-
2
-
-
0030038634
-
Topology prediction for helical transmembrane proteins at 86% accuracy
-
Rost B., Fariselli P., Casadio R. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 5:1996;1704-1718.
-
(1996)
Protein Sci
, vol.5
, pp. 1704-1718
-
-
Rost, B.1
Fariselli, P.2
Casadio, R.3
-
3
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
-
Krogh A., Larsson B., von Heijne G., Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 305:2001;567-580.
-
(2001)
J Mol Biol
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
Von Heijne, G.3
Sonnhammer, E.L.4
-
4
-
-
0034141371
-
Turning a reference inside-out: Commentary on an article by Stevens and Arkin entitled: "Are membrane proteins 'inside-out' proteins?"
-
Proteins 1999, 36:135-143
-
Rees DC, Eisenberg D: Turning a reference inside-out: Commentary on an article by Stevens and Arkin entitled: "Are membrane proteins 'inside-out' proteins?" (Proteins 1999, 36:135-143). Proteins 2000, 38:121-122.
-
(2000)
Proteins
, vol.38
, pp. 121-122
-
-
Rees, D.C.1
Eisenberg, D.2
-
5
-
-
0034663513
-
Turning an opinion inside-out: Rees and Eisenberg's commentary (Proteins 2000;38:121-122) on "Are membrane proteins 'inside-out' proteins?"
-
Proteins 1999;36:135-143
-
Stevens TJ, Arkin IT: Turning an opinion inside-out: Rees and Eisenberg's commentary (Proteins 2000;38:121-122) on "Are membrane proteins 'inside-out' proteins?" (Proteins 1999;36:135-143). Proteins 2000, 40:463-464.
-
(2000)
Proteins
, vol.40
, pp. 463-464
-
-
Stevens, T.J.1
Arkin, I.T.2
-
6
-
-
0034621834
-
Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution
-
Toyoshima C., Nakasako M., Nomura O.H. Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution. Nature. 405:2000;647.
-
(2000)
Nature
, vol.405
, pp. 647
-
-
Toyoshima, C.1
Nakasako, M.2
Nomura, O.H.3
-
7
-
-
0035943429
-
Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins
-
note
-
Adamian L., Liang J. Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins. J Mol Biol. 311:2001;891-907. This work surveys the packing geometry of TM helices in membrane proteins, including the distribution of voids and pockets, packing efficiencies, residue coordination numbers, and helix-helix interactions. It was found that there are extensive specific pairwise interhelical interactions, including aromatic-basic and polar-polar interactions. In addition, a membrane helical interfacial pairwise propensity scale was developed.
-
(2001)
J Mol Biol
, vol.311
, pp. 891-907
-
-
Adamian, L.1
Liang, J.2
-
8
-
-
0033609904
-
Structure of bacteriorhodopsin at 1.55 Å resolution
-
Luecke H., Schobert B., Richter H.-T., Cartailler J.-P., Lanyi J.K. Structure of bacteriorhodopsin at 1.55 Å resolution. J Mol Biol. 291:1999;899-911.
-
(1999)
J Mol Biol
, vol.291
, pp. 899-911
-
-
Luecke, H.1
Schobert, B.2
Richter, H.-T.3
Cartailler, J.-P.4
Lanyi, J.K.5
-
9
-
-
0034705142
-
Internal packing of helical membrane proteins
-
Using the technique of occluded surface, membrane proteins are found to have higher packing values than soluble proteins.
-
Eilers M., Shekar S.C., Shieh T., Smith S.O., Fleming P.J. Internal packing of helical membrane proteins. Proc Natl Acad Sci USA. 97:2000;5796-5801. Using the technique of occluded surface, membrane proteins are found to have higher packing values than soluble proteins.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 5796-5801
-
-
Eilers, M.1
Shekar, S.C.2
Shieh, T.3
Smith, S.O.4
Fleming, P.J.5
-
10
-
-
0036226583
-
Comparison of helix interactions in membrane and soluble alpha-bundle proteins
-
Eilers M., Patel A.B., Liu W., Smith S.O. Comparison of helix interactions in membrane and soluble alpha-bundle proteins. Biophys J. 82:2002;2720-2736.
-
(2002)
Biophys J
, vol.82
, pp. 2720-2736
-
-
Eilers, M.1
Patel, A.B.2
Liu, W.3
Smith, S.O.4
-
11
-
-
0034901412
-
Are proteins well-packed?
-
Liang J., Dill K.A. Are proteins well-packed? Biophys J. 81:2001;751-766.
-
(2001)
Biophys J
, vol.81
, pp. 751-766
-
-
Liang, J.1
Dill, K.A.2
-
12
-
-
0037172965
-
Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein
-
The first quantitative measurements of thermodynamics of sequence variants of TM helical bundle domains with a large number of helices. The effects of single mutations at core positions of the homotetramer TM domain of the M2 protein from influenza A virus were measured by analytical ultracentrifugation. Many of the mutations are found to increase the stability of helical association, suggesting that natural membrane proteins are not optimized by evolution for maximum stability for oligomerization.
-
Howard K.P., Lear J.D., DeGrado W.F. Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein. Proc Natl Acad Sci USA. 99:2002;8568-8572. The first quantitative measurements of thermodynamics of sequence variants of TM helical bundle domains with a large number of helices. The effects of single mutations at core positions of the homotetramer TM domain of the M2 protein from influenza A virus were measured by analytical ultracentrifugation. Many of the mutations are found to increase the stability of helical association, suggesting that natural membrane proteins are not optimized by evolution for maximum stability for oligomerization.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 8568-8572
-
-
Howard, K.P.1
Lear, J.D.2
DeGrado, W.F.3
-
13
-
-
0031954925
-
Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
-
Wallin E., von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 7:1998;1029-1038.
-
(1998)
Protein Sci
, vol.7
, pp. 1029-1038
-
-
Wallin, E.1
Von Heijne, G.2
-
14
-
-
0032987478
-
Membrane protein folding and stability: Physical principles
-
White S.H., Wimley W.C. Membrane protein folding and stability: physical principles. Annu Rev Biophys Biomol Struct. 28:1999;319-365.
-
(1999)
Annu Rev Biophys Biomol Struct
, vol.28
, pp. 319-365
-
-
White, S.H.1
Wimley, W.C.2
-
15
-
-
0034284386
-
How proteins adapt to a membrane-water interface
-
Killian J.A., von Heijne G. How proteins adapt to a membrane-water interface. Trends Biochem Sci. 25:2000;429-434.
-
(2000)
Trends Biochem Sci
, vol.25
, pp. 429-434
-
-
Killian, J.A.1
Von Heijne, G.2
-
16
-
-
0035427377
-
Proline-induced hinges in transmembrane helices: Possible roles in ion channel gating
-
Tieleman D.P., Shrivastava I.H., Ulmschneider M.R., Sansom M.S. Proline-induced hinges in transmembrane helices: possible roles in ion channel gating. Proteins. 44:2001;63-72.
-
(2001)
Proteins
, vol.44
, pp. 63-72
-
-
Tieleman, D.P.1
Shrivastava, I.H.2
Ulmschneider, M.R.3
Sansom, M.S.4
-
17
-
-
0035895421
-
Non-alpha-helical elements modulate polytopic membrane protein architecture
-
Riek R.P., Rigoutsos I., Novotny J., Graham R.M. Non-alpha-helical elements modulate polytopic membrane protein architecture. J Mol Biol. 306:2001;349-362.
-
(2001)
J Mol Biol
, vol.306
, pp. 349-362
-
-
Riek, R.P.1
Rigoutsos, I.2
Novotny, J.3
Graham, R.M.4
-
18
-
-
0032817780
-
Helix packing in polytopic membrane proteins: Role of glycine in transmembrane helix association
-
Javadpour M.M., Eilers M., Groesbeek M., Smith S.O. Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association. Biophysical J. 77:1999;1609-1618.
-
(1999)
Biophysical J
, vol.77
, pp. 1609-1618
-
-
Javadpour, M.M.1
Eilers, M.2
Groesbeek, M.3
Smith, S.O.4
-
19
-
-
0034711953
-
The GxxxG motif: A framework for transmembrane helix-helix association
-
Russ W.P., Engelman D.M. The GxxxG motif: a framework for transmembrane helix-helix association. J Mol Biol. 296:2000;911-919.
-
(2000)
J Mol Biol
, vol.296
, pp. 911-919
-
-
Russ, W.P.1
Engelman, D.M.2
-
20
-
-
0036240805
-
A protein sequence that can encode native structure by disfavoring alternate conformations
-
A Pro residue in the centre of the third TM helix of the cystic fibrosis conductance regulator is found to promote folding by disfavouring misfolded β-sheet aggregate. On the basis of genome-wide TM sequence analysis, the authors suggest that this is a general mechanism selected by membrane proteins.
-
Wigley W.C., Corboy M.J., Cutler T.D., Thibodeau P.H., Oldan J., Lee M.G., Rizo J., Hunt J.F., Thomas P.J. A protein sequence that can encode native structure by disfavoring alternate conformations. Nat Struct Biol. 9:2002;381-388. A Pro residue in the centre of the third TM helix of the cystic fibrosis conductance regulator is found to promote folding by disfavouring misfolded β-sheet aggregate. On the basis of genome-wide TM sequence analysis, the authors suggest that this is a general mechanism selected by membrane proteins.
-
(2002)
Nat Struct Biol
, vol.9
, pp. 381-388
-
-
Wigley, W.C.1
Corboy, M.J.2
Cutler, T.D.3
Thibodeau, P.H.4
Oldan, J.5
Lee, M.G.6
Rizo, J.7
Hunt, J.F.8
Thomas, P.J.9
-
21
-
-
0036240798
-
Putting the beta-breaks on membrane protein misfolding
-
Deber C.M., Therien A.G. Putting the beta-breaks on membrane protein misfolding. Nat Struct Biol. 9:2002;318-319.
-
(2002)
Nat Struct Biol
, vol.9
, pp. 318-319
-
-
Deber, C.M.1
Therien, A.G.2
-
22
-
-
0033544689
-
KPROT a knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction
-
Pilpel Y., Ben-Tal N., Lancet D. kPROT a knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction. J Mol Biol. 294:1999;921-935.
-
(1999)
J Mol Biol
, vol.294
, pp. 921-935
-
-
Pilpel, Y.1
Ben-Tal, N.2
Lancet, D.3
-
23
-
-
0030932407
-
A transmembrane helix dimer: Structure and implications
-
MacKenzie K.R., Prestegard J.H., Engelman D.M. A transmembrane helix dimer: structure and implications. Science. 276:1997;131-133.
-
(1997)
Science
, vol.276
, pp. 131-133
-
-
MacKenzie, K.R.1
Prestegard, J.H.2
Engelman, D.M.3
-
24
-
-
0033515557
-
A heptad motif of leucine residues found in membrane proteins can drive self-assembly of artificial transmembrane segments
-
Gurezka R., Laage R., Brosig B., Langosch D. A heptad motif of leucine residues found in membrane proteins can drive self-assembly of artificial transmembrane segments. J Biol Chem. 274:1999;9265-9270.
-
(1999)
J Biol Chem
, vol.274
, pp. 9265-9270
-
-
Gurezka, R.1
Laage, R.2
Brosig, B.3
Langosch, D.4
-
25
-
-
0033983453
-
Asparagine-mediated self-association of a model transmembrane helix
-
One of the first studies elucidating the important role of polar-polar interactions in TM helix assembly. A two-stranded coiled-coil peptide based on yeast transcription factor GCN4 leucine zipper was engineered to be membrane-soluble. The oligomerization of this peptide was found to critically depend on the presence of a single Asn residue. Mutation to Val essentially abolishes oligomerization.
-
Choma C., Gratkowski H., Lear J.D., DeGrado W.F. Asparagine-mediated self-association of a model transmembrane helix. Nat Struct Biol. 7:2000;161-166. One of the first studies elucidating the important role of polar-polar interactions in TM helix assembly. A two-stranded coiled-coil peptide based on yeast transcription factor GCN4 leucine zipper was engineered to be membrane-soluble. The oligomerization of this peptide was found to critically depend on the presence of a single Asn residue. Mutation to Val essentially abolishes oligomerization.
-
(2000)
Nat Struct Biol
, vol.7
, pp. 161-166
-
-
Choma, C.1
Gratkowski, H.2
Lear, J.D.3
DeGrado, W.F.4
-
26
-
-
0007949690
-
Interhelical hydrogen bonding drives strong interactions in membrane proteins
-
One of the first studies demonstrating the important role of polar residues in the association of TM helices. Using engineered leucine zipper, the Asn residue was found to be essential for helix association in both detergent and biological membrane.
-
Zhou F.X., Cocco M.J., Russ W.P., Brunger A.T., Engelman D.M. Interhelical hydrogen bonding drives strong interactions in membrane proteins. Nat Struct Biol. 7:2000;154-160. One of the first studies demonstrating the important role of polar residues in the association of TM helices. Using engineered leucine zipper, the Asn residue was found to be essential for helix association in both detergent and biological membrane.
-
(2000)
Nat Struct Biol
, vol.7
, pp. 154-160
-
-
Zhou, F.X.1
Cocco, M.J.2
Russ, W.P.3
Brunger, A.T.4
Engelman, D.M.5
-
27
-
-
0035969998
-
Polar side chains drive the association of model transmembrane peptides
-
Building on oligomerization experiments of a model TM helix of engineered GCN4-P1, this work showed that residues with two polar atoms can drive oligomerization, whereas Ser and Thr cannot. The authors also discuss these results in light of the frequencies of polar residues appearing in TM helices.
-
Gratkowski H., Lear J.D., DeGrado W.F. Polar side chains drive the association of model transmembrane peptides. Proc Natl Acad Sci USA. 98:2001;880-885. Building on oligomerization experiments of a model TM helix of engineered GCN4-P1, this work showed that residues with two polar atoms can drive oligomerization, whereas Ser and Thr cannot. The authors also discuss these results in light of the frequencies of polar residues appearing in TM helices.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 880-885
-
-
Gratkowski, H.1
Lear, J.D.2
DeGrado, W.F.3
-
29
-
-
0035895356
-
Polar group burial contributes more to protein stability than nonpolar group burial
-
Pace C.N. Polar group burial contributes more to protein stability than nonpolar group burial. Biochemistry. 40:2001;310-313.
-
(2001)
Biochemistry
, vol.40
, pp. 310-313
-
-
Pace, C.N.1
-
30
-
-
0032406838
-
Statistical analysis of predicted transmembrane α-helices
-
Arkin I.T., Brunger A.T. Statistical analysis of predicted transmembrane α-helices. Biochim Biophy Acta. 1429:1998;113-128.
-
(1998)
Biochim Biophy Acta
, vol.1429
, pp. 113-128
-
-
Arkin, I.T.1
Brunger, A.T.2
-
31
-
-
0034711958
-
Statistical analysis of amino acid patterns in transmembrane helices: The GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions
-
Residue pairs and triplets with different sequence separation in individual TM helices were exhaustively examined for a large set of predicted TM helices. Many sequence motifs that are significantly over-represented were found, including GG4, SS4 and many others involving small residues.
-
Senes A., Gerstein M., Engelman D.M. Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. J Mol Biol. 296:2000;921-936. Residue pairs and triplets with different sequence separation in individual TM helices were exhaustively examined for a large set of predicted TM helices. Many sequence motifs that are significantly over-represented were found, including GG4, SS4 and many others involving small residues.
-
(2000)
J Mol Biol
, vol.296
, pp. 921-936
-
-
Senes, A.1
Gerstein, M.2
Engelman, D.M.3
-
32
-
-
0034604451
-
Crystal structure of rhodopsin: A G protein-coupled receptor
-
Palczewski K., Kumasaka T., Hori T., Behnke C.A., Motoshima H., Fox B.A., Trong I., Teller D.C., Okada T., Stenkamp R.E., et al. Crystal structure of rhodopsin: a G protein-coupled receptor. Science. 289:2000;739-745.
-
(2000)
Science
, vol.289
, pp. 739-745
-
-
Palczewski, K.1
Kumasaka, T.2
Hori, T.3
Behnke, C.A.4
Motoshima, H.5
Fox, B.A.6
Trong, I.7
Teller, D.C.8
Okada, T.9
Stenkamp, R.E.10
-
33
-
-
0029881315
-
Strong hydrogen bonding interactions involving a buried glutamic acid in the transmembrane sequence of the neu/erbB-2 receptor
-
Smith S.O., Smith C.S., Bormann B. Strong hydrogen bonding interactions involving a buried glutamic acid in the transmembrane sequence of the neu/erbB-2 receptor. Nat Struct Biol. 3:1996;252-258.
-
(1996)
Nat Struct Biol
, vol.3
, pp. 252-258
-
-
Smith, S.O.1
Smith, C.S.2
Bormann, B.3
-
34
-
-
0036568229
-
Interhelical hydrogen bonds and spatial motifs in membrane proteins: Polar clamps and serine zippers
-
A comprehensive survey of interhelical H-bond interactions shows that there are extensive H-bond connections between interacting TM helices. Almost all TM helices have one or more interhelical H-bond, and about 50% of interacting helical pairs contain H-bonds. Interhelical interfaces with H-bonds, in general, are packed tighter than those without H-bonds. Several spatial interhelical motifs, including serine zipper and polar clamps, are discovered.
-
Adamian L., Liang J. Interhelical hydrogen bonds and spatial motifs in membrane proteins: polar clamps and serine zippers. Proteins. 47:2002;209-218. A comprehensive survey of interhelical H-bond interactions shows that there are extensive H-bond connections between interacting TM helices. Almost all TM helices have one or more interhelical H-bond, and about 50% of interacting helical pairs contain H-bonds. Interhelical interfaces with H-bonds, in general, are packed tighter than those without H-bonds. Several spatial interhelical motifs, including serine zipper and polar clamps, are discovered.
-
(2002)
Proteins
, vol.47
, pp. 209-218
-
-
Adamian, L.1
Liang, J.2
-
35
-
-
0036224950
-
Implications of threonine hydrogen bonding in the glycophorin a transmembrane helix dimer
-
Smith S.O., Eilers M., Song D., Crocker E., Ying W., Groesbeek M., Metz G., Ziliox M., Aimoto S. Implications of threonine hydrogen bonding in the glycophorin a transmembrane helix dimer. Biophys J. 82:2002;2476-2486.
-
(2002)
Biophys J
, vol.82
, pp. 2476-2486
-
-
Smith, S.O.1
Eilers, M.2
Song, D.3
Crocker, E.4
Ying, W.5
Groesbeek, M.6
Metz, G.7
Ziliox, M.8
Aimoto, S.9
-
36
-
-
0034079112
-
Selective constraints, amino acid composition, and the rate of protein evolution
-
A careful comparative study of substitution rates of amino acid residues in the TM region and in soluble proteins. Using a set of homologous membrane proteins that have not yet experienced extensive multiple mutation, the authors found that polar residues Gln, Asn and His in TM regions experience purifying selection pressure and are highly conserved.
-
Tourasse N.J., Li W.H. Selective constraints, amino acid composition, and the rate of protein evolution. Mol Biol Evol. 17:2000;656-664. A careful comparative study of substitution rates of amino acid residues in the TM region and in soluble proteins. Using a set of homologous membrane proteins that have not yet experienced extensive multiple mutation, the authors found that polar residues Gln, Asn and His in TM regions experience purifying selection pressure and are highly conserved.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 656-664
-
-
Tourasse, N.J.1
Li, W.H.2
-
37
-
-
0032817780
-
Helix packing in polytopic membrane proteins: Role of glycine in transmembrane helix association
-
Javadpour M.M., Eilers M., Groesbeek M., Smith S.O. Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association. Biophys J. 77:1999;1609-1618.
-
(1999)
Biophys J
, vol.77
, pp. 1609-1618
-
-
Javadpour, M.M.1
Eilers, M.2
Groesbeek, M.3
Smith, S.O.4
-
38
-
-
0033790343
-
Helical membrane protein folding, stability, and evolution
-
Popot J.L., Engelman D.M. Helical membrane protein folding, stability, and evolution. Annu Rev Biochem. 69:2000;881-922.
-
(2000)
Annu Rev Biochem
, vol.69
, pp. 881-922
-
-
Popot, J.L.1
Engelman, D.M.2
-
41
-
-
0036301006
-
Motifs of serine and threonine can drive association of transmembrane helices
-
Dawson J.P., Weinger J.S., Engelman D.M. Motifs of serine and threonine can drive association of transmembrane helices. J Mol Biol. 316:2002;799-805.
-
(2002)
J Mol Biol
, vol.316
, pp. 799-805
-
-
Dawson, J.P.1
Weinger, J.S.2
Engelman, D.M.3
-
42
-
-
0037076540
-
GXXXG and AXXXA: Common α-helical interaction motifs in proteins, particularly in extremophiles
-
Kleiger G., Grothe R., Mallick P., Eisenberg D. GXXXG and AXXXA: common α-helical interaction motifs in proteins, particularly in extremophiles. Biochemistry. 41:2002;5990-5997.
-
(2002)
Biochemistry
, vol.41
, pp. 5990-5997
-
-
Kleiger, G.1
Grothe, R.2
Mallick, P.3
Eisenberg, D.4
-
43
-
-
0035979146
-
α - H.O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions
-
α-H-O bond interactions are important for the stability and specificity of helix-helix association in membrane proteins.
-
α-H-O bond interactions are important for the stability and specificity of helix-helix association in membrane proteins.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 9056-9061
-
-
Senes, A.1
Ubarretxena-Belandia, I.2
Engelman, D.M.3
-
44
-
-
0035423934
-
Stabilizing membrane proteins
-
An insightful review on how stability-enhancing mutations are relatively easy to find. The author suggests that membrane proteins are not optimized for stability, and points to experimental demonstration that a hyperstable membrane protein can be obtained by a quadruple mutation.
-
Bowie J.U. Stabilizing membrane proteins. Curr Opin Struct Biol. 11:2001;397-402. An insightful review on how stability-enhancing mutations are relatively easy to find. The author suggests that membrane proteins are not optimized for stability, and points to experimental demonstration that a hyperstable membrane protein can be obtained by a quadruple mutation.
-
(2001)
Curr Opin Struct Biol
, vol.11
, pp. 397-402
-
-
Bowie, J.U.1
-
45
-
-
0034629489
-
Building a thermostable membrane protein
-
Zhou Y., Bowie J.U. Building a thermostable membrane protein. J Biol Chem. 275:2000;6975-6979.
-
(2000)
J Biol Chem
, vol.275
, pp. 6975-6979
-
-
Zhou, Y.1
Bowie, J.U.2
-
46
-
-
0034687802
-
Deciphering the folding kinetics of transmembrane helical proteins
-
α representation of the first 66 amino acid residues from bacteriorhodopsin, which are known to fold independently, a Monte Carlo simulation was carried out to assess the folding kinetics and equilibrium thermodynamics of these two TM helices. Under Go-like potential encoding information about native contacts, the results of simulation suggest the existence of intermediates and multi-state folding kinetics.
-
α representation of the first 66 amino acid residues from bacteriorhodopsin, which are known to fold independently, a Monte Carlo simulation was carried out to assess the folding kinetics and equilibrium thermodynamics of these two TM helices. Under Go-like potential encoding information about native contacts, the results of simulation suggest the existence of intermediates and multi-state folding kinetics.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 14229-14234
-
-
Orlandini, E.1
Seno, F.2
Banavar, J.R.3
Laio, A.4
Maritan, A.5
-
47
-
-
4243379922
-
Lattice model of transmembrane polypeptide folding
-
Chen C-M: Lattice model of transmembrane polypeptide folding. Phys Rev E 2001, 63:01090.1-4.
-
(2001)
Phys Rev E
, vol.63
, pp. 010901-010904
-
-
Chen, C.-M.1
-
49
-
-
0034141931
-
Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?
-
Vendruscolo M., Najmanovich R., Domany E. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading? Proteins. 38:2000;134-148.
-
(2000)
Proteins
, vol.38
, pp. 134-148
-
-
Vendruscolo, M.1
Najmanovich, R.2
Domany, E.3
-
50
-
-
0034237798
-
On the design and analysis of protein folding potentials
-
Tobi D., Shafran G., Linial N., Elber R. On the design and analysis of protein folding potentials. Proteins. 40:2000;71-85.
-
(2000)
Proteins
, vol.40
, pp. 71-85
-
-
Tobi, D.1
Shafran, G.2
Linial, N.3
Elber, R.4
-
51
-
-
0037079580
-
Maximum feasibility guideline in the design and analysis of protein folding potentials
-
Meller J., Wagner M., Elber R. Maximum feasibility guideline in the design and analysis of protein folding potentials. J Comput Chem. 23:2002;111-118.
-
(2002)
J Comput Chem
, vol.23
, pp. 111-118
-
-
Meller, J.1
Wagner, M.2
Elber, R.3
-
52
-
-
0035889689
-
Linear programming optimization and a double statistical filter for protein threading protocols
-
Meller J., Elber R. Linear programming optimization and a double statistical filter for protein threading protocols. Proteins. 45:2001;241-261.
-
(2001)
Proteins
, vol.45
, pp. 241-261
-
-
Meller, J.1
Elber, R.2
-
53
-
-
0033457943
-
Helix-bundle membrane protein fold templates
-
This work explored the size of the space for conformational search in packing canonical helices into bundles. Fold template can be generated computationally for up to seven helices. The number of possible fold templates is found to increase exponentially with the number of helices.
-
Bowie J.U. Helix-bundle membrane protein fold templates. Protein Sci. 8:1999;2711-2719. This work explored the size of the space for conformational search in packing canonical helices into bundles. Fold template can be generated computationally for up to seven helices. The number of possible fold templates is found to increase exponentially with the number of helices.
-
(1999)
Protein Sci
, vol.8
, pp. 2711-2719
-
-
Bowie, J.U.1
-
54
-
-
0000799811
-
Scanning method as an unbiased simulation technique and its application to the study of self-attracting random walks
-
Meirovitch H. Scanning method as an unbiased simulation technique and its application to the study of self-attracting random walks. Physical Rev A. 32:1985;3699-3708.
-
(1985)
Physical Rev A
, vol.32
, pp. 3699-3708
-
-
Meirovitch, H.1
-
55
-
-
0035342441
-
Lattice protein folding with two and four-body statistical potentials
-
Gan H.H., Tropsha A., Schlick T. Lattice protein folding with two and four-body statistical potentials. Proteins. 43:2001;161-174.
-
(2001)
Proteins
, vol.43
, pp. 161-174
-
-
Gan, H.H.1
Tropsha, A.2
Schlick, T.3
-
56
-
-
0037103826
-
Statistical geometry of packing defects of lattice chain polymer from enumeration and sequential Monte Carlo method
-
Liang J., Zhang J., Chen R. Statistical geometry of packing defects of lattice chain polymer from enumeration and sequential Monte Carlo method. J Chem Phys. 117:2002;3511-3521.
-
(2002)
J Chem Phys
, vol.117
, pp. 3511-3521
-
-
Liang, J.1
Zhang, J.2
Chen, R.3
-
57
-
-
0037110551
-
Optimal potentials for predicting inter-helical packing in transmembrane proteins
-
Dobbs H., Orlandini E., Bonaccini R., Seno F. Optimal potentials for predicting inter-helical packing in transmembrane proteins. Proteins. 49:2002;342-349.
-
(2002)
Proteins
, vol.49
, pp. 342-349
-
-
Dobbs, H.1
Orlandini, E.2
Bonaccini, R.3
Seno, F.4
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