Assessing the relative importance of the biophysical properties of amino acid substitutions associated with human genetic disease

TY - JOUR

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

SN - 1059-7794

VL - 20

SP - 98

EP - 109

JO - Human Mutation

JF - Human Mutation

IS - 2

ER -