Characterization of interactions and metal ion binding sites in proteins

Abstract Recent investigations show that as a class of interactions for designing proteins, hydrophobic interactions are not specific enough, hydrophilic interactions are typically too weak, and water interactions are always on the exterior. In terms of overall protein stability, there is a substantial advantage to a nucleus with strong, directional interactions. Metal ion sites in proteins exhibit strong directional preferences for their coordinate ligands, and the specificities manifested by ions have been demonstrated to be useful in reducing molecular fluctuations. The engineered introduction of zinc binding sites has been shown to improve the stabilities of designed proteins. Metal binding sites can therefore provide important structural building blocks for protein design.

[1]  H. Weinstein,et al.  On the ion selectivity in Ca-binding proteins: the cyclo(-L-Pro-Gly-)3 peptide as a model. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[2]  J. G. Grossmann,et al.  Metal-induced conformational changes in transferrins. , 1993, Journal of molecular biology.

[3]  J. Falke,et al.  Novel ion specificity of a carboxylate cluster Mg(II) binding site: strong charge selectivity and weak size selectivity. , 1993, Biochemistry.

[4]  R L Jernigan,et al.  Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions. , 1994, Biophysical journal.

[5]  S. N. Timasheff.  Water as ligand: preferential binding and exclusion of denaturants in protein unfolding. , 1992, Biochemistry.

[6]  J. Berg,et al.  Independence of metal binding between tandem Cys2His2 zinc finger domains , 1993, Protein science : a publication of the Protein Society.

[7]  D. Lilley,et al.  Nuclear magnetic resonance study of a deoxyoligonucleotide duplex containing a three base bulge. , 1993, Journal of molecular biology.

[8]  D A Agard,et al.  Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. , 1993, Journal of molecular biology.

[9]  A. Lane,et al.  Effects of calcium binding on the internal dynamic properties of bovine brain calmodulin, studied by NMR and optical spectroscopy. , 1992, Biochemistry.

[10]  F A Quiocho,et al.  Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex. , 1992, Science.

[11]  A. Palmer,et al.  Backbone dynamics of calcium-loaded calbindin D9k studied by two-dimensional proton-detected 15N NMR spectroscopy. , 1992, Biochemistry.

[12]  K. Karlin.  Metalloenzymes, structural motifs, and inorganic models. , 1993, Science.

[13]  R. Huber,et al.  Refined 1.8 A X-ray crystal structure of astacin, a zinc-endopeptidase from the crayfish Astacus astacus L. Structure determination, refinement, molecular structure and comparison with thermolysin. , 1994, Journal of molecular biology.

[14]  G. Rose,et al.  Protein folding--what's the question? , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[15]  J. Glusker.  Structural aspects of metal liganding to functional groups in proteins. , 1991, Advances in protein chemistry.

[16]  K. Dill,et al.  The Protein Folding Problem , 1993 .

[17]  P Argos,et al.  A method to configure protein side-chains from the main-chain trace in homology modelling. , 1993, Journal of molecular biology.

[18]  D Eisenberg,et al.  Where metal ions bind in proteins. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[19]  W. Chazin,et al.  Two-dimensional 1H nuclear magnetic resonance studies of the half-saturated (Ca2+)1 state of calbindin D9k. Further implications for the molecular basis of cooperative Ca2+ binding. , 1993, Journal of molecular biology.

[20]  H. Weinstein,et al.  Structural dynamics of calmodulin and troponin C. , 1991, Protein engineering.

[21]  P. Chakrabarti.  Systematics in the interaction of metal ions with the main-chain carbonyl group in protein structures. , 1990, Biochemistry.

[22]  R. Jernigan,et al.  Solvent effect on binding thermodynamics of biopolymers , 1990, Biopolymers.

[23]  H. Weinstein,et al.  Structural Specificity in the Engineering of Biological Function: Insights from the Dynamics of Calmodulin , 1992 .

[24]  D. T. Jones,et al.  A new approach to protein fold recognition , 1992, Nature.

[25]  J. Berg,et al.  Metal binding properties of single amino acid deletion mutants of zinc finger peptides: studies using cobalt(II) as a spectroscopic probe. , 1993, Biophysical journal.

[26]  A. Persechini,et al.  The linker of des-Glu84-calmodulin is bent. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[27]  H. Weinstein,et al.  Consequences of Sequential Ca2+ Occupancy for the Structure and Dynamics of CalbindinD9K: Computational Simulations and Comparison to Experimental Determinations in Solution , 1993 .

[28]  Roland L. Dunbrack,et al.  Backbone-dependent rotamer library for proteins. Application to side-chain prediction. , 1993, Journal of molecular biology.

[29]  R. Jernigan,et al.  Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .

[30]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[31]  C Sander,et al.  Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. , 1993, Journal of molecular biology.

[32]  J. Gao,et al.  A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations. , 1992, Science.

[33]  T M Handel,et al.  Metal ion-dependent modulation of the dynamics of a designed protein. , 1993, Science.

[34]  M J Sternberg,et al.  Empirical scale of side-chain conformational entropy in protein folding. , 1993, Journal of molecular biology.

[35]  F A Quiocho,et al.  Calmodulin structure refined at 1.7 A resolution. , 1992, Journal of molecular biology.

[36]  D A Dougherty,et al.  A mechanism for ion selectivity in potassium channels: computational studies of cation-pi interactions. , 1993, Science.

[37]  Anna Tramontano,et al.  A designed metal-binding protein with a novel fold , 1993, Nature.

[38]  G. Petsko,et al.  Weakly polar interactions in proteins. , 1988, Advances in protein chemistry.

[39]  M Ikura,et al.  Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible. , 1992, Biochemistry.

[40]  P. Chakrabarti.  Anion binding sites in protein structures. , 1993, Journal of molecular biology.

[41]  S. Roe,et al.  Patterns for prediction of hydration around polar residues in proteins. , 1993, Journal of molecular biology.

[42]  M. Akke,et al.  Molecular basis for co-operativity in Ca2+ binding to calbindin D9k. 1H nuclear magnetic resonance studies of (Cd2+)1-bovine calbindin D9k. , 1991, Journal of molecular biology.

[43]  P. Bryan,et al.  Calcium‐independent subtilisin by design , 1993, Proteins.

[44]  D. Woolfson,et al.  Protein folding in the absence of the solvent ordering contribution to the hydrophobic interaction. , 1993, Journal of molecular biology.

[45]  A. Palmer,et al.  Effects of ion binding on the backbone dynamics of calbindin D9k determined by 15N NMR relaxation. , 1993, Biochemistry.

[46]  J Skolnick,et al.  Computer modeling and folding of four‐helix bundles , 1993, Proteins.

[47]  J M Goodfellow,et al.  Distribution of solvent molecules around apolar side-chains in protein crystals. , 1993, Journal of molecular biology.

[48]  C. Miller.  Potassium selectivity in proteins: oxygen cage or pi in the face? , 1993, Science.

[49]  O. Berg,et al.  The divalent cation is obligatory for the binding of ligands to the catalytic site of secreted phospholipase A2. , 1993, Biochemistry.