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Items: 28

1.

Constrained Mutational Sampling of Amino Acids in HIV-1 Protease Evolution.

Boucher JI, Whitfield TW, Dauphin A, Nachum G, Hollins C, Zeldovich KB, Swanstrom R, Schiffer CA, Luban J, Bolon DNA.

Mol Biol Evol. 2019 Apr 1;36(4):798-810. doi: 10.1093/molbev/msz022.

PMID:
30721995
2.

Mutations in Influenza A Virus Neuraminidase and Hemagglutinin Confer Resistance against a Broadly Neutralizing Hemagglutinin Stem Antibody.

Prachanronarong KL, Canale AS, Liu P, Somasundaran M, Hou S, Poh YP, Han T, Zhu Q, Renzette N, Zeldovich KB, Kowalik TF, Kurt-Yilmaz N, Jensen JD, Bolon DNA, Marasco WA, Finberg RW, Schiffer CA, Wang JP.

J Virol. 2019 Jan 4;93(2). pii: e01639-18. doi: 10.1128/JVI.01639-18. Print 2019 Jan 15.

3.

Synonymous Mutations at the Beginning of the Influenza A Virus Hemagglutinin Gene Impact Experimental Fitness.

Canale AS, Venev SV, Whitfield TW, Caffrey DR, Marasco WA, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Zeldovich KB, Wang JP, Bolon DNA.

J Mol Biol. 2018 Apr 13;430(8):1098-1115. doi: 10.1016/j.jmb.2018.02.009. Epub 2018 Feb 18.

PMID:
29466705
4.

Thermophilic Adaptation in Prokaryotes Is Constrained by Metabolic Costs of Proteostasis.

Venev SV, Zeldovich KB.

Mol Biol Evol. 2018 Jan 1;35(1):211-224. doi: 10.1093/molbev/msx282.

5.

Elucidating the Interdependence of Drug Resistance from Combinations of Mutations.

Ragland DA, Whitfield TW, Lee SK, Swanstrom R, Zeldovich KB, Kurt-Yilmaz N, Schiffer CA.

J Chem Theory Comput. 2017 Nov 14;13(11):5671-5682. doi: 10.1021/acs.jctc.7b00601. Epub 2017 Oct 9.

6.

Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints.

Chan YH, Venev SV, Zeldovich KB, Matthews CR.

Nat Commun. 2017 Mar 6;8:14614. doi: 10.1038/ncomms14614.

7.

Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase.

Prachanronarong KL, Özen A, Thayer KM, Yilmaz LS, Zeldovich KB, Bolon DN, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Kurt-Yilmaz N, Schiffer CA.

J Chem Theory Comput. 2016 Dec 13;12(12):6098-6108. Epub 2016 Nov 17.

PMID:
27951676
8.

An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy.

Bank C, Renzette N, Liu P, Matuszewski S, Shim H, Foll M, Bolon DN, Zeldovich KB, Kowalik TF, Finberg RW, Wang JP, Jensen JD.

Evolution. 2016 Nov;70(11):2470-2484. doi: 10.1111/evo.13041. Epub 2016 Sep 13.

PMID:
27566611
9.

A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance.

Jiang L, Liu P, Bank C, Renzette N, Prachanronarong K, Yilmaz LS, Caffrey DR, Zeldovich KB, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Bolon DNA.

J Mol Biol. 2016 Feb 13;428(3):538-553. doi: 10.1016/j.jmb.2015.11.027. Epub 2015 Dec 4.

PMID:
26656922
10.

Massively parallel sampling of lattice proteins reveals foundations of thermal adaptation.

Venev SV, Zeldovich KB.

J Chem Phys. 2015 Aug 7;143(5):055101. doi: 10.1063/1.4927565.

PMID:
26254668
11.

Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment.

Zeldovich KB, Liu P, Renzette N, Foll M, Pham ST, Venev SV, Gallagher GR, Bolon DN, Kurt-Jones EA, Jensen JD, Caffrey DR, Schiffer CA, Kowalik TF, Wang JP, Finberg RW.

Mol Biol Evol. 2015 Jun;32(6):1519-32. doi: 10.1093/molbev/msv044. Epub 2015 Feb 23.

12.

Influenza virus drug resistance: a time-sampled population genetics perspective.

Foll M, Poh YP, Renzette N, Ferrer-Admetlla A, Bank C, Shim H, Malaspinas AS, Ewing G, Liu P, Wegmann D, Caffrey DR, Zeldovich KB, Bolon DN, Wang JP, Kowalik TF, Schiffer CA, Finberg RW, Jensen JD.

PLoS Genet. 2014 Feb 27;10(2):e1004185. doi: 10.1371/journal.pgen.1004185. eCollection 2014 Feb.

13.

Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro.

Renzette N, Caffrey DR, Zeldovich KB, Liu P, Gallagher GR, Aiello D, Porter AJ, Kurt-Jones EA, Bolon DN, Poh YP, Jensen JD, Schiffer CA, Kowalik TF, Finberg RW, Wang JP.

J Virol. 2014 Jan;88(1):272-81. doi: 10.1128/JVI.01067-13. Epub 2013 Oct 23.

14.

Latent effects of Hsp90 mutants revealed at reduced expression levels.

Jiang L, Mishra P, Hietpas RT, Zeldovich KB, Bolon DN.

PLoS Genet. 2013 Jun;9(6):e1003600. doi: 10.1371/journal.pgen.1003600. Epub 2013 Jun 27.

15.

Segment self-repulsion is the major driving force of influenza genome packaging.

Venev SV, Zeldovich KB.

Phys Rev Lett. 2013 Mar 1;110(9):098104. Epub 2013 Feb 28.

PMID:
23496749
16.

Analyses of the effects of all ubiquitin point mutants on yeast growth rate.

Roscoe BP, Thayer KM, Zeldovich KB, Fushman D, Bolon DN.

J Mol Biol. 2013 Apr 26;425(8):1363-77. doi: 10.1016/j.jmb.2013.01.032. Epub 2013 Jan 30.

17.

Understanding protein evolution: from protein physics to Darwinian selection.

Zeldovich KB, Shakhnovich EI.

Annu Rev Phys Chem. 2008;59:105-27. Review.

PMID:
17937598
18.

Protein stability imposes limits on organism complexity and speed of molecular evolution.

Zeldovich KB, Chen P, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2007 Oct 9;104(41):16152-7. Epub 2007 Oct 3.

19.

A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds.

Zeldovich KB, Chen P, Shakhnovich BE, Shakhnovich EI.

PLoS Comput Biol. 2007 Jul;3(7):e139.

20.

Positive and negative design in stability and thermal adaptation of natural proteins.

Berezovsky IN, Zeldovich KB, Shakhnovich EI.

PLoS Comput Biol. 2007 Mar 23;3(3):e52. Epub 2007 Feb 1.

21.

The folding mechanics of a knotted protein.

Wallin S, Zeldovich KB, Shakhnovich EI.

J Mol Biol. 2007 May 4;368(3):884-93. Epub 2007 Feb 22.

22.

Protein and DNA sequence determinants of thermophilic adaptation.

Zeldovich KB, Berezovsky IN, Shakhnovich EI.

PLoS Comput Biol. 2007 Jan 12;3(1):e5. Epub 2006 Nov 30.

23.

Statistically enhanced self-attraction of random patterns.

Lukatsky DB, Zeldovich KB, Shakhnovich EI.

Phys Rev Lett. 2006 Oct 27;97(17):178101. Epub 2006 Oct 25.

PMID:
17155509
24.

Collective dynamics of interacting molecular motors.

Campàs O, Kafri Y, Zeldovich KB, Casademunt J, Joanny JF.

Phys Rev Lett. 2006 Jul 21;97(3):038101. Epub 2006 Jul 19. Review.

PMID:
16907545
25.

Physical origins of protein superfamilies.

Zeldovich KB, Berezovsky IN, Shakhnovich EI.

J Mol Biol. 2006 Apr 7;357(4):1335-43. Epub 2006 Feb 6.

PMID:
16483605
26.

Motor proteins transporting cargos.

Zeldovich KB, Joanny JF, Prost J.

Eur Phys J E Soft Matter. 2005 Jun;17(2):155-63. Epub 2005 May 9.

PMID:
15880289
27.

Motion of single long DNA molecules through arrays of magnetic columns.

Minc N, Bokov P, Zeldovich KB, Fütterer C, Viovy JL, Dorfman KD.

Electrophoresis. 2005 Jan;26(2):362-75.

PMID:
15657884
28.

Cooperative extraction of membrane nanotubes by molecular motors.

Leduc C, Campàs O, Zeldovich KB, Roux A, Jolimaitre P, Bourel-Bonnet L, Goud B, Joanny JF, Bassereau P, Prost J.

Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17096-101. Epub 2004 Nov 29.

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