Atom-wise statistics and prediction of solvent accessibility in proteins

Singh, Yumlembam H.; Gromiha, M. Michael; Sarai, Akinori; Ahmad, Shandar

doi:10.1016/j.bpc.2006.06.013

Cited by 12 publications

(12 citation statements)

References 30 publications

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“…Because of the involvement in the interactions with other biological molecules, surface residues have been under extensive investigations, especially in the area of protein drug design 7. Accordingly, accessible surface area (ASA) has been widely adopted to define surface residues8 and based on it, a large number of sequence‐based prediction methods have been developed during recent years 9–20. However, the knowledge of ASA cannot provide information about the structural arrangements of buried residues, when their ASAs are zeros or near zeros.…”

Section: Introductionmentioning

confidence: 99%

Quantifying the relationship of protein burying depth and sequence

Wang

2007

Proteins

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Protein burying depth (BD) is a structural descriptor that is exploited not only to find whether a residue is exposed or buried, but also to determine how deep a residue is buried. The widely used solvent accessible surface area is mainly focusing on the study of protein surface residues, while protein BD can provide more detailed information about the arrangement of buried residues, which may be used to study protein deep level structure and the formation of protein folding nucleus. In this work, we analyse the relationship of protein BD and sequences, and describe it by nonlinear functions estimated by support vector machines. We examine the functions by crossvalidation tests and find strong correlation between residue BD and local sequence environment. By further taking account the size of the molecule where a residue is located, we find that the correlation coefficient between predicted and observed depths improves from 0.60 to 0.65. Moreover, nearly half of the deepest 10% residues in a protein sequence can be correctly predicted. Our study suggests that a residue's burying extent is able to be predicted, to some degree, by itself and its local neighbouring residues. The methods used to estimate the sequence-depth functions are expected to become more useful in the investigation of protein structures and folding mechanism.

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Section: Introductionmentioning

confidence: 99%

Quantifying the relationship of protein burying depth and sequence

Wang

2007

Proteins

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“…Gohlke et al 2000;Kelley et al 2000;Ahmad et al 2004;Raih et al 2005;Ofran et al 2007). Based on its importance, methods to predict burial classes and real values at single residue as well as atomic level using sequence and evolutionary profiles have been developed (Rost and Sander 1994;Ahmad and Gromiha 2002;Ahmad et al 2003;Garg et al 2005;Araúzo-Bravo et al 2006;Xu et al 2006;Singh et al, 2006;Wang et al 2007;Chen et al 2008;) and it has been shown that even predicted values of ASA can be helpful in improving some of the functional properties of amino acid residues (Ofran et al 2007). ASA has also been used as an important descriptor to predict deleterious mutations in proteins (Saunders and Baker 2002), especially because other well-known local structural descriptors such as secondary structure are less sensitive to single residue changes.…”

Section: Introductionmentioning

confidence: 98%

Sequence-dependence and prediction of nucleotide solvent accessibility in double stranded DNA

Ahmad

2009

Gene

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“…Protein-solvent interaction is believed to contribute largely to the solvation, folding and structure of a water-soluble protein [1,2,3,4,5] and plays an important role in its function such as ligand binding [6]. However it is challenging to quantify such contributions [7,8] using either experimental approach [9,10] or theoretical model [11,12,13,14,15] or molecular dynamic (MD 1 ) simulation [16,17] or structural information [18,19]. For example, due to the difficulty to evaluate protein-solvent interaction it is not clear at present how evolution has optimized the surfaces of naturallyoccurring water-soluble proteins to make them best adapted to aqueous solvent.…”

Section: Introductionmentioning

confidence: 99%

The solvent-excluded surfaces of water-soluble proteins

Wang¹

2018

Preprint

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The solvent-excluded surface (SES) of a protein is determined by and in turn affects protein-solvent interaction and consequently plays important roles in its solvation, folding and function. However, accurate quantitative relationships between them remain largely unknown at present. To evaluate SES's contribution to protein-solvent interaction we have applied our accurate and robust SES computation algorithm to various sets of proteins and ligand-protein interfaces. Our results show that each of the analyzed water-soluble proteins has a negative net charge on its SES. In addition we have identified a list of SES-defined physical and geometrical properties that likely pertain to protein solvation and folding based on their characteristic changes with protein size, their differences between folded and extended conformations, and their correlations with known hydrophobicity scales and with experimentally-determined protein solubility. The relevance of the list of SES-defined properties to protein structure and function is supported by their differences between water-soluble proteins and transmembrane proteins and between solvent-accessible regions and ligand-binding interfaces. Taken together our analyses reveal the importance of SES for protein solvation, folding and function. In particular the universal enrichment of negative charge and the larger than average SES area for a polar atom on the surface of a water-soluble protein suggest that from a protein-solvent interaction perspective to fold into a native state is to optimize the electrostatic and hydrogen-bonding interactions between solvent molecules and the surface polar atoms of a protein rather than to only minimize its apolar surface area.

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Atom-wise statistics and prediction of solvent accessibility in proteins

Cited by 12 publications

References 30 publications

Quantifying the relationship of protein burying depth and sequence

Quantifying the relationship of protein burying depth and sequence

Sequence-dependence and prediction of nucleotide solvent accessibility in double stranded DNA

The solvent-excluded surfaces of water-soluble proteins

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