-
2
-
-
0037062424
-
A monomeric red fluorescent protein
-
Campbell RE, et al. (2002) A monomeric red fluorescent protein. Proc Natl Acad Sci USA 99(12):7877-7882.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, Issue.12
, pp. 7877-7882
-
-
Campbell, R.E.1
-
3
-
-
67650287695
-
In the light of directed evolution: Pathways of adaptive protein evolution
-
Suppl 1
-
Bloom JD, Arnold FH (2009) In the light of directed evolution: Pathways of adaptive protein evolution. Proc Natl Acad Sci USA 106(Suppl 1):9995-10000.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 9995-10000
-
-
Bloom, J.D.1
Arnold, F.H.2
-
4
-
-
0037041420
-
Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases
-
Bucciantini M, et al. (2002) Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature 416(6880):507-511.
-
(2002)
Nature
, vol.416
, Issue.6880
, pp. 507-511
-
-
Bucciantini, M.1
-
5
-
-
0042467550
-
Rationalization of the effects of mutations on peptide and protein aggregation rates
-
Chiti F, Stefani M, Taddei N, Ramponi G, Dobson CM (2003) Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature 424(6950): 805-808.
-
(2003)
Nature
, vol.424
, Issue.6950
, pp. 805-808
-
-
Chiti, F.1
Stefani, M.2
Taddei, N.3
Ramponi, G.4
Dobson, C.M.5
-
6
-
-
47549097539
-
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
-
Drummond DA, Wilke CO (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134(2):341-352.
-
(2008)
Cell
, vol.134
, Issue.2
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
7
-
-
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(2):680-685.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.2
, pp. 680-685
-
-
Geiler-Samerotte, K.A.1
-
8
-
-
34248674895
-
The stability effects of protein mutations appear to be universally distributed
-
Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS (2007) The stability effects of protein mutations appear to be universally distributed. J Mol Biol 369(5):1318-1332.
-
(2007)
J Mol Biol
, vol.369
, Issue.5
, pp. 1318-1332
-
-
Tokuriki, N.1
Stricher, F.2
Schymkowitz, J.3
Serrano, L.4
Tawfik, D.S.5
-
9
-
-
40149099484
-
How protein stability and new functions trade off
-
Tokuriki N, Stricher F, Serrano L, Tawfik DS (2008) How protein stability and new functions trade off. PLOS Comput Biol 4(2):e1000002.
-
(2008)
PLOS Comput Biol
, vol.4
, Issue.2
, pp. e1000002
-
-
Tokuriki, N.1
Stricher, F.2
Serrano, L.3
Tawfik, D.S.4
-
10
-
-
0036295508
-
Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs
-
Wang X, Minasov G, Shoichet BK (2002) Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol 320(1):85-95.
-
(2002)
J Mol Biol
, vol.320
, Issue.1
, pp. 85-95
-
-
Wang, X.1
Minasov, G.2
Shoichet, B.K.3
-
11
-
-
84880000622
-
Mutational analysis of 48G7 reveals that somatic hypermutation affects both antibody stability and binding affinity
-
Sun SB, et al. (2013) Mutational analysis of 48G7 reveals that somatic hypermutation affects both antibody stability and binding affinity. J Am Chem Soc 135(27):9980-9983.
-
(2013)
J Am Chem Soc
, vol.135
, Issue.27
, pp. 9980-9983
-
-
Sun, S.B.1
-
12
-
-
0036139093
-
Why are proteins marginally stable?
-
Taverna DM, Goldstein RA (2002) Why are proteins marginally stable? Proteins 46(1): 105-109.
-
(2002)
Proteins
, vol.46
, Issue.1
, pp. 105-109
-
-
Taverna, D.M.1
Goldstein, R.A.2
-
13
-
-
36049027813
-
Protein stability imposes limits on organism complexity and speed of molecular evolution
-
Zeldovich KB, Chen P, Shakhnovich EI (2007) Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci USA 104(41): 16152-16157.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.41
, pp. 16152-16157
-
-
Zeldovich, K.B.1
Chen, P.2
Shakhnovich, E.I.3
-
14
-
-
33645811495
-
Protein stability promotes evolvability
-
Bloom JD, Labthavikul ST, Otey CR, Arnold FH (2006) Protein stability promotes evolvability. Proc Natl Acad Sci USA 103(15):5869-5874.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.15
, pp. 5869-5874
-
-
Bloom, J.D.1
Labthavikul, S.T.2
Otey, C.R.3
Arnold, F.H.4
-
15
-
-
23944490117
-
Missense meanderings in sequence space: A biophysical view of protein evolution
-
DePristo MA, Weinreich DM, Hartl DL (2005) Missense meanderings in sequence space: A biophysical view of protein evolution. Nat Rev Genet 6(9):678-687.
-
(2005)
Nat Rev Genet
, vol.6
, Issue.9
, pp. 678-687
-
-
DePristo, M.A.1
Weinreich, D.M.2
Hartl, D.L.3
-
16
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH (2005) Why highly expressed proteins evolve slowly. Proc Natl Acad Sci USA 102(40):14338-14343.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.40
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
17
-
-
84865730325
-
Protein biophysics explains why highly abundant proteins evolve slowly
-
Serohijos AWR, Rimas Z, Shakhnovich EI (2012) Protein biophysics explains why highly abundant proteins evolve slowly. Cell Reports 2(2):249-256.
-
(2012)
Cell Reports
, vol.2
, Issue.2
, pp. 249-256
-
-
Serohijos, A.W.R.1
Rimas, Z.2
Shakhnovich, E.I.3
-
18
-
-
79551667508
-
Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks
-
Johnson ME, Hummer G (2011) Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks. Proc Natl Acad Sci USA 108(2):603-608.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.2
, pp. 603-608
-
-
Johnson, M.E.1
Hummer, G.2
-
19
-
-
79952744659
-
Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions
-
Heo M, Maslov S, Shakhnovich E (2011) Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions. Proc Natl Acad Sci USA 108(10):4258-4263.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.10
, pp. 4258-4263
-
-
Heo, M.1
Maslov, S.2
Shakhnovich, E.3
-
20
-
-
0018692402
-
The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme
-
Gould SJ, Lewontin RC (1979) The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme. Proc R Soc Lond B Biol Sci 205(1161): 581-598.
-
(1979)
Proc R Soc Lond B Biol Sci
, vol.205
, Issue.1161
, pp. 581-598
-
-
Gould, S.J.1
Lewontin, R.C.2
-
21
-
-
0034144568
-
The fall and rise of Dr Pangloss: Adaptationism and the Spandrels paper 20 years later
-
Pigliucci I, Kaplan I (2000) The fall and rise of Dr Pangloss: Adaptationism and the Spandrels paper 20 years later. Trends Ecol Evol 15(2):66-70.
-
(2000)
Trends Ecol Evol
, vol.15
, Issue.2
, pp. 66-70
-
-
Pigliucci, I.1
Kaplan, I.2
-
22
-
-
0037154126
-
Protein structure and the spandrels of San Marco: Insulin's receptor-binding surface is buttressed by an invariant leucine essential for its stability
-
Weiss MA, et al. (2002) Protein structure and the spandrels of San Marco: Insulin's receptor-binding surface is buttressed by an invariant leucine essential for its stability. Biochemistry 41(3):809-819.
-
(2002)
Biochemistry
, vol.41
, Issue.3
, pp. 809-819
-
-
Weiss, M.A.1
-
23
-
-
80054759105
-
Molecular spandrels: Tests of adaptation at the genetic level
-
Barrett RDH, Hoekstra HE (2011) Molecular spandrels: Tests of adaptation at the genetic level. Nat Rev Genet 12(11):767-780.
-
(2011)
Nat Rev Genet
, vol.12
, Issue.11
, pp. 767-780
-
-
Barrett, R.D.H.1
Hoekstra, H.E.2
-
24
-
-
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(5770):111-114.
-
(2006)
Science
, vol.312
, Issue.5770
, pp. 111-114
-
-
Weinreich, D.M.1
Delaney, N.F.2
Depristo, M.A.3
Hartl, D.L.4
-
25
-
-
79957958115
-
Diminishing returns epistasis among beneficial mutations decelerates adaptation
-
Chou HH, Chiu HC, Delaney NF, Segrè D, Marx CJ (2011) Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332(6034):1190-1192.
-
(2011)
Science
, vol.332
, Issue.6034
, pp. 1190-1192
-
-
Chou, H.H.1
Chiu, H.C.2
Delaney, N.F.3
Segrè, D.4
Marx, C.J.5
-
26
-
-
84883140639
-
Path-based approach to random walks on networks characterizes how proteins evolve new functions
-
Manhart M, Morozov AV (2013) Path-based approach to random walks on networks characterizes how proteins evolve new functions. Phys Rev Lett 111(8):088102.
-
(2013)
Phys Rev Lett
, vol.111
, Issue.8
, pp. 088102
-
-
Manhart, M.1
Morozov, A.V.2
-
27
-
-
85014205842
-
-
Metzler R, Oshanin G, Redner S World Scientific, Singapore
-
Manhart M, Morozov AV (2014) First-Passage Phenomena and Their Applications, eds Metzler R, Oshanin G, Redner S (World Scientific, Singapore).
-
(2014)
First-Passage Phenomena and their Applications
-
-
Manhart, M.1
Morozov, A.V.2
-
29
-
-
84903957091
-
Introducing protein intrinsic disorder
-
Habchi J, Tompa P, Longhi S, Uversky VN (2014) Introducing protein intrinsic disorder. Chem Rev 114(13):6561-6588.
-
(2014)
Chem Rev
, vol.114
, Issue.13
, pp. 6561-6588
-
-
Habchi, J.1
Tompa, P.2
Longhi, S.3
Uversky, V.N.4
-
30
-
-
0028916599
-
A hot spot of binding energy in a hormone-receptor interface
-
Clackson T, Wells JA (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267(5196):383-386.
-
(1995)
Science
, vol.267
, Issue.5196
, pp. 383-386
-
-
Clackson, T.1
Wells, J.A.2
-
31
-
-
34548779127
-
Hot spots-A review of the proteinprotein interface determinant amino-acid residues
-
Moreira IS, Fernandes PA, Ramos MJ (2007) Hot spots-a review of the proteinprotein interface determinant amino-acid residues. Proteins 68(4):803-812.
-
(2007)
Proteins
, vol.68
, Issue.4
, pp. 803-812
-
-
Moreira, I.S.1
Fernandes, P.A.2
Ramos, M.J.3
-
32
-
-
0025082684
-
Additivity of mutational effects in proteins
-
Wells JA (1990) Additivity of mutational effects in proteins. Biochemistry 29(37): 8509-8517.
-
(1990)
Biochemistry
, vol.29
, Issue.37
, pp. 8509-8517
-
-
Wells, J.A.1
-
33
-
-
33745758856
-
A microscopic interpretation for adaptive dynamics trait substitution sequence models
-
Champagnat N (2006) A microscopic interpretation for adaptive dynamics trait substitution sequence models. Stoch Proc Appl 116(8):1127-1160.
-
(2006)
Stoch Proc Appl
, vol.116
, Issue.8
, pp. 1127-1160
-
-
Champagnat, N.1
-
35
-
-
60349093708
-
Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation
-
Charlesworth B (2009) Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation. Nat Rev Genet 10(3):195-205.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.3
, pp. 195-205
-
-
Charlesworth, B.1
-
36
-
-
84861663597
-
Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space
-
Shoval O, et al. (2012) Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space. Science 336(6085):1157-1160.
-
(2012)
Science
, vol.336
, Issue.6085
, pp. 1157-1160
-
-
Shoval, O.1
-
37
-
-
34548724489
-
The evolution of genetic networks by non-adaptive processes
-
Lynch M(2007) The evolution of genetic networks by non-adaptive processes. Nat Rev Genet 8(10):803-813.
-
(2007)
Nat Rev Genet
, vol.8
, Issue.10
, pp. 803-813
-
-
Lynch, M.1
-
38
-
-
84874923658
-
Cofactors and metabolites as protein folding helpers in metabolic diseases
-
Rodrigues JV, Henriques BJ, Lucas TG, Gomes CM (2012) Cofactors and metabolites as protein folding helpers in metabolic diseases. Curr Top Med Chem 12(22):2546-2559.
-
(2012)
Curr Top Med Chem
, vol.12
, Issue.22
, pp. 2546-2559
-
-
Rodrigues, J.V.1
Henriques, B.J.2
Lucas, T.G.3
Gomes, C.M.4
-
39
-
-
33644873184
-
BioGRID: A general repository for interaction datasets
-
Stark C, et al. (2006) BioGRID: A general repository for interaction datasets. Nucleic Acids Res 34(Database issue):D535-D539.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D535-D539
-
-
Stark, C.1
-
40
-
-
84859473329
-
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly
-
Yang JR, Liao BY, Zhuang SM, Zhang J (2012) Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. Proc Natl Acad Sci USA 109(14):E831-E840.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.14
, pp. E831-E840
-
-
Yang, J.R.1
Liao, B.Y.2
Zhuang, S.M.3
Zhang, J.4
-
41
-
-
84876896201
-
Evolutionary capacitance and control of protein stability in protein-protein interaction networks
-
Dixit PD, Maslov S (2013) Evolutionary capacitance and control of protein stability in protein-protein interaction networks. PLOS Comput Biol 9(4):e1003023.
-
(2013)
PLOS Comput Biol
, vol.9
, Issue.4
, pp. e1003023
-
-
Dixit, P.D.1
Maslov, S.2
-
42
-
-
79960652801
-
Molecular chaperones in protein folding and proteostasis
-
Hartl FU, Bracher A, Hayer-Hartl M (2011) Molecular chaperones in protein folding and proteostasis. Nature 475(7356):324-332.
-
(2011)
Nature
, vol.475
, Issue.7356
, pp. 324-332
-
-
Hartl, F.U.1
Bracher, A.2
Hayer-Hartl, M.3
-
43
-
-
33846551980
-
Empirical fitness landscapes reveal accessible evolutionary paths
-
Poelwijk FJ, Kiviet DJ, Weinreich DM, Tans SJ (2007) Empirical fitness landscapes reveal accessible evolutionary paths. Nature 445(7126):383-386.
-
(2007)
Nature
, vol.445
, Issue.7126
, pp. 383-386
-
-
Poelwijk, F.J.1
Kiviet, D.J.2
Weinreich, D.M.3
Tans, S.J.4
-
44
-
-
84874460493
-
Quantitative analyses of empirical fitness landscapes
-
Szendro IG, Schenk MF, Franke J, Krug J, de Visser JA (2013) Quantitative analyses of empirical fitness landscapes. J Stat Mech 2013:P01005.
-
(2013)
J Stat Mech
, vol.2013
, pp. 01005
-
-
Szendro, I.G.1
Schenk, M.F.2
Franke, J.3
Krug, J.4
De Visser, J.A.5
-
46
-
-
84876090839
-
Replaying the tape of life: Quantification of the predictability of evolution
-
Lobkovsky AE, Koonin EV (2012) Replaying the tape of life: Quantification of the predictability of evolution. Front Genet 3:246.
-
(2012)
Front Genet
, vol.3
, pp. 246
-
-
Lobkovsky, A.E.1
Koonin, E.V.2
-
47
-
-
0035066602
-
ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions
-
Thorn KS, Bogan AA (2001) ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 17(3):284-285.
-
(2001)
Bioinformatics
, vol.17
, Issue.3
, pp. 284-285
-
-
Thorn, K.S.1
Bogan, A.A.2
|