-
1
-
-
23944490117
-
Missense meanderings in sequence space: A biophysical view of protein evolution
-
DOI 10.1038/nrg1672
-
DePristo MA, Weinreich DM, Hartl DL (2005) Missense meanderings insequence space: A biophysical view of protein evolution. Nat Rev Genet 6:678-687. (Pubitemid 41192319)
-
(2005)
Nature Reviews Genetics
, vol.6
, Issue.9
, pp. 678-687
-
-
DePristo, M.A.1
Weinreich, D.M.2
Hartl, D.L.3
-
4
-
-
77954743785
-
Mutational effects and the evolution of new protein functions
-
Soskine M, Tawfik DS (2010) Mutational effects and the evolution of new protein functions. Nat Rev Genet 11:572-582.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 572-582
-
-
Soskine, M.1
Tawfik, D.S.2
-
5
-
-
33645666942
-
Darwinian evolution can follow only very few mutational paths to fitter proteins
-
Weinreich DM, Delaney NF, DePristo MA, Hartl DL (2006) Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312:111-114.
-
(2006)
Science
, vol.312
, pp. 111-114
-
-
Weinreich, D.M.1
Delaney, N.F.2
DePristo, M.A.3
Hartl, D.L.4
-
6
-
-
34547607777
-
A first-principles model of early evolution: Emergence of gene families, species, and preferred protein folds
-
DOI 10.1371/journal.pcbi.0030139
-
Zeldovich KB, Chen P, Shakhnovich BE, Shakhnovich EI (2007) A first-principles model of early evolution: Emergence of gene families, species, and preferred protein folds. PLoS Comput Biol 3:1224-1238. (Pubitemid 47196166)
-
(2007)
PLoS Computational Biology
, vol.3
, Issue.7
, pp. 1224-1238
-
-
Zeldovich, K.B.1
Chen, P.2
Shakhnovich, B.E.3
Shakhnovich, E.I.4
-
8
-
-
47549097539
-
Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution
-
DOI 10.1016/j.cell.2008.05.042, PII S0092867408007058
-
Drummond DA, Wilke CO (2008) Mistranslation-induced proteinmisfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352. (Pubitemid 352010328)
-
(2008)
Cell
, vol.134
, Issue.2
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
9
-
-
33846515095
-
Thermodynamics of neutral protein evolution
-
Bloom JD, Raval A, Wilke CO (2007) Thermodynamics of neutral protein evolution. Genetics 175:255-266.
-
(2007)
Genetics
, vol.175
, pp. 255-266
-
-
Bloom, J.D.1
Raval, A.2
Wilke, C.O.3
-
10
-
-
77955670221
-
Evolutionary fates within amicrobial population highlight an essential role for protein folding during natural selection
-
Pena MI, Davlieva M, Bennett MR, Olson JS, Shamoo Y (2010) Evolutionary fates within amicrobial population highlight an essential role for protein folding during natural selection. Mol Sys Biol 6:1-12.
-
(2010)
Mol Sys Biol
, vol.6
, pp. 1-12
-
-
Pena, M.I.1
Davlieva, M.2
Bennett, M.R.3
Olson, J.S.4
Shamoo, Y.5
-
11
-
-
79959992592
-
A biophysical protein folding model accounts for most mutational fitness effects in viruses
-
Wylie CS, Shakhnovich EI (2011) A biophysical protein folding model accounts for most mutational fitness effects in viruses. Proc Natl Acad Sci USA 108:9916-9921.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 9916-9921
-
-
Wylie, C.S.1
Shakhnovich, E.I.2
-
13
-
-
0023847706
-
Insights into enzyme function from studies on mutants of dihydrofolate reductase
-
Benkovic SJ, Fierke CA, Naylor AM (1988) Insights into enzyme function from studies on mutants of dihydrofolate reductase. Science 239:1105-1110. (Pubitemid 18084316)
-
(1988)
Science
, vol.239
, Issue.4844
, pp. 1105-1110
-
-
Benkovic, S.J.1
Fierke, C.A.2
Naylor, A.M.3
-
14
-
-
77955102352
-
Quantifying E.coli proteome and transcriptome with single-molecule sensitivity in single cells
-
Taniguchi Y, et al. (2010) Quantifying E.coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329:533-538.
-
(2010)
Science
, vol.329
, pp. 533-538
-
-
Taniguchi, Y.1
-
15
-
-
33845864966
-
Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein
-
DOI 10.1038/nature05385, PII NATURE05385
-
Bershtein S, Segal M, Bekerman R, Tokuriki N, Tawfik DS (2006) Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444:929-932. (Pubitemid 46025005)
-
(2006)
Nature
, vol.444
, Issue.7121
, pp. 929-932
-
-
Bershtein, S.1
Segal, M.2
Bekerman, R.3
Tokuriki, N.4
Tawfik, D.S.5
-
16
-
-
79551674254
-
Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast
-
Geiler-Samerotte KA, et al. (2011) Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Proc Natl Acad Sci USA 108:680-685.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 680-685
-
-
Geiler-Samerotte, K.A.1
-
17
-
-
0018588511
-
Stability of proteins: Small globular proteins
-
Privalov PL (1979) Stability of proteins: Small globular proteins. Adv Protein Chem 33:167-241.
-
(1979)
Adv Protein Chem
, vol.33
, pp. 167-241
-
-
Privalov, P.L.1
-
18
-
-
0000159569
-
Protein structure and the energetics of protein stability
-
Robertson AD, Murphy KP (1997) Protein structure and the energetics of protein stability. Chem Rev 97:1251-1268.
-
(1997)
Chem Rev
, vol.97
, pp. 1251-1268
-
-
Robertson, A.D.1
Murphy, K.P.2
-
20
-
-
0038441327
-
Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation
-
DOI 10.1038/nrg1088
-
Elena SF, Lenski RE (2003) Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation. Nat Rev Genet 4:457-469. (Pubitemid 36648145)
-
(2003)
Nature Reviews Genetics
, vol.4
, Issue.6
, pp. 457-469
-
-
Elena, S.F.1
Lenski, R.E.2
-
21
-
-
0016224361
-
A thermodynamic approach to the problem of stabilization of globular protein structure: A calorimetric study
-
Privalov PL, Khechinashvili NN (1974) A thermodynamic approach to the problem of stabilization of globular protein structure: A calorimetric study. J Mol Biol 86:665-684.
-
(1974)
J Mol Biol
, vol.86
, pp. 665-684
-
-
Privalov, P.L.1
Khechinashvili, N.N.2
-
22
-
-
33646931471
-
Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
-
Shakhnovich E (2006) Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet. Chem Rev 106:1559-1588.
-
(2006)
Chem Rev
, vol.106
, pp. 1559-1588
-
-
Shakhnovich, E.1
-
23
-
-
0024554228
-
The structural stability of a protein is an important determinant of its proteolytic susceptibility in Escherichia coli
-
Parsell DA, Sauer RT (1989) The structural stability of a protein is an important determinant of its proteolytic susceptibility in Escherichia coli. J Biol Chem 264:7590-7595. (Pubitemid 19119177)
-
(1989)
Journal of Biological Chemistry
, vol.264
, Issue.13
, pp. 7590-7595
-
-
Parsell, D.A.1
Sauer, R.T.2
-
24
-
-
18744391410
-
Pulse proteolysis: A simple method for quantitative determination of protein stability and ligand binding
-
DOI 10.1038/nmeth740
-
Park C, Marqusee S (2005) Pulse proteolysis: Asimple method for quantitative determination of protein stability and ligand binding. Nat Methods 2:207-212. (Pubitemid 41122128)
-
(2005)
Nature Methods
, vol.2
, Issue.3
, pp. 207-212
-
-
Park, C.1
Marqusee, S.2
-
25
-
-
79955613183
-
Impact of gene expression noise on organismal fitness and the efficacy of natural selection
-
Wang Z, Zhang J (2011) Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc Natl Acad Sci USA 108:E67-E76.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
-
-
Wang, Z.1
Zhang, J.2
-
26
-
-
0034737320
-
The crystal structure of dihydrofolate reductase from Thermotoga maritima: Molecular features of thermostability
-
Dams T, et al. (2000) The crystal structure of dihydrofolate reductase from Thermotoga maritima: Molecular features of thermostability. J Mol Biol 297:659-672.
-
(2000)
J Mol Biol
, vol.297
, pp. 659-672
-
-
Dams, T.1
-
27
-
-
79959543603
-
Non-adaptive origins of interactome complexity
-
Fernandez A, Lynch M (2011) Non-adaptive origins of interactome complexity. Nature 474:502-505.
-
(2011)
Nature
, vol.474
, pp. 502-505
-
-
Fernandez, A.1
Lynch, M.2
-
28
-
-
0036923039
-
Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism
-
DOI 10.1016/S0022-2836(02)01112-9
-
Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI (2002) Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J Mol Biol 324:851-857. (Pubitemid 36044117)
-
(2002)
Journal of Molecular Biology
, vol.324
, Issue.4
, pp. 851-857
-
-
Ding, F.1
Dokholyan, N.V.2
Buldyrev, S.V.3
Stanley, H.E.4
Shakhnovich, E.I.5
-
29
-
-
49349104659
-
Mechanism and energy landscape of domain swapping in the B1 domain of protein G
-
Malevanets A, Sirota FL, Wodak SJ (2008) Mechanism and energy landscape of domain swapping in the B1 domain of protein G. J Mol Biol 382:223-235.
-
(2008)
J Mol Biol
, vol.382
, pp. 223-235
-
-
Malevanets, A.1
Sirota, F.L.2
Wodak, S.J.3
-
30
-
-
23944448528
-
Protein oligomerization through domain swapping: Role of inter-molecular interactions and protein concentration
-
DOI 10.1016/j.jmb.2005.06.062, PII S0022283605007461
-
Yang S, Levine H, Onuchic JN (2005) Protein oligomerization through domain swapping: Role of inter-molecular interactions and protein concentration. J Mol Biol 352:202-211. (Pubitemid 41207449)
-
(2005)
Journal of Molecular Biology
, vol.352
, Issue.1
, pp. 202-211
-
-
Yang, S.1
Levine, H.2
Onuchic, J.N.3
-
31
-
-
0035826713
-
Three-dimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues
-
DOI 10.1073/pnas.101542098
-
Rousseau F, Schymkowitz JW, Wilkinson HR, Itzhaki LS (2001) Three-dimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues. Proc Natl Acad Sci USA 98:5596-5601. (Pubitemid 32435687)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.10
, pp. 5596-5601
-
-
Rousseau, F.1
Schymkowitz, J.W.H.2
Wilkinson, H.R.3
Itzhaki, L.S.4
-
32
-
-
33645521792
-
Protein aggregation and its consequences for human disease
-
Dobson CM (2006) Protein aggregation and its consequences for human disease. Protein Pept Lett 13:219-227.
-
(2006)
Protein Pept Lett
, vol.13
, pp. 219-227
-
-
Dobson, C.M.1
-
33
-
-
60449090411
-
Protein acrobatics in pairs - Dimerization via domain swapping
-
Gronenborn AM (2009) Protein acrobatics in pairs - dimerization via domain swapping. Curr Opin Struct Biol 19:39-49.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 39-49
-
-
Gronenborn, A.M.1
-
34
-
-
33748936121
-
Domain Swapping in p13suc1 Results in Formation of Native-like, Cytotoxic Aggregates
-
DOI 10.1016/j.jmb.2006.07.061, PII S0022283606009399
-
Rousseau F, et al. (2006) Domain swapping in p13suc1 results in formation of native-like, cytotoxic aggregates. J Mol Biol 363:496-505. (Pubitemid 44436250)
-
(2006)
Journal of Molecular Biology
, vol.363
, Issue.2
, pp. 496-505
-
-
Rousseau, F.1
Wilkinson, H.2
Villanueva, J.3
Serrano, L.4
Schymkowitz, J.W.H.5
Itzhaki, L.S.6
-
35
-
-
21244464335
-
Binding properties and evolution of homodimers in protein-protein interaction networks
-
DOI 10.1093/nar/gki678
-
Ispolatov I, Yuryev A, Mazo I, Maslov S (2005) Binding properties and evolution of homodimers in protein - protein interaction networks. Nucleic Acids Res 33:3629-3635. (Pubitemid 41430585)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.11
, pp. 3629-3635
-
-
Ispolatov, I.1
Yuryev, A.2
Mazo, I.3
Maslov, S.4
-
37
-
-
33845989816
-
Structural Similarity Enhances Interaction Propensity of Proteins
-
DOI 10.1016/j.jmb.2006.11.020, PII S002228360601549X
-
Lukatsky DB, Shakhnovich BE, Mintseris J, Shakhnovich EI (2007) Structural similarity enhances interaction propensity of proteins. J Mol Biol 365:1596-1606. (Pubitemid 46048849)
-
(2007)
Journal of Molecular Biology
, vol.365
, Issue.5
, pp. 1596-1606
-
-
Lukatsky, D.B.1
Shakhnovich, B.E.2
Mintseris, J.3
Shakhnovich, E.I.4
|