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1 Title:

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Title:

The Nature of Single Amino Acid Polymorphism and Substitutions

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Questions

Distribution of SAP?
1. SNP in Genome-> SNP onto cDNA -> SNP onto Proteome
Is the occurence of SAP random in terms of their location at genome/proteome?
1. Is there any favourable or unfavourable (structural) envrionment for the location of SNP in 3-D structure of protein?
2. Is occurrence related with length of a protein?
Any difference between SAPs and substitutions between proteins of a same ancestor?
1. within orgamins and between orgamism?
Difference between disease-related substitutions and (neutral) polymorphism

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Abstract

Human genetic variations arise from various sources. In this study, we investigated Single Amino acid Polymorphisms (SAPs) which occur on proteins with two fundamental questions in which we seek to answer; 1) where SAPs are located in 3-dimensional structure of proteins, 2) are there any restraints on the occurrence of SAPs in proteins. All the available SNPs are mapped onto their corresponding position of UniProt proteins and 3-dimensional structures if they are available in PDB. Within 3-domeisional structure, the locations of SAPs were analyzed by the following properties; i) solvent accessibility, ii) secondary structure, and iii) hydrogen-bonds from a side-chain to main-chain amide (NH) or carbonyl (CO) or the other side-chain. In case of non-synonymous SAPs, their likelihood of amino acid substitutions was examined by ESSTs (Environment Specific amino acid Substitution Tables) which represent general likelihood of amino-acid substitutions. In terms of functional properties of a protein, the occurrence of SAPs was examined to see whether they are at the same location of residues annotated by CSA and following UniProt keywords; DISULFID, ACT_SITE, CA_BIND, ZN_FING, DNA_BIND, NP_BIND, METAL, BINDING, and LIPID. We believe this study will help understanding the restraints affecting the landscape of SAPs at proteome level

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Main Table of Contents

The difference between observed and predicted occurrence of SAP
The 3D structural environments of SAPs
The likelihood of amino acid substitution for nsSNPs

Results

Local structural environments of SAPs and mutations
1. Solvent accessibility
2. Hydrogen bonds from side-chain to main-chain NH, CO and the other side-chains
3. Elements of secondary structures
Probability of substitution by SAPs and mutation with regard to their local structure environments
Degree of sequence conservation at SAP positions (Shannon's sequence entropy)Amino acid polymorphism and
Correlation between protein length and the number of SAPs (or mutation)