IBBR Publications

Found 365 results
Filters: Keyword is Protein Conformation  [Clear All Filters]
2020
Tyukhtenko S, Ma X, Rajarshi G, Karageorgos I, Anderson KW, Hudgens JW, Guo JJ, Nasr ML, Zvonok N, Vemuri K, et al. Conformational gating, dynamics and allostery in human monoacylglycerol lipase. Sci Rep. 2020 ;10(1):18531.
Sesterhenn F, Yang C, Bonet J, Cramer JT, Wen X, Wang Y, Chiang C-I, Abriata LA, Kucharska I, Castoro G, et al. De novo protein design enables the precise induction of RSV-neutralizing antibodies. Science. 2020 ;368(6492).
2019
Bester SM, Adipietro KA, Funk VL, Myslinski JM, Keul ND, Cheung J, Wilder PT, Wood ZA, Weber DJ, Height JJ, et al. The structural and biochemical impacts of monomerizing human acetylcholinesterase. Protein Sci. 2019 ;28(6):1106-1114.
2018
Zhang S-Q, Huang H, Yang J, Kratochvil HT, Lolicato M, Liu Y, Shu X, Liu L, DeGrado WF. Designed peptides that assemble into cross-α amyloid-like structures. Nat Chem Biol. 2018 ;14(9):870-875.
S Hasan S, Sevvana M, Kuhn RJ, Rossmann MG. Structural biology of Zika virus and other flaviviruses. Nat Struct Mol Biol. 2018 ;25(1):13-20.
2017
Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, Mackerell AD. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat Methods. 2017 ;14(1):71-73.
2016
Lakkaraju SKaushik, Lemkul JA, Huang J, Mackerell AD. DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR. J Comput Chem. 2016 ;37(4):416-25.
Anderson KW, Mast N, Hudgens JW, Lin JB, Turko IV, Pikuleva IA. Mapping of the Allosteric Site in Cholesterol Hydroxylase CYP46A1 for Efavirenz, a Drug That Stimulates Enzyme Activity. J Biol Chem. 2016 ;291(22):11876-86.
Deshmukh L, Schwieters CD, Grishaev A, G Clore M. Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering. Chemphyschem. 2016 ;17(11):1548-52.
Cavalier MC, Ansari MImran, Pierce AD, Wilder PT, McKnight LE, E Raman P, Neau DB, Bezawada P, Alasady MJ, Charpentier TH, et al. Small Molecule Inhibitors of Ca(2+)-S100B Reveal Two Protein Conformations. J Med Chem. 2016 ;59(2):592-608.
2015
Vanommeslaeghe K, Mackerell AD. CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. Biochim Biophys Acta. 2015 ;1850(5):861-71.
Chen W, Shi C, Mackerell AD, Shen J. Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields. J Phys Chem B. 2015 ;119(25):7902-10.
Lakkaraju SK, Mbatia H, Hanscom M, Zhao Z, Wu J, Stoica B, Mackerell AD, Faden AI, Xue F. Cyclopropyl-containing positive allosteric modulators of metabotropic glutamate receptor subtype 5. Bioorg Med Chem Lett. 2015 ;25(11):2275-9.
Lakkaraju SKaushik, Yu W, E Raman P, Hershfeld AV, Fang L, Deshpande DA, Mackerell AD. Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors. J Chem Inf Model. 2015 ;55(3):700-8.
Lee JHo, Li F, Grishaev A, Bax A. Quantitative residue-specific protein backbone torsion angle dynamics from concerted measurement of 3J couplings. J Am Chem Soc. 2015 ;137(4):1432-5.
E Raman P, Mackerell AD. Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability. J Am Chem Soc. 2015 ;137(7):2608-21.
2014
Georgiev IS, Rudicell RS, Saunders KO, Shi W, Kirys T, McKee K, O'Dell S, Chuang G-Y, Yang Z-Y, Ofek GA, et al. Antibodies VRC01 and 10E8 neutralize HIV-1 with high breadth and potency even with Ig-framework regions substantially reverted to germline. J Immunol. 2014 ;192(3):1100-6.
Haidar JN, Zhu W, Lypowy J, Pierce BG, Bari A, Persaud K, Luna X, Snavely M, Ludwig D, Weng Z. Backbone flexibility of CDR3 and immune recognition of antigens. J Mol Biol. 2014 ;426(7):1583-99.
Jo S, Cheng X, Islam SM, Huang L, Rui H, Zhu A, Lee HSun, Qi Y, Han W, Vanommeslaeghe K, et al. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Adv Protein Chem Struct Biol. 2014 ;96:235-65.
Singh NKumar, S Hasan S, Kumar J, Raj I, Pathan AA, Parmar A, Shakil S, Gourinath S, Madamwar D. Crystal structure and interaction of phycocyanin with β-secretase: A putative therapy for Alzheimer's disease. CNS Neurol Disord Drug Targets. 2014 ;13(4):691-8.
Trastoy B, Lomino JV, Pierce BG, Carter LG, Günther S, Giddens JP, Snyder GA, Weiss TM, Weng Z, Wang L-X, et al. Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies. Proc Natl Acad Sci U S A. 2014 ;111(18):6714-9.
Roche J, Louis JM, Grishaev A, Ying J, Bax A. Dissociation of the trimeric gp41 ectodomain at the lipid-water interface suggests an active role in HIV-1 Env-mediated membrane fusion. Proc Natl Acad Sci U S A. 2014 ;111(9):3425-30.
Min W, Angileri F, Luo H, Lauria A, Shanmugasundaram M, Almerico AMaria, Cappello F, de Macario EConway, Lednev IK, Macario AJL, et al. A human CCT5 gene mutation causing distal neuropathy impairs hexadecamer assembly in an archaeal model. Sci Rep. 2014 ;4:6688.
Maltsev AS, Grishaev A, Roche J, Zasloff M, Bax A. Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase. J Am Chem Soc. 2014 ;136(10):3752-5.
Mallajosyula SS, Vanommeslaeghe K, Mackerell AD. Perturbation of long-range water dynamics as the mechanism for the antifreeze activity of antifreeze glycoprotein. J Phys Chem B. 2014 ;118(40):11696-706.