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A point mutation may not be causing a disease, but it can still have an effect on the structure and function of the protein. Consequences due to such point mutations often go undetected, as they do not result in a disease phenotype, although they do affect the protein and may perturb normal human physiology. In addition to the examples described herein, it is easy to imagine that other consequences related to SNV changes will be found as more experimentally determined 3D structures become available and our understanding of protein structure-function relationships continues to grow.

For example, the impact of genetic variation on protein-protein interactions is not well represented in the current dataset. A comprehensive understanding of three-dimensional structure, dynamics, and biophysics of wild-type and mutant proteins will be required to develop better tools that can make accurate predictions regarding the consequences of genetic changes manifested at the atomic level in protein gene products. Distribution of the SNVs in the dataset, for which no structural and functional consequence was found in existing literature, based on structural position and secondary structure elements left.


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Distribution based on structural position and secondary structure elements for SNVs with structural and functional consequence information right. A CSV file containing the annotated dataset that has been used for this manuscript. Conceptualization: AP. Data curation: RB. Formal analysis: RB. Funding acquisition: SKB. Investigation: RB. Software: AP RB. Supervision: AP. Writing — original draft: RB AP. Browse Subject Areas? Click through the PLOS taxonomy to find articles in your field. Introduction With the ever-growing importance of genomics for human health, considerable efforts have been devoted to linking human phenotypes to genotypic variations at the nucleotide level and changes in 3D protein structure [ 1 , 2 ].

Describe the structure and function proteins

Download: PPT. Table 1. Six popular training datasets for tools predicting the effect of single point mutations. Methodology 2. Construction of the dataset The data set used in this paper is a semi-automatically derived and hand-curated collection of proteins, each of which possess an amino acid that has been changed by a SNV and 3D atomic coordinates are available in the PDB. For each PDB entry, the amino acid sequence of the crystallized protein experimentally observed in 3D differs from the corresponding UniProt sequence at the position of the variation.

From these structures, we selected only those structures for which the dbSNP mutation information matched information coming from UniProt and the 3D structure.

When multiple PDB entries with the same mutation are available, preference was been given to structures determined by X-ray crystallography. In a few cases it was not possible to do so, and the dataset contains 49 structures determined by NMR. Manual annotation of SNVs To enumerate the consequence s of a given SNV on a gene product, we systematically reviewed the available literature to identify experimentally verified functional effects.

Whether the amino acid substitution falls within Loop vs. What effect or consequence does the SNV have on the protein? Software tools for mapping of genetic variation to protein sequence and 3D structure. Mapping tool from human genomic position to protein sequence and 3D structure —This tool allows to map coordinates from the human reference assemblies versions 37, or 38 as provided by the Genome Reference Consortium to the correct UniProt isoforms and 3D structures. Protein Feature View —Provides a rich graphical summary of protein sequence features, including identification of genomic positions mapped to protein sequences.

Protein Structure and Function

Aggregation—The SNV renders the protein aggregation prone. Stability—The SNV causes a change in protein stability. It may make the protein susceptible to proteolytic cleavage, or cause a change in thermal inactivation temperature, or cause a change in the energy of stabilization of the protein.

It can also lead to destabilization of a protein oligomer, loss of packing or hydrophobic interactions, or change a mode s of protein-protein interaction. It can also cause structural changes in the binding site or affect specificity for a binding partner s. Assembly—The SNV affects the oligomeric assembly properties of the protein.

Rearrangement—The SNV causes local structural rearrangements conformational changes in the neighborhood of the amino acid change arising from the SNV. Results and discussion 3. Location of SNVs within 3D structures We first investigated whether it is possible to identify patterns concerning sites at which point mutations occur. Fig 2.

SNV consequences map to various locations within protein structures. Consequences of SNVs related changes By systematically reviewing relevant peer-reviewed literature, we determined that a broad range of possible effects could be attributed to a single residue change. Table 2. Consequence of SNVs on protein structure and function for a dataset of SNVs for which experimentally obtained atomic level data for the variation is available in the Protein Data Bank.

To exemplify how a mutation can influence protein stability, we analyze the following case: DJ-1 mutant PDB: 2RK4 is a small conserved protein amino acids , whose absence or inactivation leads to rare forms of familial Parkinsonism in humans [ 52 ]. Close-up view of the nucleotide-binding region of LysArg.

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Fig 7. In manganese superoxide dismutase, a SNV can affect protein assembly. Fig 8. SNVs not implicated in disease. Paucity of structural and functional data for SNVs For the majority of SNVs represented in our dataset, we found no information about the structural or the functional changes caused by the SNV published in peer-reviewed literature. The active site surfaces of elastase and thrombin are sufficiently similar so that wild-type alpha1-antitrypsin Met binds to the active site of elastase which is specific for methionine at the cleavage site and mutant alpha1-antitrypsin Arg binds to the active site of thrombin which is specific for arginine or lysine at the cleavage site [ 60 ] Fig 9A.

The polymorphism generates a cryptic mitochondrial targeting sequence [ 63 ]. When the GR mutation is present, AGT no longer forms a stable dimer, and the resulting enzyme monomer is able to cross the mitochondrial membrane Fig 9B. The disease phenotype is caused by depletion of the enzyme within the peroxisome.

I-TASSER server for protein structure and function prediction

Even this relatively modest change in bending angle can have significant effects on longer-range interactions among other proteins bound near SRY recognition site Fig 9C [ 64 ]. Frequency in population One important question of human genetic studies is how the frequency with which a genetic variation can be found in a population is correlated with the risk for a disease. Conclusion The focus of this study are protein structures in the PDB archive for which 3D structures of genetic variant proteins have been determined.

Supporting information. S1 Fig. Experimental procedures. S2 Fig. Resolution plot. S3 Fig. Distribution of SNVs. S1 File. Dataset of SNVs. Author Contributions Conceptualization: AP. References 1. Genetic Mapping in Human Disease. View Article Google Scholar 2.

Botstein D, Risch N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nature Genetics. View Article Google Scholar 3. Kimura M, Takahata N. Selective constraint in protein polymorphism: study of the effectively neutral mutation model by using an improved pseudosampling method.

Wang Z, Moult J.

SNPs, protein structure, and disease. Human Mutation. Pirmohamed M, Park BK. Genetic susceptibility to adverse drug reactions. Trends Pharmacological Sciences. View Article Google Scholar 6. Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci.