Atom depth in protein structure and function.

Atom depth, originally defined as the distance between a protein atom and the nearest water molecule surrounding a protein, is a simple but valuable geometrical descriptor of the protein interior. It can be easily computed from the 3D structure of a protein, thus complementing the information provided by the calculation of the solvent accessible surface area and buried surface area. Depth has been found to be correlated with several molecular, residue and atomic properties, such as average protein domain size, protein stability, free energy of formation of protein complexes, amino acid type hydrophobicity, residue conservation and hydrogen/deuterium amide proton exchange rates.

[1]  S. Marqusee,et al.  Hydrogen exchange studies of protein structure. , 1998, Current opinion in biotechnology.

[2]  F M Poulsen,et al.  A nuclear magnetic resonance study of the hydrogen-exchange behaviour of lysozyme in crystals and solution. , 1991, Journal of molecular biology.

[3]  Oliviero Carugo,et al.  DPX: for the analysis of the protein core , 2003, Bioinform..

[4]  M L Connolly,et al.  The molecular surface package. , 1993, Journal of molecular graphics.

[5]  Simon J. Hubbard,et al.  Department of Biochemistry and Molecular Biology , 2006 .

[6]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[7]  Mark Gerstein,et al.  Determining the minimum number of types necessary to represent the sizes of protein atoms , 2001, Bioinform..

[8]  H. Senn,et al.  The three-dimensional high resolution structure of human interferon alpha-2a determined by heteronuclear NMR spectroscopy in solution. , 1997, Journal of molecular biology.

[9]  R. Grantham.  Amino Acid Difference Formula to Help Explain Protein Evolution , 1974, Science.

[10]  L. Mirny,et al.  Evolutionary conservation of the folding nucleus. , 2000, Journal of molecular biology.

[11]  Shandar Ahmad,et al.  NETASA: neural network based prediction of solvent accessibility , 2002, Bioinform..

[12]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[13]  K. B. Ward,et al.  Occluded molecular surface: Analysis of protein packing , 1995, Journal of molecular recognition : JMR.

[14]  D. Cooper,et al.  Human Gene Mutation Database , 1996, Human Genetics.

[15]  Oliviero Carugo,et al.  Atom depth as a descriptor of the protein interior. , 2003, Biophysical journal.

[16]  L Serrano,et al.  The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. , 1992, Journal of molecular biology.

[17]  R. Nussinov,et al.  Favorable domain size in proteins. , 1998, Folding & design.

[18]  A. Fersht,et al.  The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. , 1992, Journal of molecular biology.

[19]  O. Carugo,et al.  How many water molecules can be detected by protein crystallography? , 1999, Acta crystallographica. Section D, Biological crystallography.

[20]  M Krawczak,et al.  Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes. , 1998, American journal of human genetics.

[21]  Stephen H. Bryant,et al.  Domain size distributions can predict domain boundaries , 2000, Bioinform..

[22]  R. Varadarajan,et al.  Residue depth: a novel parameter for the analysis of protein structure and stability. , 1999, Structure.