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Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps.

Bitran A, Jacobs WM, Zhai X, Shakhnovich E.

Proc Natl Acad Sci U S A. 2020 Jan 21;117(3):1485-1495. doi: 10.1073/pnas.1913207117. Epub 2020 Jan 7.


Common activation mechanism of class A GPCRs.

Zhou Q, Yang D, Wu M, Guo Y, Guo W, Zhong L, Cai X, Dai A, Jang W, Shakhnovich EI, Liu ZJ, Stevens RC, Lambert NA, Babu MM, Wang MW, Zhao S.

Elife. 2019 Dec 19;8. pii: e50279. doi: 10.7554/eLife.50279.


Semi-rational design and molecular dynamics simulations study of the thermostability enhancement of cellobiose 2-epimerases.

Chen Q, Xiao Y, Shakhnovich EI, Zhang W, Mu W.

Int J Biol Macromol. 2019 Nov 13. pii: S0141-8130(19)37163-6. doi: 10.1016/j.ijbiomac.2019.11.015. [Epub ahead of print]


Adaptation to mutational inactivation of an essential gene converges to an accessible suboptimal fitness peak.

Rodrigues JV, Shakhnovich EI.

Elife. 2019 Oct 1;8. pii: e50509. doi: 10.7554/eLife.50509.


The Early Phase of β2m Aggregation: An Integrative Computational Study Framed on the D76N Mutant and the ΔN6 Variant.

J S Loureiro R, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, F N Faísca P.

Biomolecules. 2019 Aug 14;9(8). pii: E366. doi: 10.3390/biom9080366.


Simulation-guided enzyme discovery: A new microbial source of cellobiose 2-epimerase.

Xiao Y, Chen Q, Shakhnovich EI, Zhang W, Mu W.

Int J Biol Macromol. 2019 Oct 15;139:1002-1008. doi: 10.1016/j.ijbiomac.2019.08.075. Epub 2019 Aug 8.


Substrate inhibition imposes fitness penalty at high protein stability.

Adkar BV, Bhattacharyya S, Gilson AI, Zhang W, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2019 Jun 4;116(23):11265-11274. doi: 10.1073/pnas.1821447116. Epub 2019 May 16.


Chimeric dihydrofolate reductases display properties of modularity and biophysical diversity.

Rodrigues JV, Ogbunugafor CB, Hartl DL, Shakhnovich EI.

Protein Sci. 2019 Jul;28(7):1359-1367. doi: 10.1002/pro.3646. Epub 2019 May 30.


Mutation rate variability as a driving force in adaptive evolution.

Engelhardt D, Shakhnovich EI.

Phys Rev E. 2019 Feb;99(2-1):022424. doi: 10.1103/PhysRevE.99.022424.


Dynamic disulfide exchange in a crystallin protein in the human eye lens promotes cataract-associated aggregation.

Serebryany E, Yu S, Trauger SA, Budnik B, Shakhnovich EI.

J Biol Chem. 2018 Nov 16;293(46):17997-18009. doi: 10.1074/jbc.RA118.004551. Epub 2018 Sep 21.


Growth tradeoffs produce complex microbial communities on a single limiting resource.

Manhart M, Shakhnovich EI.

Nat Commun. 2018 Aug 10;9(1):3214. doi: 10.1038/s41467-018-05703-6.


Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape.

Jacobs WM, Shakhnovich EI.

J Phys Chem B. 2018 Dec 13;122(49):11126-11136. doi: 10.1021/acs.jpcb.8b05842. Epub 2018 Aug 22.


ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.

Razban RM, Gilson AI, Durfee N, Strobelt H, Dinkla K, Choi JM, Pfister H, Shakhnovich EI.

Bioinformatics. 2018 Dec 1;34(23):4140. doi: 10.1093/bioinformatics/bty516. No abstract available.


Evolution on the Biophysical Fitness Landscape of an RNA Virus.

Rotem A, Serohijos AWR, Chang CB, Wolfe JT, Fischer AE, Mehoke TS, Zhang H, Tao Y, Lloyd Ung W, Choi JM, Rodrigues JV, Kolawole AO, Koehler SA, Wu S, Thielen PM, Cui N, Demirev PA, Giacobbi NS, Julian TR, Schwab K, Lin JS, Smith TJ, Pipas JM, Wobus CE, Feldman AB, Weitz DA, Shakhnovich EI.

Mol Biol Evol. 2018 Oct 1;35(10):2390-2400. doi: 10.1093/molbev/msy131.


Accessibility of the Shine-Dalgarno Sequence Dictates N-Terminal Codon Bias in E. coli.

Bhattacharyya S, Jacobs WM, Adkar BV, Yan J, Zhang W, Shakhnovich EI.

Mol Cell. 2018 Jun 7;70(5):894-905.e5. doi: 10.1016/j.molcel.2018.05.008. Epub 2018 Jun 7.


ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.

Razban RM, Gilson AI, Durfee N, Strobelt H, Dinkla K, Choi JM, Pfister H, Shakhnovich EI.

Bioinformatics. 2018 Oct 15;34(20):3557-3565. doi: 10.1093/bioinformatics/bty370. Erratum in: Bioinformatics. 2018 Dec 1;34(23):4140.


Correction to Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants.

Srinivasan B, Rodrigues JV, Tonddast-Navaei S, Shakhnovich E, Skolnick J.

ACS Chem Biol. 2018 May 18;13(5):1407. doi: 10.1021/acschembio.7b00759. Epub 2018 Apr 24. No abstract available.


Differential Enzyme Flexibility Probed Using Solid-State Nanopores.

Hu R, Rodrigues JV, Waduge P, Yamazaki H, Cressiot B, Chishti Y, Makowski L, Yu D, Shakhnovich E, Zhao Q, Wanunu M.

ACS Nano. 2018 May 22;12(5):4494-4502. doi: 10.1021/acsnano.8b00734. Epub 2018 Apr 17.


Trade-offs between microbial growth phases lead to frequency-dependent and non-transitive selection.

Manhart M, Adkar BV, Shakhnovich EI.

Proc Biol Sci. 2018 Feb 14;285(1872). pii: 20172459. doi: 10.1098/rspb.2017.2459.


Stability of the Influenza Virus Hemagglutinin Protein Correlates with Evolutionary Dynamics.

Klein EY, Blumenkrantz D, Serohijos A, Shakhnovich E, Choi JM, Rodrigues JV, Smith BD, Lane AP, Feldman A, Pekosz A.

mSphere. 2018 Jan 3;3(1). pii: e00554-17. doi: 10.1128/mSphereDirect.00554-17. eCollection 2018 Jan-Feb.


Absence of Selection for Quantum Coherence in the Fenna-Matthews-Olson Complex: A Combined Evolutionary and Excitonic Study.

Valleau S, Studer RA, Häse F, Kreisbeck C, Saer RG, Blankenship RE, Shakhnovich EI, Aspuru-Guzik A.

ACS Cent Sci. 2017 Oct 25;3(10):1086-1095. doi: 10.1021/acscentsci.7b00269. Epub 2017 Aug 30.


Evidence of evolutionary selection for cotranslational folding.

Jacobs WM, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11434-11439. doi: 10.1073/pnas.1705772114. Epub 2017 Oct 10.


Optimization of lag phase shapes the evolution of a bacterial enzyme.

Adkar BV, Manhart M, Bhattacharyya S, Tian J, Musharbash M, Shakhnovich EI.

Nat Ecol Evol. 2017 Apr 28;1(6):149. doi: 10.1038/s41559-017-0149.


A tale of two tails: The importance of unstructured termini in the aggregation pathway of β2-microglobulin.

Loureiro RJS, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, Faísca PFN.

Proteins. 2017 Nov;85(11):2045-2057. doi: 10.1002/prot.25358. Epub 2017 Aug 8.


Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations.

Chéron N, Shakhnovich EI.

J Comput Chem. 2017 Aug 15;38(22):1941-1951. doi: 10.1002/jcc.24839. Epub 2017 Jun 1.


Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants.

Srinivasan B, Rodrigues JV, Tonddast-Navaei S, Shakhnovich E, Skolnick J.

ACS Chem Biol. 2017 Jul 21;12(7):1848-1857. doi: 10.1021/acschembio.7b00175. Epub 2017 May 31. Erratum in: ACS Chem Biol. 2018 May 18;13(5):1407.


The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution.

Gilson AI, Marshall-Christensen A, Choi JM, Shakhnovich EI.

Biophys J. 2017 Apr 11;112(7):1350-1365. doi: 10.1016/j.bpj.2017.02.029.


Graph's Topology and Free Energy of a Spin Model on the Graph.

Choi JM, Gilson AI, Shakhnovich EI.

Phys Rev Lett. 2017 Feb 24;118(8):088302. doi: 10.1103/PhysRevLett.118.088302. Epub 2017 Feb 24.


A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016.

Debroise T, Shakhnovich EI, Chéron N.

J Chem Inf Model. 2017 Mar 27;57(3):584-593. doi: 10.1021/acs.jcim.6b00610. Epub 2017 Feb 27.


Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighborhoods in Sequence Space.

Zhou Q, Sun X, Xia X, Fan Z, Luo Z, Zhao S, Shakhnovich E, Liang H.

J Phys Chem Lett. 2017 Jan 19;8(2):407-414. doi: 10.1021/acs.jpclett.6b02769. Epub 2017 Jan 5.


Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity.

Bhattacharyya S, Bershtein S, Yan J, Argun T, Gilson AI, Trauger SA, Shakhnovich EI.

Elife. 2016 Dec 10;5. pii: e20309. doi: 10.7554/eLife.20309.


Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.

Bershtein S, Serohijos AW, Shakhnovich EI.

Curr Opin Struct Biol. 2017 Feb;42:31-40. doi: 10.1016/ Epub 2016 Oct 31. Review.


Structure-Based Prediction of Protein-Folding Transition Paths.

Jacobs WM, Shakhnovich EI.

Biophys J. 2016 Sep 6;111(5):925-36. doi: 10.1016/j.bpj.2016.06.031.


An Internal Disulfide Locks a Misfolded Aggregation-prone Intermediate in Cataract-linked Mutants of Human γD-Crystallin.

Serebryany E, Woodard JC, Adkar BV, Shabab M, King JA, Shakhnovich EI.

J Biol Chem. 2016 Sep 2;291(36):19172-83. doi: 10.1074/jbc.M116.735977. Epub 2016 Jul 14.


A Simple Model of Protein Domain Swapping in Crowded Cellular Environments.

Woodard JC, Dunatunga S, Shakhnovich EI.

Biophys J. 2016 Jun 7;110(11):2367-2376. doi: 10.1016/j.bpj.2016.04.033.


Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models.

Jacquin H, Gilson A, Shakhnovich E, Cocco S, Monasson R.

PLoS Comput Biol. 2016 May 13;12(5):e1004889. doi: 10.1371/journal.pcbi.1004889. eCollection 2016 May.


Evolutionary dynamics of viral escape under antibodies stress: A biophysical model.

Chéron N, Serohijos AW, Choi JM, Shakhnovich EI.

Protein Sci. 2016 Jul;25(7):1332-40. doi: 10.1002/pro.2915. Epub 2016 Mar 24.


Biophysical principles predict fitness landscapes of drug resistance.

Rodrigues JV, Bershtein S, Li A, Lozovsky ER, Hartl DL, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):E1470-8. doi: 10.1073/pnas.1601441113. Epub 2016 Feb 29. Erratum in: Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):E1964.


Searching the Sequence Space for Potent Aptamers Using SELEX in Silico.

Zhou Q, Xia X, Luo Z, Liang H, Shakhnovich E.

J Chem Theory Comput. 2015 Dec 8;11(12):5939-46. doi: 10.1021/acs.jctc.5b00707. Epub 2015 Nov 5.


Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria.

Bershtein S, Serohijos AW, Bhattacharyya S, Manhart M, Choi JM, Mu W, Zhou J, Shakhnovich EI.

PLoS Genet. 2015 Oct 20;11(10):e1005612. doi: 10.1371/journal.pgen.1005612. eCollection 2015 Oct.


OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands.

Chéron N, Jasty N, Shakhnovich EI.

J Med Chem. 2016 May 12;59(9):4171-88. doi: 10.1021/acs.jmedchem.5b00886. Epub 2015 Sep 23.


Repurposing of rutin for the inhibition of norovirus replication.

Chéron N, Yu C, Kolawole AO, Shakhnovich EI, Wobus CE.

Arch Virol. 2015 Sep;160(9):2353-8. doi: 10.1007/s00705-015-2495-y. Epub 2015 Jun 26.


Isolation and Analysis of Rare Norovirus Recombinants from Coinfected Mice Using Drop-Based Microfluidics.

Zhang H, Cockrell SK, Kolawole AO, Rotem A, Serohijos AW, Chang CB, Tao Y, Mehoke TS, Han Y, Lin JS, Giacobbi NS, Feldman AB, Shakhnovich E, Weitz DA, Wobus CE, Pipas JM.

J Virol. 2015 Aug;89(15):7722-34. doi: 10.1128/JVI.01137-15. Epub 2015 May 13.


Thermal stabilization of dihydrofolate reductase using monte carlo unfolding simulations and its functional consequences.

Tian J, Woodard JC, Whitney A, Shakhnovich EI.

PLoS Comput Biol. 2015 Apr 23;11(4):e1004207. doi: 10.1371/journal.pcbi.1004207. eCollection 2015 Apr.


Systems-level response to point mutations in a core metabolic enzyme modulates genotype-phenotype relationship.

Bershtein S, Choi JM, Bhattacharyya S, Budnik B, Shakhnovich E.

Cell Rep. 2015 Apr 28;11(4):645-56. doi: 10.1016/j.celrep.2015.03.051. Epub 2015 Apr 16.


Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding.

Choi JM, Serohijos AWR, Murphy S, Lucarelli D, Lofranco LL, Feldman A, Shakhnovich EI.

Biophys J. 2015 Feb 17;108(4):795-798. doi: 10.1016/j.bpj.2015.01.001.


Is catalytic activity of chaperones a selectable trait for the emergence of heat shock response?

Çetinbaş M, Shakhnovich EI.

Biophys J. 2015 Jan 20;108(2):438-48. doi: 10.1016/j.bpj.2014.11.3468.


The influence of selection for protein stability on dN/dS estimations.

Dasmeh P, Serohijos AW, Kepp KP, Shakhnovich EI.

Genome Biol Evol. 2014 Oct 28;6(10):2956-67. doi: 10.1093/gbe/evu223.


Evolution of specificity in protein-protein interactions.

Peleg O, Choi JM, Shakhnovich EI.

Biophys J. 2014 Oct 7;107(7):1686-96. doi: 10.1016/j.bpj.2014.08.004.


Gene Dosage Experiments in Enterobacteriaceae Using Arabinose-regulated Promoters.

Bhattacharyya S, Bershtein S, Shakhnovich EI.

Bio Protoc. 2014 Jul 20;7(14). pii: e2396. doi: 10.21769/BioProtoc.2396.

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