Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases

Gert Vriend; Vincent Eijsink

doi:10.1007/bf02337558

journal article Aug 01, 1993

Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases

Gert Vriend

Vincent Eijsink

Journal of Computer-Aided Molecular Design Vol. 7 No. 4 pp. 367-396 · Springer Science and Business Media LLC

View at Publisher Save 10.1007/bf02337558

Topics

No keywords indexed for this article. Browse by subject →

References

215

[1]

Giege, R. and Mikol, V., Trends Biotechnol., 7 (1989) 277. 10.1016/0167-7799(89)90047-4

[2]

Swindells, M.B. and Thornton, J.M., Curr. Opin. Struct. Biol., 1 (1991) 219. 10.1016/0959-440x(91)90064-z

[3]

Evolution and the Tertiary Structure of Proteins

M Bajaj, T Blundell

Annual Review of Biophysics and Bioengineering 1984 10.1146/annurev.bb.13.060184.002321

[4]

Determinants of a protein fold

Donald Bashford, Cyrus Chothia, Arthur M. Lesk

Journal of Molecular Biology 1987 10.1016/0022-2836(87)90521-3

[5]

The relation between the divergence of sequence and structure in proteins.

C. Chothia, A.M. Lesk

The EMBO Journal 1986 10.1002/j.1460-2075.1986.tb04288.x

[6]

Database of homology‐derived protein structures and the structural meaning of sequence alignment

Chris Sander, Reinhard Schneider

Proteins: Structure, Function, and Bioinformatics 1991 10.1002/prot.340090107

[7]

Knowledge-based prediction of protein structures and the design of novel molecules

T. L. BLUNDELL, B. L. Sibanda, M. J. E. Sternberg et al.

Nature 1987 10.1038/326347a0

[8]

Van den Burg, B., Enequist, H.G., Van der Haar, M.E., Eijsink, V.G.H., Stulp, B.K. and Venema, G., J. Bacteriol., 173 (1991) 4107. 10.1128/jb.173.13.4107-4115.1991

[9]

Eijsink, V.G.H., Vriend, G., Van der Vinne, B., Van den Burg, B. and Venema, G., Proteins, 14 (1992) 224. 10.1002/prot.340140209

[10]

Eijsink, V.G.H., Dijkstra, B.W., Vriend, G., Van der Zee, J.R., Veltman, O.R., Van der Vinne, B., Van den Burg, B., Kempe, S. and Venema, G., Protein Eng., 5 (1992) 421. 10.1093/protein/5.5.421

[11]

Fontana, A., Biophys. Chem., 29 (1988) 181. 10.1016/0301-4622(88)87038-8

[12]

Identification of protein sequence homology by consensus template alignment

William Ramsay Taylor

Journal of Molecular Biology 1986 10.1016/0022-2836(86)90308-6

[13]

Criteria that discriminate between native proteins and incorrectly folded models

Jiří Novotný, A. A. Rashin, R. E. Bruccoleri

Proteins: Structure, Function, and Bioinformatics 1988 10.1002/prot.340040105

[14]

Environment‐specific amino acid substitution tables: Tertiary templates and prediction of protein folds

John OVERINGTON, Dan Donnelly, Mark S. Johnson et al.

Protein Science 1992 10.1002/pro.5560010203

[15]

Crippen, G.M., Biochemistry, 30 (1990) 4232. 10.1021/bi00231a018

[16]

Detection of native‐like models for amino acid sequences of unknown three‐dimensional structure in a data base of known protein conformations

Manfred J. Sippl, Sabine Weitckus

Proteins: Structure, Function, and Bioinformatics 1992 10.1002/prot.340130308

[17]

Secondary structure‐based profiles: Use of structure‐conserving scoring tables in searching protein sequence databases for structural similarities

Roland Lüthy, Andrew D. McLachlan, David Eisenberg

Proteins: Structure, Function, and Bioinformatics 1991 10.1002/prot.340100307

[18]

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

James U. Bowie, Roland Lüthy, David Eisenberg

Science 1991 10.1126/science.1853201

[19]

Assessment of protein models with three-dimensional profiles

Roland Lüthy, James U. Bowie, David Eisenberg

Nature 1992 10.1038/356083a0

[20]

A new approach to protein fold recognition

David T. Jones, W. R. Taylort, J. M. Thornton

Nature 1992 10.1038/358086a0

[21]

Scharf, M., Ph.D. Thesis, University of Heidelberg, 1989.

[22]

Prediction of progress at last

Janet M. Thornton, Tomas P. Flores, David T. Jones et al.

Nature 1991 10.1038/354105a0

[23]

Analysis of the relationship between side-chain conformation and secondary structure in globular proteins

Malcolm J. McGregor, Suhail A. Islam, Michael J.E. Sternberg

Journal of Molecular Biology 1987 10.1016/0022-2836(87)90314-7

[24]

Tertiary templates for proteins

Jay W. Ponder, Frederic M. Richards

Journal of Molecular Biology 1987 10.1016/0022-2836(87)90358-5

[25]

Read, L.S. and Thornton, J.M., Proteins, 5 (1989) 170. 10.1002/prot.340050212

[26]

Construction of side-chains in homology modelling

Neena L. Summers, Martin Karplus

Journal of Molecular Biology 1989 10.1016/0022-2836(89)90109-5

[27]

Eisenmenger, F., Argos, P. and Abagyan, R., J. Mol. Biol., 231 (1993) 849. 10.1006/jmbi.1993.1331

[28]

Using known substructures in protein model building and crystallography.

T.Alwyn Jones, S. Thirup

The EMBO Journal 1986 10.1002/j.1460-2075.1986.tb04287.x

[29]

Schomburg, D. and Reichelt, J., J. Mol. Graphics, 6 (1988) 161. 10.1016/0263-7855(88)80069-9

[30]

Interactive program for visualization and modelling of proteins, nucleic acids and small molecules

H E Dayringer, A Tramontano, S R Sprang et al.

Journal of Molecular Graphics 1986 10.1016/0263-7855(86)80002-9

[31]

WHAT IF: A molecular modeling and drug design program

G. Vriend

Journal of Molecular Graphics 1990 10.1016/0263-7855(90)80070-v

[32]

A graphics model building and refinement system for macromolecules

T. Alwyn Jones

Journal of Applied Crystallography 1978 10.1107/s0021889878013308

[33]

Hubbard, R.E., In Fletterick, R.J. and Zoller, M. (Eds), Computer Graphics and Molecular Modelling, Cold Spring Harbor, 1986, pp. 9–12.

[34]

Improved methods for building protein models in electron density maps and the location of errors in these models

T. Alwyn Jones, J. Y. Zou, S. W. Cowan et al.

Acta Crystallographica Section A Foundations of Cr... 1991 10.1107/s0108767390010224

[35]

An algorithm for determining the conformation of polypeptide segments in proteins by systematic search

J. Moult, M. N. G. James

Proteins: Structure, Function, and Bioinformatics 1986 10.1002/prot.340010207

[36]

Prediction of the folding of short polypeptide segments by uniform conformational sampling

Robert E. Bruccoleri, Martin Karplus

Biopolymers 1987 10.1002/bip.360260114

[37]

Predicting antibody hypervariable loop conformations II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations

R. M. Fine, H. Wang, P. S. Shenkin et al.

Proteins: Structure, Function, and Bioinformatics 1986 10.1002/prot.340010408

[38]

A new method for building protein conformations from sequence alignments with homologues of known structure

Timothy F. Havel, Mark E. Snow

Journal of Molecular Biology 1991 10.1016/0022-2836(91)90603-4

[39]

Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: Development of strategies and construction of models for myoglobin, lysozyme, and thymosin β4

Manfred J. Sippl, Manfred Hendlich, Peter Lackner

Protein Science 1992 10.1002/pro.5560010509

[40]

Simon, I., Glasser, L. and Scheraga, H.A., Proc. Natl. Acad. Sci. U.S.A., 88 (1991) 3661. 10.1073/pnas.88.9.3661

[41]

On the multiple‐minima problem in the conformational analysis of polypeptides. IV. Application of the electrostatically driven monte carlo method to the 20‐residue membrane‐bound portion of melittin

Daniel R. Ripoll, Harold A. Scheraca

Biopolymers 1990 10.1002/bip.360300116

[42]

How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins

Arthur M. Lesk, Cyrus Chothia

Journal of Molecular Biology 1980 10.1016/0022-2836(80)90373-3

[43]

Helix movements and the reconstruction of the haem pocket during the evolution of the cytochrome c family

Cyrus Chothia, Arthur M. Lesk

Journal of Molecular Biology 1985 10.1016/0022-2836(85)90033-6

[44]

Chothia, C. and Lesk, A.M., Trends Biochem. Sci., 190 (1985) 116. 10.1016/0968-0004(85)90270-1

[45]

Richardson, J.S., In Anfinsen, C.B., Edsall, J.T. and Richards, R.M. (Eds), Advances in Protein Chemistry, Vol. 34, Academic Press, pp. 167–339.

[46]

Ashida, T., Tsunogae, Y., Tanaka, I. and Yamane, T., Acta Cryst., B43 (1987) 212. 10.1107/s0108768187098045

[47]

Islam, S.A. and Sternberg, M.J.E., Protein Eng., 2 (1989) 431. 10.1093/protein/2.6.431

[48]

Akrigg, D., Bleasby, A.J., Dix, N.I.M., Findlay, J.B.C., North, A.C.T., Parry-Smith, D., Wootton, J.C., Blundell, T.L., Gardner, S.P., Hayes, F., Islam, S., Sternberg, M.J.E., Thornton, J.M. and Tickle, I.J., Nature, 335 (1988) 745. 10.1038/335745a0

[49]

Huysmans, M., Richelle, J. and Wodak, S.J., Proteins, 11 (1991) 59. 10.1002/prot.340110108

[50]

Vriend, G., Stouten, P. and Sander, C., submitted.

Showing 50 of 215 references

Cited By

74

Computational Library Design for Increasing Haloalkane Dehalogenase Stability

Robert J. Floor, Hein J. Wijma · 2014

ChemBioChem

Enhanced activity and stability in the presence of organic solvents by increased active site polarity and stabilization of a surface loop in a metalloprotease

A. Badoei-Dalfard, K. Khajeh · 2010

The Journal of Biochemistry

The stability of engineered thermostable neutral proteases from Bacillus stearothermophilus in organic solvents and detergents

Johanna Mansfeld, Renate Ulbrich‐Hofmann · 2007

Biotechnology and Bioengineering

Rational engineering of enzyme stability

Vincent G. H. Eijsink, Alexandra Bjørk · 2004

Journal of Biotechnology

Molecular Mechanisms of Stabilization of Proteolytic Enzymes: A Model of Thermolysin-Like Microbial Metalloproteases

I. V. Demidyuk, M. V. Zabolotskaya · 2003

Russian Journal of Bioorganic Chemi...

Directed evolution converts subtilisin E into a functional equivalent of thermitase

Huimin Zhao, Frances H. Arnold · 1999

Protein Engineering, Design and Sel...

Characterization of a novel stable biocatalyst obtained by protein engineering

Bertus Van den Burg, Arno De Kreij · 1999

Biotechnology and Applied Biochemis...

Engineering an enzyme to resist boiling

Bertus Van den Burg, Gert Vriend · 1998

Proceedings of the National Academy...

Core-packing constraints, hydrophobicity and protein design

Enoch P Baldwin, Brian W Matthews · 1994

Current Opinion in Biotechnology

Modeling studies of the change in conformation required for cleavage of limited proteolytic sites

S.J. Hubbard, F Eisenmenger · 1994

Protein Science

Metrics

74

Citations

215

References

Details

Published: Aug 01, 1993
Vol/Issue: 7(4)
Pages: 367-396
License: View

Authors

G

Gert Vriend

Radboud University Nijmegen

V

Vincent Eijsink

Cite This Article

Gert Vriend, Vincent Eijsink (1993). Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases. Journal of Computer-Aided Molecular Design, 7(4), 367-396. https://doi.org/10.1007/bf02337558

Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases

You May Also Like