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Results: 1 to 20 of 198

1.

Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics.

Serohijos AW, Shakhnovich EI.

Curr Opin Struct Biol. 2014 Jun;26C:84-91. doi: 10.1016/j.sbi.2014.05.005. Epub 2014 Jun 19. Review.

PMID:
24952216
[PubMed - as supplied by publisher]
2.

A simulated intermediate state for folding and aggregation provides insights into ΔN6 β2-microglobulin amyloidogenic behavior.

Estácio SG, Krobath H, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, Faísca PF.

PLoS Comput Biol. 2014 May 8;10(5):e1003606. doi: 10.1371/journal.pcbi.1003606. eCollection 2014 May.

PMID:
24809460
[PubMed - in process]
Free PMC Article
3.

Influenza A H1N1 pandemic strain evolution--divergence and the potential for antigenic drift variants.

Klein EY, Serohijos AW, Choi JM, Shakhnovich EI, Pekosz A.

PLoS One. 2014 Apr 3;9(4):e93632. doi: 10.1371/journal.pone.0093632. eCollection 2014.

PMID:
24699432
[PubMed - in process]
Free PMC Article
4.

Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations.

Cetinbaş M, Shakhnovich EI.

PLoS Comput Biol. 2013;9(11):e1003269. doi: 10.1371/journal.pcbi.1003269. Epub 2013 Nov 7.

PMID:
24244114
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions.

Serohijos AW, Shakhnovich EI.

Mol Biol Evol. 2014 Jan;31(1):165-76. doi: 10.1093/molbev/mst189. Epub 2013 Oct 11.

PMID:
24124208
[PubMed - in process]
Free PMC Article
6.

Assessing the effect of loop mutations in the folding space of β2-microglobulin with molecular dynamics simulations.

Estácio SG, Shakhnovich EI, Faísca PF.

Int J Mol Sci. 2013 Aug 22;14(9):17256-78. doi: 10.3390/ijms140917256.

PMID:
23975166
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Structural and energetic determinants of co-translational folding.

Krobath H, Shakhnovich EI, Faísca PF.

J Chem Phys. 2013 Jun 7;138(21):215101. doi: 10.1063/1.4808044.

PMID:
23758397
[PubMed - indexed for MEDLINE]
8.

Positively selected sites in cetacean myoglobins contribute to protein stability.

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

PLoS Comput Biol. 2013;9(3):e1002929. doi: 10.1371/journal.pcbi.1002929. Epub 2013 Mar 7.

PMID:
23505347
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A one-shot germinal center model under protein structural stability constraints.

Raoof S, Heo M, Shakhnovich EI.

Phys Biol. 2013 Apr;10(2):025001. doi: 10.1088/1478-3975/10/2/025001. Epub 2013 Mar 15.

PMID:
23492682
[PubMed - indexed for MEDLINE]
10.

Highly abundant proteins favor more stable 3D structures in yeast.

Serohijos AW, Lee SY, Shakhnovich EI.

Biophys J. 2013 Feb 5;104(3):L1-3. doi: 10.1016/j.bpj.2012.11.3838.

PMID:
23442924
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A universal trend among proteomes indicates an oily last common ancestor.

Mannige RV, Brooks CL, Shakhnovich EI.

PLoS Comput Biol. 2012;8(12):e1002839. doi: 10.1371/journal.pcbi.1002839. Epub 2012 Dec 27.

PMID:
23300421
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness.

Bershtein S, Mu W, Serohijos AW, Zhou J, Shakhnovich EI.

Mol Cell. 2013 Jan 10;49(1):133-44. doi: 10.1016/j.molcel.2012.11.004. Epub 2012 Dec 6.

PMID:
23219534
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Collapse of unfolded proteins in a mixture of denaturants.

Xia Z, Das P, Shakhnovich EI, Zhou R.

J Am Chem Soc. 2012 Nov 7;134(44):18266-74. doi: 10.1021/ja3031505. Epub 2012 Oct 24.

PMID:
23057830
[PubMed - indexed for MEDLINE]
14.

Protein biophysics explains why highly abundant proteins evolve slowly.

Serohijos AW, Rimas Z, Shakhnovich EI.

Cell Rep. 2012 Aug 30;2(2):249-56. doi: 10.1016/j.celrep.2012.06.022. Epub 2012 Aug 2.

PMID:
22938865
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Robustness of atomistic Gō models in predicting native-like folding intermediates.

Estácio SG, Fernandes CS, Krobath H, Faísca PF, Shakhnovich EI.

J Chem Phys. 2012 Aug 28;137(8):085102.

PMID:
22938266
[PubMed - indexed for MEDLINE]
16.

Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation.

Wylie CS, Shakhnovich EI.

PLoS Comput Biol. 2012;8(8):e1002609. doi: 10.1371/journal.pcbi.1002609. Epub 2012 Aug 2.

PMID:
22876168
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Identification of a conserved aggregation-prone intermediate state in the folding pathways of Spc-SH3 amyloidogenic variants.

Krobath H, Estácio SG, Faísca PF, Shakhnovich EI.

J Mol Biol. 2012 Oct 5;422(5):705-22. doi: 10.1016/j.jmb.2012.06.020. Epub 2012 Jun 20.

PMID:
22727745
[PubMed - indexed for MEDLINE]
18.

Is there an en route folding intermediate for Cold shock proteins?

Huang L, Shakhnovich EI.

Protein Sci. 2012 May;21(5):677-85. doi: 10.1002/pro.2053. Epub 2012 Mar 29.

PMID:
22467601
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations.

Bershtein S, Mu W, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4857-62. doi: 10.1073/pnas.1118157109. Epub 2012 Mar 12. Erratum in: Proc Natl Acad Sci U S A. 2012 May 1;109(18):7126. Wu, Wanmeng [corrected to Mu, Wanmeng].

PMID:
22411825
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Sequence correlations shape protein promiscuity.

Lukatsky DB, Afek A, Shakhnovich EI.

J Chem Phys. 2011 Aug 14;135(6):065104. doi: 10.1063/1.3624332.

PMID:
21842953
[PubMed - indexed for MEDLINE]

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