-
1
-
-
13844299144
-
The family feud: do proteins with similar structures fold via the same pathway?
-
Zarrine-Afsar A., Larson S.M., and Davidson A.R. The family feud: do proteins with similar structures fold via the same pathway?. Curr. Opin. Struct. Biol. 15 (2005) 42-49
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 42-49
-
-
Zarrine-Afsar, A.1
Larson, S.M.2
Davidson, A.R.3
-
2
-
-
0034695407
-
Conservation of folding and stability within a protein family: the tyrosine corner as an evolutionary cul-de-sac
-
Hamill S.J., Cota E., Chothia C., and Clarke J. Conservation of folding and stability within a protein family: the tyrosine corner as an evolutionary cul-de-sac. J. Mol. Biol. 295 (2000) 641-649
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 641-649
-
-
Hamill, S.J.1
Cota, E.2
Chothia, C.3
Clarke, J.4
-
3
-
-
0037053429
-
Sequence conservation in Ig-like domains: the role of highly conserved proline residues in the fibronectin type III superfamily
-
Steward A., Adhya S., and Clarke J. Sequence conservation in Ig-like domains: the role of highly conserved proline residues in the fibronectin type III superfamily. J. Mol. Biol. 318 (2002) 935-940
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 935-940
-
-
Steward, A.1
Adhya, S.2
Clarke, J.3
-
4
-
-
0028961335
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
5
-
-
9144257886
-
The Pfam protein families database
-
Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., et al. The Pfam protein families database. Nucleic Acids Res. 32 (2004) D138-D141
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Bateman, A.1
Coin, L.2
Durbin, R.3
Finn, R.D.4
Hollich, V.5
Griffiths-Jones, S.6
-
6
-
-
0024844388
-
Conformations of immunoglobulin hypervariable regions
-
[see comments]
-
Chothia C., Lesk A.M., Tramontano A., Levitt M., Smith-Gill S.J., Air G., et al. Conformations of immunoglobulin hypervariable regions. [see comments]. Nature 342 (1989) 877-883
-
(1989)
Nature
, vol.342
, pp. 877-883
-
-
Chothia, C.1
Lesk, A.M.2
Tramontano, A.3
Levitt, M.4
Smith-Gill, S.J.5
Air, G.6
-
7
-
-
0028361540
-
Many of the immunoglobulin superfamily domains in cell adhesion molecules and surface receptors belong to a new structural set which is close to that containing variable domains
-
Harpaz Y., and Chothia C. Many of the immunoglobulin superfamily domains in cell adhesion molecules and surface receptors belong to a new structural set which is close to that containing variable domains. J. Mol. Biol. 238 (1994) 528-539
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 528-539
-
-
Harpaz, Y.1
Chothia, C.2
-
8
-
-
0033200251
-
Folding studies of immunoglobulin-like beta-sandwich proteins suggest that they share a common folding pathway
-
Clarke J., Cota E., Fowler S.B., and Hamill S.J. Folding studies of immunoglobulin-like beta-sandwich proteins suggest that they share a common folding pathway. Struct. Fold. Des. 7 (1999) 1145-1153
-
(1999)
Struct. Fold. Des.
, vol.7
, pp. 1145-1153
-
-
Clarke, J.1
Cota, E.2
Fowler, S.B.3
Hamill, S.J.4
-
9
-
-
0031214363
-
A comparison of the folding kinetics and thermodynamics of two homologous fibronectin type III modules
-
Plaxco K.W., Spitzfaden C., Campbell I.D., and Dobson C.M. A comparison of the folding kinetics and thermodynamics of two homologous fibronectin type III modules. J. Mol. Biol. 270 (1997) 763-770
-
(1997)
J. Mol. Biol.
, vol.270
, pp. 763-770
-
-
Plaxco, K.W.1
Spitzfaden, C.2
Campbell, I.D.3
Dobson, C.M.4
-
10
-
-
0031556949
-
Module-module interactions in the cell binding region of fibronectin: stability, flexibility and specificity
-
Spitzfaden C., Grant R.P., Mardon H.J., and Campbell I.D. Module-module interactions in the cell binding region of fibronectin: stability, flexibility and specificity. J. Mol. Biol. 265 (1997) 565-579
-
(1997)
J. Mol. Biol.
, vol.265
, pp. 565-579
-
-
Spitzfaden, C.1
Grant, R.P.2
Mardon, H.J.3
Campbell, I.D.4
-
11
-
-
1242341404
-
Approaching the speed limit for Greek Key beta-barrel formation: transition-state movement tunes folding rate of zinc-substituted azurin
-
Pozdnyakova I., and Wittung-Stafshede P. Approaching the speed limit for Greek Key beta-barrel formation: transition-state movement tunes folding rate of zinc-substituted azurin. Biochim. Biophys. Acta 1651 (2003) 1-4
-
(2003)
Biochim. Biophys. Acta
, vol.1651
, pp. 1-4
-
-
Pozdnyakova, I.1
Wittung-Stafshede, P.2
-
12
-
-
0034677663
-
The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology
-
Hamill S.J., Steward A., and Clarke J. The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology. J. Mol. Biol. 297 (2000) 165-178
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 165-178
-
-
Hamill, S.J.1
Steward, A.2
Clarke, J.3
-
13
-
-
0028791393
-
An integrated kinetic analysis of intermediates and transition states in protein folding reactions
-
Parker M.J., Spencer J., and Clarke A.R. An integrated kinetic analysis of intermediates and transition states in protein folding reactions. J. Mol. Biol. 253 (1995) 771-786
-
(1995)
J. Mol. Biol.
, vol.253
, pp. 771-786
-
-
Parker, M.J.1
Spencer, J.2
Clarke, A.R.3
-
14
-
-
0034984382
-
Mapping the folding pathway of an immunoglobulin domain: structural detail from Phi value analysis and movement of the transition state
-
Fowler S.B., and Clarke J. Mapping the folding pathway of an immunoglobulin domain: structural detail from Phi value analysis and movement of the transition state. Structure 9 (2001) 355-366
-
(2001)
Structure
, vol.9
, pp. 355-366
-
-
Fowler, S.B.1
Clarke, J.2
-
15
-
-
0033604845
-
Effects of core mutations on the folding of a beta-sheet protein: implications for backbone organization in the I-state
-
Lorch M., Mason J.M., Clarke A.R., and Parker M.J. Effects of core mutations on the folding of a beta-sheet protein: implications for backbone organization in the I-state. Biochemistry 38 (1999) 1377-1385
-
(1999)
Biochemistry
, vol.38
, pp. 1377-1385
-
-
Lorch, M.1
Mason, J.M.2
Clarke, A.R.3
Parker, M.J.4
-
16
-
-
0035793212
-
The folding nucleus of a fibronectin type III domain is composed of core residues of the immunoglobulin-like fold
-
Cota E., Steward A., Fowler S.B., and Clarke J. The folding nucleus of a fibronectin type III domain is composed of core residues of the immunoglobulin-like fold. J. Mol. Biol. 305 (2001) 1185-1194
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 1185-1194
-
-
Cota, E.1
Steward, A.2
Fowler, S.B.3
Clarke, J.4
-
17
-
-
0032474435
-
The effect of boundary selection on the stability and folding of the third fibronectin type III domain from human tenascin
-
Hamill S.J., Meekhof A.E., and Clarke J. The effect of boundary selection on the stability and folding of the third fibronectin type III domain from human tenascin. Biochemistry 37 (1998) 8071-8079
-
(1998)
Biochemistry
, vol.37
, pp. 8071-8079
-
-
Hamill, S.J.1
Meekhof, A.E.2
Clarke, J.3
-
18
-
-
0033957144
-
Folding of beta-sandwich proteins: three-state transition of a fibronectin type III module
-
Cota E., and Clarke J. Folding of beta-sandwich proteins: three-state transition of a fibronectin type III module. Protein Sci. 9 (2000) 112-120
-
(2000)
Protein Sci.
, vol.9
, pp. 112-120
-
-
Cota, E.1
Clarke, J.2
-
19
-
-
0034703474
-
Two proteins with the same structure respond very differently to mutation: the role of plasticity in protein stability
-
Cota E., Hamill S.J., Fowler S.B., and Clarke J. Two proteins with the same structure respond very differently to mutation: the role of plasticity in protein stability. J. Mol. Biol. 302 (2000) 713-725
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 713-725
-
-
Cota, E.1
Hamill, S.J.2
Fowler, S.B.3
Clarke, J.4
-
20
-
-
0031214818
-
Folding and stability of a fibronectin type III domain of human tenascin
-
Clarke J., Hamill S.J., and Johnson C.M. Folding and stability of a fibronectin type III domain of human tenascin. J. Mol. Biol. 270 (1997) 771-778
-
(1997)
J. Mol. Biol.
, vol.270
, pp. 771-778
-
-
Clarke, J.1
Hamill, S.J.2
Johnson, C.M.3
-
21
-
-
0031571127
-
Backbone dynamics of homologous fibronectin type III cell adhesion domains from fibronectin and tenascin
-
Carr P.A., Erickson H.P., and Palmer III A.G. Backbone dynamics of homologous fibronectin type III cell adhesion domains from fibronectin and tenascin. Structure 5 (1997) 949-959
-
(1997)
Structure
, vol.5
, pp. 949-959
-
-
Carr, P.A.1
Erickson, H.P.2
Palmer III, A.G.3
-
22
-
-
0842283895
-
Hydrophobic core fluidity of homologous protein domains: relation of side-chain dynamics to core composition and packing
-
Best R.B., Rutherford T.J., Freund S.M., and Clarke J. Hydrophobic core fluidity of homologous protein domains: relation of side-chain dynamics to core composition and packing. Biochemistry 43 (2004) 1145-1155
-
(2004)
Biochemistry
, vol.43
, pp. 1145-1155
-
-
Best, R.B.1
Rutherford, T.J.2
Freund, S.M.3
Clarke, J.4
-
23
-
-
18144378006
-
What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis
-
Best R.B., Clarke J., and Karplus M. What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis. J. Mol. Biol. 349 (2005) 185-203
-
(2005)
J. Mol. Biol.
, vol.349
, pp. 185-203
-
-
Best, R.B.1
Clarke, J.2
Karplus, M.3
-
24
-
-
20544465799
-
Mechanical unfolding of TNfn3: the unfolding pathway of a fnIII domain probed by protein engineering. AFM and MD simulation
-
Ng S.P., Rounsevell R.W., Steward A., Geierhaas C.D., Williams P.M., Paci E., and Clarke J. Mechanical unfolding of TNfn3: the unfolding pathway of a fnIII domain probed by protein engineering. AFM and MD simulation. J. Mol. Biol. 350 (2005) 776-789
-
(2005)
J. Mol. Biol.
, vol.350
, pp. 776-789
-
-
Ng, S.P.1
Rounsevell, R.W.2
Steward, A.3
Geierhaas, C.D.4
Williams, P.M.5
Paci, E.6
Clarke, J.7
-
26
-
-
34547094880
-
Designing an extracellular matrix protein with enhanced mechanical stability
-
Ng S.P., Billings K.S., Ohashi T., Allen M.D., Best R.B., Randles L.G., et al. Designing an extracellular matrix protein with enhanced mechanical stability. Proc. Natl Acad. Sci. USA 104 (2007) 9633-9637
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 9633-9637
-
-
Ng, S.P.1
Billings, K.S.2
Ohashi, T.3
Allen, M.D.4
Best, R.B.5
Randles, L.G.6
-
27
-
-
0008863560
-
Some factors in the interpretation of protein denaturation
-
Kauzmann W. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14 (1959) 1-63
-
(1959)
Adv. Protein Chem.
, vol.14
, pp. 1-63
-
-
Kauzmann, W.1
-
28
-
-
5244245983
-
A correlation of reaction rates
-
Hammond G.S. A correlation of reaction rates. J. Am. Chem. Soc. 77 (1955) 334-338
-
(1955)
J. Am. Chem. Soc.
, vol.77
, pp. 334-338
-
-
Hammond, G.S.1
-
29
-
-
0027171034
-
Application of physical organic chemistry to engineered mutants of proteins: Hammond postulate behavior in the transition state of protein folding
-
Matouschek A., and Fersht A.R. Application of physical organic chemistry to engineered mutants of proteins: Hammond postulate behavior in the transition state of protein folding. Proc. Natl Acad. Sci. USA 90 (1993) 7814-7818
-
(1993)
Proc. Natl Acad. Sci. USA
, vol.90
, pp. 7814-7818
-
-
Matouschek, A.1
Fersht, A.R.2
-
30
-
-
0035252685
-
Characterisation of the transition states for protein folding: towards a new level of mechanistic detail in protein engineering analysis
-
Oliveberg M. Characterisation of the transition states for protein folding: towards a new level of mechanistic detail in protein engineering analysis. Curr. Opin. Struct. Biol. 11 (2001) 94-100
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 94-100
-
-
Oliveberg, M.1
-
32
-
-
0032574698
-
Context-dependent nature of destabilizing mutations on the stability of FKBP12
-
Main E.R., Fulton K.F., and Jackson S.E. Context-dependent nature of destabilizing mutations on the stability of FKBP12. Biochemistry 37 (1998) 6145-6153
-
(1998)
Biochemistry
, vol.37
, pp. 6145-6153
-
-
Main, E.R.1
Fulton, K.F.2
Jackson, S.E.3
-
33
-
-
0026553768
-
The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability
-
Serrano L., Kellis J., Cann P., Matouschek A., and Fersht A.R. The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J. Mol. Biol. 224 (1992) 783-804
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 783-804
-
-
Serrano, L.1
Kellis, J.2
Cann, P.3
Matouschek, A.4
Fersht, A.R.5
-
35
-
-
0001917325
-
Deuterium exchange between peptides and water
-
Linderstrøm-Lang K. Deuterium exchange between peptides and water. Chem Soc., Spec. Publ. 2 (1955) 1-20
-
(1955)
Chem Soc., Spec. Publ.
, vol.2
, pp. 1-20
-
-
Linderstrøm-Lang, K.1
-
36
-
-
0034100848
-
Two exposed amino acids confer thermostability on a cold shock protein
-
Perl D., Mueller U., Heinemann U., and Schmidt F.X. Two exposed amino acids confer thermostability on a cold shock protein. Nat. Struct. Biol. 7 (2000) 380-383
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 380-383
-
-
Perl, D.1
Mueller, U.2
Heinemann, U.3
Schmidt, F.X.4
-
37
-
-
34848905895
-
Conformational dynamics in loop swap mutants of homologous fibronectin type III domains
-
Siggers K.F., Soto C., and Palmer A.G.R. Conformational dynamics in loop swap mutants of homologous fibronectin type III domains. Biophys. J. 93 (2007) 2447-2456
-
(2007)
Biophys. J.
, vol.93
, pp. 2447-2456
-
-
Siggers, K.F.1
Soto, C.2
Palmer, A.G.R.3
-
38
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco K.W., Simons K.T., and Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277 (1998) 985-994
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 985-994
-
-
Plaxco, K.W.1
Simons, K.T.2
Baker, D.3
-
39
-
-
0035173844
-
The roles of stability and contact order in determining protein folding rates
-
Dinner A.R., and Karplus M. The roles of stability and contact order in determining protein folding rates. Nat. Struct. Biol. 8 (2001) 21-22
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 21-22
-
-
Dinner, A.R.1
Karplus, M.2
-
40
-
-
0037225280
-
Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding
-
Sanchez I.E., and Kiefhaber T. Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding. J. Mol. Biol. 325 (2003) 367-376
-
(2003)
J. Mol. Biol.
, vol.325
, pp. 367-376
-
-
Sanchez, I.E.1
Kiefhaber, T.2
-
41
-
-
0036293485
-
Conformational plasticity in folding of the split beta-alpha-beta protein S6: evidence for burst-phase disruption of the native state
-
Otzen D.E., and Oliveberg M. Conformational plasticity in folding of the split beta-alpha-beta protein S6: evidence for burst-phase disruption of the native state. J. Mol. Biol. 317 (2002) 613-627
-
(2002)
J. Mol. Biol.
, vol.317
, pp. 613-627
-
-
Otzen, D.E.1
Oliveberg, M.2
-
42
-
-
22444436625
-
Spectrin R16: Broad energy barrier or sequential transition states?
-
Scott K.A., and Clarke J. Spectrin R16: Broad energy barrier or sequential transition states?. Protein Sci. 14 (2005) 1617-1629
-
(2005)
Protein Sci.
, vol.14
, pp. 1617-1629
-
-
Scott, K.A.1
Clarke, J.2
-
43
-
-
0026511656
-
The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
-
Fersht A.R., Matouschek A., and Serrano L. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224 (1992) 771-782
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 771-782
-
-
Fersht, A.R.1
Matouschek, A.2
Serrano, L.3
-
44
-
-
0029400480
-
NMRPipe: a multidimensional spectral processing system based on UNIX pipes
-
Delaglio F., Grzesiek S., Vuister G.W., Zhu G., Pfeifer J., and Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6 (1995) 277-293
-
(1995)
J. Biomol. NMR
, vol.6
, pp. 277-293
-
-
Delaglio, F.1
Grzesiek, S.2
Vuister, G.W.3
Zhu, G.4
Pfeifer, J.5
Bax, A.6
-
45
-
-
36549010109
-
-
Goddard, T. D. & Kneller, D. G. SPARKY 3. University of California, San Francisco, CA.
-
-
-
-
46
-
-
0347722841
-
Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients
-
Sattler M., Schleucher J., and Griesinger C. Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog. Nuclear Magn. Reson. Spectrosc. 34 (1999) 93-158
-
(1999)
Prog. Nuclear Magn. Reson. Spectrosc.
, vol.34
, pp. 93-158
-
-
Sattler, M.1
Schleucher, J.2
Griesinger, C.3
-
48
-
-
45149138663
-
Comparison of different modes of two-dimensional reverse-correlation NMR for the study of proteins
-
Bax A., Ikura M., Kay L.E., Torchia D.A., and Tschudin R. Comparison of different modes of two-dimensional reverse-correlation NMR for the study of proteins. J. Magn. Reson. 86 (1990) 304-318
-
(1990)
J. Magn. Reson.
, vol.86
, pp. 304-318
-
-
Bax, A.1
Ikura, M.2
Kay, L.E.3
Torchia, D.A.4
Tschudin, R.5
-
49
-
-
0027250665
-
Primary structure effects on peptide group hydrogen exchange
-
Bai Y., Milne J.S., Mayne L., and Englander S.W. Primary structure effects on peptide group hydrogen exchange. Proteins: Struct., Funct., Genet. 17 (1993) 75-86
-
(1993)
Proteins: Struct., Funct., Genet.
, vol.17
, pp. 75-86
-
-
Bai, Y.1
Milne, J.S.2
Mayne, L.3
Englander, S.W.4
-
51
-
-
36549010890
-
-
Zhang, Y.-Z. Protein and peptide structure and interactions studied by hydrogen exchange and NMR. PhD Thesis, University of Pennsylvania.
-
-
-
|