Literature DB >> 8378312

What determines the strength of noncovalent association of ligands to proteins in aqueous solution?

S Miyamoto1, P A Kollman.   

Abstract

Free energy perturbation methods using molecular dynamics have been used to calculate the absolute free energy of association of two ligand-protein complexes. The calculations reproduce the significantly more negative free energy of association of biotin to streptavidin, compared to N-L-acetyltryptophanamide/alpha-chymotrypsin. This difference in free energy of association is due to van der Waals/dispersion effects in the nearly ideally performed cavity that streptavidin presents to biotin, which involves four tryptophan residues.

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Year:  1993        PMID： 8378312      PMCID： PMC47364          DOI： 10.1073/pnas.90.18.8402

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  20 in total

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Authors:  D L Beveridge; F M DiCapua
Journal:  Annu Rev Biophys Biophys Chem       Date:  1989

2.  Hidden thermodynamics of mutant proteins: a molecular dynamics analysis.

Authors:  J Gao; K Kuczera; B Tidor; M Karplus
Journal:  Science       Date:  1989-06-02       Impact factor: 47.728

3.  Free energy calculations by computer simulation.

Authors:  P A Bash; U C Singh; R Langridge; P A Kollman
Journal:  Science       Date:  1987-05-01       Impact factor: 47.728

4.  Semiquantitative calculations of catalytic free energies in genetically modified enzymes.

Authors:  J K Hwang; A Warshel
Journal:  Biochemistry       Date:  1987-05-19       Impact factor: 3.162

5.  Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin.

Authors:  S N Rao; U C Singh; P A Bash; P A Kollman
Journal:  Nature       Date:  1987 Aug 6-12       Impact factor: 49.962

6.  Structural origins of high-affinity biotin binding to streptavidin.

Authors:  P C Weber; D H Ohlendorf; J J Wendoloski; F R Salemme
Journal:  Science       Date:  1989-01-06       Impact factor: 47.728

7.  Energetics of enzyme catalysis.

Authors:  A Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  1978-11       Impact factor: 11.205

8.  Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 A resolution.

Authors:  M Fujinaga; A R Sielecki; R J Read; W Ardelt; M Laskowski; M N James
Journal:  J Mol Biol       Date:  1987-05-20       Impact factor: 5.469

9.  Calculation of the relative change in binding free energy of a protein-inhibitor complex.

Authors:  P A Bash; U C Singh; F K Brown; R Langridge; P A Kollman
Journal:  Science       Date:  1987-01-30       Impact factor: 47.728

10.  A mutant T4 lysozyme (Val 131----Ala) designed to increase thermostability by the reduction of strain within an alpha-helix.

Authors:  S Dao-Pin; W A Baase; B W Matthews
Journal:  Proteins       Date:  1990
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  21 in total

1.  The maximal affinity of ligands.

Authors:  I D Kuntz; K Chen; K A Sharp; P A Kollman
Journal:  Proc Natl Acad Sci U S A       Date:  1999-08-31       Impact factor: 11.205

2.  Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study.

Authors:  Nathalie Basdevant; Harel Weinstein; Marco Ceruso
Journal:  J Am Chem Soc       Date:  2006-10-04       Impact factor: 15.419

3.  Minimalist explicit solvation models for surface loops in proteins.

Authors:  Ronald P White; Hagai Meirovitch
Journal:  J Chem Theory Comput       Date:  2006       Impact factor: 6.006

4.  Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.

Authors:  P A Rejto; G M Verkhivker
Journal:  Proc Natl Acad Sci U S A       Date:  1996-08-20       Impact factor: 11.205

5.  Force generation, work, and coupling in molecular motors.

Authors:  R M Krupka
Journal:  Biophys J       Date:  1996-04       Impact factor: 4.033

6.  The statistical-thermodynamic basis for computation of binding affinities: a critical review.

Authors:  M K Gilson; J A Given; B L Bush; J A McCammon
Journal:  Biophys J       Date:  1997-03       Impact factor: 4.033

Review 7.  Beauty is skin deep: a surface monolayer perspective on nanoparticle interactions with cells and bio-macromolecules.

Authors:  Krishnendu Saha; Avinash Bajaj; Bradley Duncan; Vincent M Rotello
Journal:  Small       Date:  2011-06-14       Impact factor: 13.281

8.  Site-directed mutagenesis studies of the high-affinity streptavidin-biotin complex: contributions of tryptophan residues 79, 108, and 120.

Authors:  A Chilkoti; P H Tan; P S Stayton
Journal:  Proc Natl Acad Sci U S A       Date:  1995-02-28       Impact factor: 11.205

Review 9.  Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.

Authors:  Hagai Meirovitch; Srinath Cheluvaraja; Ronald P White
Journal:  Curr Protein Pept Sci       Date:  2009-06       Impact factor: 3.272

10.  Effects of tryptophan residue fluorination on streptavidin stability and biotin-streptavidin interactions via molecular dynamics simulations.

Authors:  Jarosław J Panek; Thomas R Ward; Aneta Jezierska; Marjana Novic
Journal:  J Mol Model       Date:  2008-12-04       Impact factor: 1.810
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