In this work, eight different scoring functions have been combined with the aim of improving the prediction of protein-ligand binding conformations and affinities. The obtained scores were analyzed using multivariate statistical methods to generate expressions, with the ability (1) to select the best candidate between different docked conformations of an inhibitor (MultiSelect) and (2) to quantify the protein-ligand binding affinity (MultiScore). By use of the docking program GOLD, 40 different inhibitors were docked into the active site of three matrix metalloproteinases (MMP's), yielding a total of 120 enzyme-inhibitor complexes. For each complex, a single conformation of the inhibitor was selected using principal component analysis (PCA) for the scores obtained by the eight functions SCORE, LUDI, GRID, PMF_Score, D_Score, G_Score, ChemScore, and F_Score. Binding affinities were estimated based on partial least-squares projections onto latent structures (PLS) on the eight scores of each selected inhibitor conformation. By use of this procedure, R(2) = 0.78 and Q(2) = 0.78 were obtained when comparing experimental and calculated binding affinities. MultiSelect was evaluated by applying the same method for selecting docked conformations for 18 different protein-ligand complexes of known three-dimensional structure. In all cases, the selected ligand conformations were found to be very similar to the experimentally determined ligand conformations. A more general evaluation of MultiScore was performed using a set of 120 different protein-ligand complexes for which both the three-dimensional structures and the binding affinities were known. This approach allowed an evaluation of MultiScore independently of MultiSelect. The generality of the method was verified by obtaining R(2) = 0.68 and Q(2) = 0.67, when comparing calculated and experimental binding affinities for the 120 X-ray structures. In all cases, LUDI, SCORE, GRID, and F_Score were included as important functions, whereas the fifth function was PMF_Score and ChemScore for the MMP and X-ray models, respectively.

Severe protein C deficiency is a rare, early onset, venous thrombotic condition that is inherited as an autosomal recessive trait. The protein C (PROC) genes of nine unrelated individuals with severe protein C deficiency were sequenced yielding a total of 13 different lesions. Eight of these were novel, including a gross gene deletion, three missense mutations, two micro-deletions, a splicing mutation and a single base-pair substitution in the HNF-3 binding site in the PROC gene promoter. Evidence for the pathogenicity of the mutations detected was obtained by molecular modelling, in vitro splicing assay and reporter gene assay. Neither the plasma protein C activity level nor the nature of the PROC gene lesions detected were found to be a good prognostic indicator of the age of onset or clinical severity of thrombotic symptoms. Other factors may thus complicate the relationship between genotype and clinical phenotype. Indeed, in two patients, the inheritance of either one or two Factor V Leiden alleles in addition to two PROC gene lesions could have served to precipitate the thrombotic events. No association was however apparent between clinical severity and the possession of a particular promoter polymorphism genotype. Despite the absence of a clear genotype-phenotype relationship, the molecular genetic analysis of the severe recessive form of protein C deficiency potentiates both the counselling of affected families and the provision of antenatal exclusion diagnosis.

No abstract

Severe protein C deficiency is a rare, early onset, venous thrombotic condition that is inherited as an autosomal recessive trait. The protein C (PROC) genes of nine unrelated individuals with severe protein C deficiency were sequenced yielding a total of 13 different lesions. Eight of these were novel, including a gross gene deletion, three missense mutations, two micro-deletions, a splicing mutation and a single base-pair substitution in the HNF-3 binding site in the PROC gene promoter. Evidence for the pathogenicity of the mutations detected was obtained by molecular modelling, in vitro splicing assay and reporter gene assay. Neither the plasma protein C activity level nor the nature of the PROC gene lesions detected were found to be a good prognostic indicator of the age of onset or clinical severity of thrombotic symptoms. Other factors may thus complicate the relationship between genotype and clinical phenotype. Indeed, in two patients, the inheritance of either one or two Factor V Leiden alleles in addition to two PROC gene lesions could have served to precipitate the thrombotic events. No association was however apparent between clinical severity and the possession of a particular promoter polymorphism genotype. Despite the absence of a clear genotype-phenotype relationship, the molecular genetic analysis of the severe recessive form of protein C deficiency potentiates both the counselling of affected families and the provision of antenatal exclusion diagnosis.

No general rules have been proposed to account for the functional consequences of gene regulatory mutations. In a first attempt to establish the nature of such rules, an analysis was performed of the DNA sequence context of 153 different single base-pair substitutions in the regulatory regions of 65 different human genes underlying inherited disease. Use of a recently proposed measure of DNA sequence complexity (taking into account the level of structural repetitiveness of a DNA sequence, rather than simply the oligonucleotide composition) has served to demonstrate that the concomitant change in local DNA sequence complexity surrounding a substituted nucleotide is related to the likelihood of a regulatory mutation coming to clinical attention. Mutations that led to an increase in complexity exhibited higher odds ratios in favour of pathological consequences than mutations that led to a decrease or left complexity unchanged. This relationship, however, was discernible only for pyrimidine-to-purine transversions. Odds ratios for other types of substitution were not found to be significantly associated with local changes in sequence complexity, even though a trend similar to that observed for Y-->R transversions was also apparent for transitions. These findings suggest that the maintenance of a defined level of DNA sequence complexity, or at least the avoidance of an increase in sequence complexity, is a critical prerequisite for the function of gene regulatory regions.