Sergi Garcia-Manyes - Related publications

2005-2011 Department of Biological Sc Columbia University, New York, NY 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Zhuravlev PI, Hinczewski M, Thirumalai D. Low Force Unfolding of a Single-Domain Protein by Parallel Pathways. The Journal of Physical Chemistry. B. PMID 33565314 DOI: 10.1021/acs.jpcb.0c11308   
2021 Mori T, Jung J, Kobayashi C, Dokainish HM, Re S, Sugita Y. Elucidation of Interactions Regulating Conformational Stability and Dynamics of SARS-CoV-2 S-Protein. Biophysical Journal. PMID 33484712 DOI: 10.1016/j.bpj.2021.01.012   
2021 Buchholz I, McDonnell T, Nestler P, Tharad S, Kulke M, Radziszewska A, Ripoll VM, Schmidt F, Hammer E, Toca-Herrera JL, Rahman A, Delcea M. Specific domain V reduction of beta-2-glycoprotein I induces protein flexibility and alters pathogenic antibody binding. Scientific Reports. 11: 4542. PMID 33633190 DOI: 10.1038/s41598-021-84021-2   
2021 Hervø-Hansen S, Højgaard C, Johansson KE, Wang Y, Wahni K, Young D, Messens J, Teilum K, Lindorff-Larsen K, Winther JR. Charge Interactions in a Highly Charge-Depleted Protein. Journal of the American Chemical Society. PMID 33529004 DOI: 10.1021/jacs.0c10789   
2021 Milorey B, Schweitzer-Stenner R, Andrews B, Schwalbe H, Urbanc B. Short peptides as predictors for the structure of polyarginine sequences in disordered proteins. Biophysical Journal. PMID 33453267 DOI: 10.1016/j.bpj.2020.12.026   
2021 Duran T, Minatovicz B, Bai J, Shin D, Mohammadiarani H, Chaudhuri B. Molecular Dynamics Simulation to Uncover the Mechanisms of Protein Instability During Freezing. Journal of Pharmaceutical Sciences. PMID 33421436 DOI: 10.1016/j.xphs.2021.01.002   
2021 Gianni S, Freiberger MI, Jemth P, Ferreiro DU, Wolynes PG, Fuxreiter M. Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly. Accounts of Chemical Research. PMID 33550810 DOI: 10.1021/acs.accounts.0c00813   
2021 Hou Q, Pucci F, Ancien F, Kwasigroch JM, Bourgeas R, Rooman M. SWOTein: a structure-based approach to predict stability Strengths and Weaknesses of prOTEINs. Bioinformatics (Oxford, England). PMID 33471089 DOI: 10.1093/bioinformatics/btab034   
2021 Sanders JC, Holmstrom ED. Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins. Essays in Biochemistry. PMID 33600559 DOI: 10.1042/EBC20200022   
2021 Gupta M, Venkatramani R, Ainavarapu SRK. Role of Ligand Binding Site in Modulating the Mechanical Stability of Proteins with β-Grasp Fold. The Journal of Physical Chemistry. B. PMID 33492970 DOI: 10.1021/acs.jpcb.0c08085   
2021 Paiz EA, Lewis KA, Whitten ST. Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins. Molecules (Basel, Switzerland). 26. PMID 33530506 DOI: 10.3390/molecules26030634   
2021 Bedford JT, Poutsma J, Diawara N, Greene LH. The nature of persistent interactions in two model β-grasp proteins reveals the advantage of symmetry in stability. Journal of Computational Chemistry. PMID 33534913 DOI: 10.1002/jcc.26477   
2021 Gopal SM, Wingbermühle S, Schnatwinkel J, Juber S, Herrmann C, Schäfer LV. Conformational Preferences of an Intrinsically Disordered Protein Domain: A Case Study for Modern Force Fields. The Journal of Physical Chemistry. B. 125: 24-35. PMID 33382616 DOI: 10.1021/acs.jpcb.0c08702   
2021 Roche R, Bhattacharya S, Bhattacharya D. Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins. Plos Computational Biology. 17: e1008753. PMID 33621244 DOI: 10.1371/journal.pcbi.1008753   
2021 Xu X, Gagné D, Aramini JM, Gardner KH. Volume and Compressibility Differences Between Protein Conformations Revealed by High-Pressure NMR. Biophysical Journal. PMID 33524371 DOI: 10.1016/j.bpj.2020.12.034   
2021 Vugmeyster L. Recent developments in deuterium solid-state NMR for the detection of slow motions in proteins. Solid State Nuclear Magnetic Resonance. 111: 101710. PMID 33450712 DOI: 10.1016/j.ssnmr.2020.101710   
2021 Romero-Tamayo S, Laplaza R, Velazquez-Campoy A, Villanueva R, Medina M, Ferreira P. W196 and the -Hairpin Motif Modulate the Redox Switch of Conformation and the Biomolecular Interaction Network of the Apoptosis-Inducing Factor. Oxidative Medicine and Cellular Longevity. 2021: 6673661. PMID 33510840 DOI: 10.1155/2021/6673661   
2021 Bhatia S, Krishnamoorthy G, Udgaonkar JB. Mapping Distinct Sequences of Structure Formation Differentiating Multiple Folding Pathways of a Small Protein. Journal of the American Chemical Society. PMID 33430589 DOI: 10.1021/jacs.0c11097   
2021 Hays JM, Boland E, Kasson PM. Inference of Joint Conformational Distributions from Separately Acquired Experimental Measurements. The Journal of Physical Chemistry Letters. 12: 1606-1611. PMID 33596657 DOI: 10.1021/acs.jpclett.0c03623   
2021 Mondal B, Nagesh J, Reddy G. Double Domain Swapping in Human γC and γD Crystallin Drives Early Stages of Aggregation. The Journal of Physical Chemistry. B. PMID 33566611 DOI: 10.1021/acs.jpcb.0c07833   
2021 Tesei G, Martins JM, Kunze MBA, Wang Y, Crehuet R, Lindorff-Larsen K. DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles. Plos Computational Biology. 17: e1008551. PMID 33481784 DOI: 10.1371/journal.pcbi.1008551   
2021 Harkness RW, Hennecker C, Grün JT, Blümler A, Heckel A, Schwalbe H, Mittermaier AK. Parallel reaction pathways accelerate folding of a guanine quadruplex. Nucleic Acids Research. PMID 33469659 DOI: 10.1093/nar/gkaa1286   
2021 Nixon CF, Lim SA, Sailer ZR, Zheludev IN, Gee CL, Kelch BA, Harms MJ, Marqusee S. Exploring the Evolutionary History of Kinetic Stability in the α-Lytic Protease Family. Biochemistry. PMID 33433210 DOI: 10.1021/acs.biochem.0c00720   
2021 Seifi B, Wallin S. The C-terminal domain of transcription factor RfaH: Folding, fold switching and energy landscape. Biopolymers. e23420. PMID 33521926 DOI: 10.1002/bip.23420   
2021 Thompson EJ, Paul A, Iavarone AT, Klinman JP. Identification of Thermal Conduits That Link the Protein-Water Interface to the Active Site Loop and Catalytic Base in Enolase. Journal of the American Chemical Society. PMID 33395523 DOI: 10.1021/jacs.0c09423   
2021 Di Luca A, Kaila VRI. Molecular strain in the active/deactive-transition modulates domain coupling in respiratory complex I. Biochimica Et Biophysica Acta. Bioenergetics. 148382. PMID 33513365 DOI: 10.1016/j.bbabio.2021.148382   
2021 Petrosyan R, Patra S, Rezajooei N, Garen CR, Woodside MT. Unfolded and intermediate states of PrP play a key role in the mechanism of action of an antiprion chaperone. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33619087 DOI: 10.1073/pnas.2010213118   
2021 Labra-Núñez A, Cofas-Vargas LF, Gutiérrez-Magdaleno G, Gómez-Velasco H, Rodríguez-Hernández A, Rodríguez-Romero A, García-Hernández E. Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Archives of Biochemistry and Biophysics. 699: 108750. PMID 33421379 DOI: 10.1016/   
2021 Labra-Núñez A, Cofas-Vargas LF, Gutiérrez-Magdaleno G, Gómez-Velasco H, Rodríguez-Hernández A, Rodríguez-Romero A, García-Hernández E. Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Archives of Biochemistry and Biophysics. 699: 108750. PMID 33421379 DOI: 10.1016/   
2021 Li J, Shen P, Zhen S, Tang C, Ye Y, Zhou D, Hong W, Zhao Z, Tang BZ. Mechanical single-molecule potentiometers with large switching factors from ortho-pentaphenylene foldamers. Nature Communications. 12: 167. PMID 33420002 DOI: 10.1038/s41467-020-20311-z   
2021 Moradi S, Ahmadi P, Karami C, Farhadian N, Balaei F, Ansari M, Shahlaei M. Evaluation of the effects of isoniazid and rifampin on the structure and activity of pepsin enzyme by multi spectroscopy and molecular modeling methods. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 253: 119523. PMID 33621938 DOI: 10.1016/j.saa.2021.119523   
2021 Dang TKL, Nguyen T, Habeck M, Gültas M, Waack S. A graph-based algorithm for detecting rigid domains in protein structures. Bmc Bioinformatics. 22: 66. PMID 33579190 DOI: 10.1186/s12859-021-03966-3   
2021 Crilly CJ, Brom JA, Kowalewski ME, Piszkiewicz S, Pielak GJ. Dried Protein Structure Revealed at the Residue Level by Liquid-Observed Vapor Exchange NMR. Biochemistry. PMID 33400518 DOI: 10.1021/acs.biochem.0c00863   
2021 Begun A, Liubimov S, Molochkov A, Niemi AJ. On topology and knotty entanglement in protein folding. Plos One. 16: e0244547. PMID 33439862 DOI: 10.1371/journal.pone.0244547   
2021 Li Y, Bedi RK, Wiedmer L, Sun X, Huang D, Caflisch A. Atomistic and Thermodynamic Analysis of N6-Methyladenosine (mA) Recognition by the Reader Domain of YTHDC1. Journal of Chemical Theory and Computation. PMID 33472367 DOI: 10.1021/acs.jctc.0c01136   
2021 Kumar R, Saran S. Comparative modelling unravels the structural features of eukaryotic TCTP implicated in its multifunctional properties: an in silico approach. Journal of Molecular Modeling. 27: 20. PMID 33410974 DOI: 10.1007/s00894-020-04630-y   
2021 Gupta D, Tiwari P, Haque MA, Sachdeva E, Hassan MI, Ethayathulla AS, Kaur P. Structural insights into the transient closed conformation and pH dependent ATPase activity of S.Typhi GyraseB N- terminal domain. Archives of Biochemistry and Biophysics. 108786. PMID 33548211 DOI: 10.1016/   
2021 Mei LC, Wang YL, Wu FX, Wang F, Hao GF, Yang GF. HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study. Briefings in Bioinformatics. PMID 33406224 DOI: 10.1093/bib/bbaa373   
2021 Steinmetz A, Yvorra T, Retailleau P, Lantz O, Schmidt F. Datasets and analyses of molecular dynamics simulations of covalent binary and ternary complexes of MHC class I-related molecule/T-cell receptor (MR1/TCR) agonists to understand complex formation and conditions of fluorescent labelling. Data in Brief. 34: 106704. PMID 33506079 DOI: 10.1016/j.dib.2020.106704   
2021 Juraszek J, Rutten L, Blokland S, Bouchier P, Voorzaat R, Ritschel T, Bakkers MJG, Renault LLR, Langedijk JPM. Stabilizing the closed SARS-CoV-2 spike trimer. Nature Communications. 12: 244. PMID 33431842 DOI: 10.1038/s41467-020-20321-x   
2021 Sellner M, Fischer A, Don CG, Smieško M. Conformational Landscape of Cytochrome P450 Reductase Interactions. International Journal of Molecular Sciences. 22. PMID 33498551 DOI: 10.3390/ijms22031023   
2021 Sharma A, Kumari S, Goel M. Uncovering the structure-function aspects of an archaeal CsaA protein. Biochimica Et Biophysica Acta. Proteins and Proteomics. 140615. PMID 33561579 DOI: 10.1016/j.bbapap.2021.140615   
2021 Quesada Moreno MM, Pinacho P, Perez C, Sekutor M, Schreiner PR, Schnell M. Do docking sites persist upon fluorination? The diadamantyl ether-aromatics challenge for rotational spectroscopy and theory. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 33512017 DOI: 10.1002/chem.202100078   
2021 Diaz DB, Appavoo SD, Bogdanchikova AF, Lebedev Y, McTiernan TJ, Dos Passos Gomes G, Yudin AK. Illuminating the dark conformational space of macrocycles using dominant rotors. Nature Chemistry. PMID 33589789 DOI: 10.1038/s41557-020-00620-y   
2021 Koculi E, Thirumalai D. Retardation of Folding Rates of Substrate Proteins in the Nanocage of GroEL. Biochemistry. PMID 33464880 DOI: 10.1021/acs.biochem.0c00903   
2021 Smith RD, Carlson HA. Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. Journal of Chemical Information and Modeling. PMID 33599485 DOI: 10.1021/acs.jcim.0c01002   
2021 You Y, Yang L, Chen H, Xiong L, Yang F. Effects of (-)-Epigallocatechin-3-gallate on the Functional and Structural Properties of Soybean Protein Isolate. Journal of Agricultural and Food Chemistry. PMID 33576221 DOI: 10.1021/acs.jafc.0c07337   
2021 Zhu M, Song LT, Liu RR, Zhai HL, Meng YJ, Ren CL. Selective inhibition mechanism of nitroxoline to the BET family: Insight from molecular simulations. Life Sciences. 119141. PMID 33529672 DOI: 10.1016/j.lfs.2021.119141   
2021 Khan FI, Song H, Hassan F, Tian J, Tang L, Lai D, Juan F. Impact of amino acid substitutions on the behavior of a photoactivatable near infrared fluorescent protein PAiRFP1. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 253: 119572. PMID 33631627 DOI: 10.1016/j.saa.2021.119572   
2021 Lindsay RJ, Mansbach RA, Gnanakaran S, Shen T. Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation. Biophysical Chemistry. 271: 106552. PMID 33581430 DOI: 10.1016/j.bpc.2021.106552