Assessing the relative importance of the biophysical properties of amino acid substitutions associated with human genetic disease
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Assessing the relative importance of the biophysical properties of amino acid substitutions associated with human genetic disease. / Terp, Bent N; Cooper, David N; Christensen, Inge T; Jørgensen, Flemming Steen; Bross, Peter Gerd; Gregersen, Niels; Krawczak, Michael.
I: Human Mutation, Bind 20, Nr. 2, 2002, s. 98-109.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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T1 - Assessing the relative importance of the biophysical properties of amino acid substitutions associated with human genetic disease
AU - Terp, Bent N
AU - Cooper, David N
AU - Christensen, Inge T
AU - Jørgensen, Flemming Steen
AU - Bross, Peter Gerd
AU - Gregersen, Niels
AU - Krawczak, Michael
N1 - Copyright 2002 Wiley-Liss, Inc.
PY - 2002
Y1 - 2002
N2 - The inclusion of a mutation in a pathology-based database such as the Human Gene Mutation Database (HGMD) is a two-stage process: first, the mutation must occur at the DNA level, then it must cause a clinically detectable disease state. The likelihood of the latter step, termed the relative clinical observation likelihood (RCOL), can be regarded as a function of the structural/functional consequences of a mutation at the protein level. Following this paradigm, we modeled in silico all amino acid replacements that could potentially have arisen from an inherited single base pair substitution in five human genes encoding arylsulphatase A (ARSA), antithrombin III (SERPINC1), protein C (PROC), phenylalanine hydroxylase (PAH), and transthyretin (TTR). These proteins were chosen on the basis of 1) the availability of a crystallographic structure, and 2) a sufficiently large number of amino acid replacements being logged in HGMD. A total of 9,795 possible mutant structures were modeled and 20 different biophysical parameters assessed. Together with the HGMD-derived spectra of clinically detected mutations, these data allowed maximum likelihood estimation of RCOL profiles for the 20 parameters studied. Nine parameters (including energy difference between wild-type and mutant structures, accessibility of the mutated residue, and distance from the binding/active site) exhibited statistically significant variability in their RCOL profiles, indicating that mutation-associated changes affected protein function. As yet, however, a biological meaning could only be attributed to the RCOL profiles of solvent accessibility and, for three proteins, local energy change, disturbed geometry, and distance from the active center. The limited ability of the biophysical properties of mutations to explain clinical consequences is probably due to our current lack of understanding as to which amino acid residues are critical for protein folding. However, since the proteins examined here were unrelated, and our findings consistent, it may nevertheless prove possible to extrapolate to other proteins whose dysfunction underlies inherited disease.
AB - The inclusion of a mutation in a pathology-based database such as the Human Gene Mutation Database (HGMD) is a two-stage process: first, the mutation must occur at the DNA level, then it must cause a clinically detectable disease state. The likelihood of the latter step, termed the relative clinical observation likelihood (RCOL), can be regarded as a function of the structural/functional consequences of a mutation at the protein level. Following this paradigm, we modeled in silico all amino acid replacements that could potentially have arisen from an inherited single base pair substitution in five human genes encoding arylsulphatase A (ARSA), antithrombin III (SERPINC1), protein C (PROC), phenylalanine hydroxylase (PAH), and transthyretin (TTR). These proteins were chosen on the basis of 1) the availability of a crystallographic structure, and 2) a sufficiently large number of amino acid replacements being logged in HGMD. A total of 9,795 possible mutant structures were modeled and 20 different biophysical parameters assessed. Together with the HGMD-derived spectra of clinically detected mutations, these data allowed maximum likelihood estimation of RCOL profiles for the 20 parameters studied. Nine parameters (including energy difference between wild-type and mutant structures, accessibility of the mutated residue, and distance from the binding/active site) exhibited statistically significant variability in their RCOL profiles, indicating that mutation-associated changes affected protein function. As yet, however, a biological meaning could only be attributed to the RCOL profiles of solvent accessibility and, for three proteins, local energy change, disturbed geometry, and distance from the active center. The limited ability of the biophysical properties of mutations to explain clinical consequences is probably due to our current lack of understanding as to which amino acid residues are critical for protein folding. However, since the proteins examined here were unrelated, and our findings consistent, it may nevertheless prove possible to extrapolate to other proteins whose dysfunction underlies inherited disease.
KW - Amino Acid Substitution
KW - Amyloid Neuropathies, Familial
KW - Antithrombin III
KW - Antithrombin III Deficiency
KW - Arylsulfatases
KW - Biophysics
KW - Databases, Genetic
KW - Databases, Protein
KW - Genetic Diseases, Inborn
KW - Genotype
KW - Humans
KW - Leukodystrophy, Metachromatic
KW - Models, Genetic
KW - Mutation, Missense
KW - Phenotype
KW - Phenylalanine Hydroxylase
KW - Phenylketonurias
KW - Prealbumin
KW - Protein C
KW - Protein C Deficiency
KW - Protein Structure, Secondary
U2 - 10.1002/humu.10095
DO - 10.1002/humu.10095
M3 - Journal article
C2 - 12124990
VL - 20
SP - 98
EP - 109
JO - Human Mutation
JF - Human Mutation
SN - 1059-7794
IS - 2
ER -
ID: 38394145