Sri Rama Koti Ainavarapu - Related publications

Affiliations: 
Tata Institute of Fundamental Research, Mumbai, Maharashtra, India 
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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 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 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 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 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 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 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 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 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 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 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 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 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 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/j.abb.2021.108786   
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 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 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 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 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/j.abb.2020.108750   
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/j.abb.2020.108750   
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 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 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 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 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 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 Ching WY, Adhikari P, Jawad B, Podgornik R. Ultra-large-scale quantum chemical computation of bio-molecular systems: the case of Spike protein of SARS-CoV-2 virus. Computational and Structural Biotechnology Journal. PMID 33623641 DOI: 10.1016/j.csbj.2021.02.004   
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 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 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 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 Saha S, Bhattacharjee S, Chowdhury J. Exploring the binding interactions of janus green blue with serum albumins from spectroscopic and calorimetric studies aided by calculations. Journal of Biomolecular Structure & Dynamics. 1-17. PMID 33410370 DOI: 10.1080/07391102.2020.1870156   
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 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 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 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 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 Aiyer S, Swapna GVT, Ma LC, Liu G, Hao J, Chalmers G, Jacobs BC, Montelione GT, Roth MJ. A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins. Structure (London, England : 1993). PMID 33592170 DOI: 10.1016/j.str.2021.01.010   
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   
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 Rocha MA, Sprague-Piercy MA, Kwok AO, Roskamp KW, Martin RW. Chemical Properties Determine Solubility and Stability in βγ-Crystallins of the Eye Lens. Chembiochem : a European Journal of Chemical Biology. PMID 33569867 DOI: 10.1002/cbic.202000739   
2021 Thompson CJ, Vu VH, Leckband DE, Schwartz DK. Cadherin cis and trans interactions are mutually cooperative. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33658369 DOI: 10.1073/pnas.2019845118   
2021 Mahmoudinobar F, Nilsson BL, Dias CL. Effects of Ions and Small Compounds on the Structure of Aβ Monomers. The Journal of Physical Chemistry. B. 125: 1085-1097. PMID 33481611 DOI: 10.1021/acs.jpcb.0c09617   
2021 Barnes CA, Starich MR, Tjandra N, Mishra P. Simultaneous measurement of H-R's for rapid acquisition of backbone and sidechain paramagnetic relaxation enhancements (PREs) in proteins. Journal of Biomolecular Nmr. PMID 33625630 DOI: 10.1007/s10858-021-00359-9   
2021 Lapenta F, Aupič J, Vezzoli M, Strmšek Ž, Da Vela S, Svergun DI, Carazo JM, Melero R, Jerala R. Self-assembly and regulation of protein cages from pre-organised coiled-coil modules. Nature Communications. 12: 939. PMID 33574245 DOI: 10.1038/s41467-021-21184-6   
2021 Wang X, Ma Q. Wzb of Vibrio vulnificus represents a new group of low molecular weight protein tyrosine phosphatases with a unique insertion in the W-loop. The Journal of Biological Chemistry. 100280. PMID 33450227 DOI: 10.1016/j.jbc.2021.100280   
2021 Salvi N, Bessa LM, Guseva S, Camacho-Zarco A, Maurin D, Perez LM, Malki A, Hengesbach M, Korn SM, Schlundt A, Schwalbe H, Blackledge M. H, C and N backbone chemical shift assignments of SARS-CoV-2 nsp3a. Biomolecular Nmr Assignments. PMID 33475934 DOI: 10.1007/s12104-020-10001-8