniga C, Huang J, Siegel D, Chang G, Varki A, Zengler K. Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates. Nat Microbiol. 2019. doi: 10.1038/s41564-019-0564-9. PubMed PMID: 31548686. PMC6879853

Kalogriopoulos NA, Rees SD, Ngo T, Kopcho NJ, Ilatovskiy AV, Sun N, Komives EA, Chang G, Ghosh P, Kufareva I. Structural basis for GPCR-independent activation of heterotrimeric Gi proteins. Proc Natl Acad Sci U S A. 2019;116(33):16394-403. doi: 10.1073/pnas.1906658116. PubMed PMID: 31363053; PMCID: PMC6697900

Maity K, Heumann JM, McGrath AP, Kopcho NJ, Hsu PK, Lee CW, Mapes JH, Garza D, Krishnan S, Morgan GP, Hendargo KJ, Klose T, Rees SD, Medrano-Soto A, Saier MH, Jr., Pineros M, Komives EA, Schroeder JI, Chang G, Stowell MHB. Cryo-EM structure of OSCA1.2 from Oryza sativa elucidates the mechanical basis of potential membrane hyperosmolality gating. Proc Natl Acad Sci U S A. 2019;116(28):14309-18. doi: 10.1073/pnas.1900774116. PMC6628804

Rob Alberstein

Email: Robert.Alberstein@ucsf.edu
Linkedin: https://www.linkedin.com/in/rob-alberstein-31486965/
Program: Chem/Biochem
Advisor: Akif Tezcan

Publications:

Zhang S*, Alberstein RG*, De Yoreo JJ, Tezcan FA. 2020 Assembly of a patchy protein into variable 2D lattices via tunable multiscale interactions. Nat Commun. 11(1):3770*co-first authors

Golub E, Subramanian RH, Esselborn J, Alberstein RG, Bailey JB, Chiong JA, Yan X, Booth T, Baker TS, Tezcan FA. 2020 Constructing protein polyhedra via orthogonal chemical interactions. Nature. 578(7793):172-176

Subramanian RH*, Smith SJ*, Alberstein RG, Bailey JB, Zhang L, Cardone G, Suominen L, Chami M, Stahlberg H, Baker TS, Tezcan FA. 2018. Self-Assembly of a Designed Nucleoprotein Architecture through Multimodal Interactions. ACS Cent Sci. 4(11):1578-1586. *co-first authors

Churchfield LA, Alberstein RG, Williamson LM, Tezcan FA. 2018. Determining the Structural and Energetic Basis of Allostery in a De Novo Designed Metalloprotein Assembly. J Am Chem Soc. 140(31):10043-10053.

Alberstein R, Suzuki Y, Paesani F, Tezcan FA. 2018. Engineering the entropy-driven free-energy landscape of a dynamic nanoporous protein assembly. Nat Chem. 10(7):732-739.

Ben Dick

Email: bdick@ucsd.edu
Linkedin: https://www.linkedin.com/in/benjamin-dick/
Program: Chem/Biochem
Advisor: Seth Cohen (Matching slot)

Publications:

Dick BL, Patel A, McCammon JA, Cohen SM. 2017. Effect of donor atom identity on metal-binding pharmacophore coordination. J Biol Inorg Chem. 22(4):605-613.

Isosteres of hydroxypyridinethione as drug-like pharmacophores for metalloenzyme inhibition. J Biol Inorg Chem. 23(7):1129-1138.

Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. 2019. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev. 119(2):1323-1455.PMC6405328

Credille CV, Dick BL, Morrison CN, Stokes RW, Adamek RN, Wu NC, Wilson IA, Cohen SM. 2018. Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease. J Med Chem. 61(22):10206-10217.

Perez C, Barkley-Levenson AM, Dick BL, Glatt PF, Martinez Y, Siegel D, Momper JD, Palmer AA, Cohen SM. 2019. Metal-Binding Pharmacophore Library Yields the Discovery of a Glyoxalase 1 Inhibitor. J Med Chem. 2019 Feb 14;62(3):1609-1625.

Credille CV, Morrison CN, Stokes RW, Dick BL, Feng Y, Sun J, Chen Y, Cohen SM. (2019) SAR Exploration of Tight-Binding Inhibitors of Influenza Virus PA Endonuclease. J Med Chem. 62(21): 9438-9449.

Noah Kopcho

Email: nkopcho@ucsd.edu
Linkedin: https://www.linkedin.com/in/noah-kopcho-7a5956193/
Program: Chem/Biochem
Advisor: Geoffrey Chang

Publications:

Kopcho N, Chang G, Komives EA. Dynamics of ABC Transporter P-glycoprotein in Three Conformational States. Sci Rep. 2019;9(1):15092. doi: 10.1038/s41598-019-50578-2. PubMed PMID: 31641149; PMCID: PMC6805939

Kalogriopoulos NA, Rees SD, Ngo T, Kopcho NJ, Ilatovskiy AV, Sun N, Komives EA, Chang G, Ghosh P, Kufareva I. Structural basis for GPCR-independent activation of heterotrimeric Gi proteins. Proc Natl Acad Sci U S A. 2019;116(33):16394-403. doi: 10.1073/pnas.1906658116. PubMed PMID: 31363053; PMCID: PMC6697900

Maity K, Heumann JM, McGrath AP, Kopcho NJ, Hsu PK, Lee CW, Mapes JH, Garza D, Krishnan S, Morgan GP, Hendargo KJ, Klose T, Rees SD, Medrano-Soto A, Saier MH, Jr., Pineros M, Komives EA, Schroeder JI, Chang G, Stowell MHB. Cryo-EM structure of OSCA1.2 from Oryza sativa elucidates the mechanical basis of potential membrane hyperosmolality gating. Proc Natl Acad Sci U S A. 2019;116(28):14309-18. doi: 10.1073/pnas.1900774116. PMC6628804

Colin Deniston

Email: cdenisto@ucsd.edu
Linkedin: https://www.linkedin.com/in/colin-deniston-38773265/
Program: Chem/Biochem
Advisor: Andres Leschziner

Publications:

Deniston C*, Salogiannis J*, Mathea S*, Snead D, Lahiri I, Matyszewski M, Donosa O, Watanabe R, Bohning J, Shiau AK, Knapp S, Villa E, Reck-Peterson SL and Leschziner AE. (2020) Parkinson’s Disease LRRK2 structure and model for microtubule interaction. Nature (accepted). (* equal contributors) PMCID in progress

Sarah Kochanek

Email: skochanek@ucsd.edu

Linkedin: https://www.linkedin.com/in/sarah-kochanek/

Program: Chem/Biochem
Advisor: Rommie Amaro

Publications:

Kochanek SE, Clymer TM, Pakkala VS, Hebert SP, Reeping K, Firestine SM, Evanseck JD. 2015. Intramolecular charge-assisted hydrogen bond strength in pseudochair carboxyphosphate. J Phys Chem B. 119(3):1184-91.PMC4306500

Benjamin Jagger

Email: skochanek@ucsd.edu

Linkedin: https://www.linkedin.com/in/benjaminjagger/

Program: Chem/Biochem
Advisor: Rommie Amaro

Publications:

Votapka LW, Jagger BR, Heyneman AL, Amaro RE. 2017. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding. J Phys Chem B. 121(15):3597-3606. PMC5562489

Jagger BR, Lee CT, Amaro RE. 2018. Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. J Phys Chem Lett. 9(17):4941-4948. PMC6443090

Sonjiala Hotchkiss

Email: shotchkiss@ucsd.edu

Linkedin: https://www.linkedin.com/in/sonjialahotchkiss

Program: Chem/Biochem
Advisor: Gourisankar Ghosh

Publications:

Hotchkiss S, Mulero M, Chan GJ,Biswas T, Polley S, Ohn C, Demir O, Amaro RE, Siegel D, Ghosh G (2021) Discovery of an IKK2/b Site that Allosterically Controls Its Activation (submitted).