scholarly journals Predicting the phenotype of Mendelian disease missense mutations using amino acid conservation and protein stability change

2016 ◽  
Author(s):  
Maria T. Chavez ◽  
Ethan O. Perlstein
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Stability ◽  
Model Organisms ◽  
Mendelian Disease ◽  
Missense Mutations ◽  
Lysosomal Storage ◽  
Mendelian Diseases ◽  
Stability Change ◽  
Jensen Shannon Divergence

AbstractMany Mendelian diseases are caused by recessive, loss-of-function missense mutations. On a gene-by-gene basis, it has been demonstrated that missense mutations cause, among other defects, protein misfolding, protein instability, protein mistransport, which strongly suggests that pathogenic missense mutations do not occur at random positions. Based on those observations, we predicted that Mendelian disease missense mutations are enriched in evolutionarily-conserved amino acids. In a pilot set of 260 Mendelian diseases genes affecting cellular organelles we show that missense mutations indeed occur in amino acids that are significantly more conserved than the average amino acid in the protein based on three different scoring methods (Jensen Shannon Divergence p = 7.78E-03, Shannon Entropy p = 1.68E-13, Sum of Pairs p = 1.55E-17). In order to understand how these results might be related to clinical phenotypes in humans or preclinical phenotypes in model organisms, we calculated the protein stability change upon mutation (ΔΔGu) using EASE-MM and found that, on average, pathogenic mutations cause a stability change of greater magnitude than benign mutations (p = 4.414428E-23). Finally, we performed a computational case study on NPC1, the gene responsible for 95% of diagnosed cases of the lysosomal storage disorder Niemann-Pick Type C using a set of 411 missense mutations from the Exome Aggregation Consortium.

scholarly journals A cDNA clone for human glucosamine-6-sulphatase reveals differences between arylsulphatases and non-arylsulphatases

1992 ◽  
Vol 288 (2) ◽  
pp. 539-544 ◽  
Author(s):  
D A Robertson ◽  
C Freeman ◽  
C P Morris ◽  
J J Hopwood
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Sequence Similarity ◽  
Genetic Disorder ◽  
Heparan Sulphate ◽  
Leader Peptide ◽  
Cdna Clones ◽  
Amino Acid Residues ◽  
Lysosomal Storage ◽  
Glycosylation Sites

Glucosamine-6-sulphatase is an exo-hydrolase required for the lysosomal degradation of heparan sulphate and keratan sulphate. Deficiency of glucosamine-6-sulphatase activity leads to the lysosomal storage of the glycosaminoglycan, heparan sulphate and the monosaccharide sulphate N-acetylglucosamine 6-sulphate and the autosomal recessive genetic disorder mucopolysaccharidosis type IIID. Glucosamine-6-sulphatase can be classified as a non-arylsulphatase since, relative to arylsulphatase B, it shows negligible activity toward 4-methylumbelliferyl sulphate. We have isolated human cDNA clones and derived amino acid sequence coding for the entire glucosamine-6-sulphatase protein. The predicted sequence has 552 amino acids with a leader peptide of 36 amino acids and contains 13 potential N-glycosylation sites, of which it is likely that 10 are used. Glucosamine-6-sulphatase shows strong sequence similarity to other sulphatases such as the family of arylsulphatases, although the degree of similarity is not as high as that between members of the arylsulphatase family. This pattern of inter- and intra-family similarity delineates regions and amino acid residues that may be critical for sulphatase function and substrate specificity.

scholarly journals A Region of the Sir1 Protein Dedicated to Recognition of a Silencer and Required for Interaction with the Orc1 Protein in Saccharomyces cerevisiae

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 31-44 ◽  
Author(s):  
Kelly A Gardner ◽  
Jasper Rine ◽  
Catherine A Fox
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acids ◽  
Amino Acid ◽  
Origin Recognition Complex ◽  
Dna Binding Domain ◽  
Missense Mutations ◽  
Macromolecular Complexes ◽  
Sequence Elements ◽  
Per Se ◽  
Amino Acid Segment

AbstractSilencing of the cryptic mating-type loci HMR and HML requires the recognition of DNA sequence elements called silencers by the Sir1p, one of four proteins dedicated to the assembly of silenced chromatin in Saccharomyces cerevisiae. The Sir1p is thought to recognize silencers indirectly through interactions with proteins that bind the silencer DNA directly, such as the origin recognition complex (ORC). Eight recessive alleles of SIR1 were discovered that encode mutant Sir1 proteins specifically defective in their ability to recognize the HMR-E silencer. The eight missense mutations all map within a 17-amino-acid segment of Sir1p, and this segment was also required for Sir1p's interaction with Orc1p. The mutant Sir1 proteins could function in silencing if tethered to a silencer directly through a heterologous DNA-binding domain. Thus the amino acids identified are required for Sir1 protein's recognition of the HMR-E silencer and interaction with Orc1p, but not for its ability to function in silencing per se. The approach used to find these mutations may be applicable to defining interaction surfaces on proteins involved in other processes that require the assembly of macromolecular complexes.

scholarly journals A Numerical Representation and Classification of Codons to Investigate Codon Alternation Patterns during Genetic Mutations on Disease Pathogenesis

2020 ◽  
Author(s):  
Antara Sengupta ◽  
Pabitra Pal Choudhury ◽  
Subhadip Chakraborty ◽  
Swarup Roy ◽  
Jayanta Kumar Das ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Chemical Properties ◽  
Numerical Representation ◽  
Missense Mutations ◽  
Disease Pathogenesis ◽  
Physical Density ◽  
Monogenic Diseases

Motivation: Alteration of amino acid is possible due to mutation in codons that could have a potential impact in a diseased condition. Effective mutation analysis can help to predict the fate of the diseased individual which can be validated later by in-vitro experimentations. It may also help an individual who is asymptomatic but having a particular genetic change for early detection and diagnosis during any terminal diseases. We try to investigate the codon alteration patterns and its impact during mutation for the genes known to be responsible for a particular disease.Results: For our current study, we consider neurodegenerative and monogenic diseases. We use numerical representation based on a determinative degree and classification of codons as well as amino acids into three different classes (Strong, Weak and Transition) for the analysis. Our analysis reveals that the strong class codons are highly mutated followed by weak and transition class. We observe that most of the mutations occur in the first or second positions in the codon rather than the third. While looking into the chemical properties of amino acid, we observe that amino acids belong to the aliphatic group are affected most during missense mutations. Our investigation further emphasises that in most of the cases the change in the determinative degree of codon due to mutation is directly proportional to the physical density property. In addition, our scheme gives a more microscopic and alternative representation of the existing codon table that helps in deciphering interesting codon alteration patterns during mutations in disease pathogenesis.

scholarly journals Structural Analysis of Four Newly Identified Extracellular Membrane-Proximal Missense Mutations in Patients with Glanzmann Thrombasthenia

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1452-1452
Author(s):  
Xavier Pillois ◽  
Mathieu Fiore ◽  
Alan Nurden
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Conflicts Of Interest ◽  
Severe Bleeding ◽  
Type I ◽  
Missense Mutations ◽  
Glanzmann Thrombasthenia ◽  
Activated State ◽  
Platelet Disorder ◽  
Β Sheets

Abstract Background: Glanzmann thrombasthenia (GT), an autosomal recessive inherited platelet disorder, is a moderate to severe bleeding syndrome caused by the absence of platelet aggregation due to quantitative and/or qualitative deficiencies of the αIIbβ3 integrin. We recently identified 41 causative missense mutations of which 24 were novel in a large cohort of 76 GT families (Genoscope project). These mutations mainly localize to the headpiece region of the integrin that has been well studied but 4 mutations although extracellular were proximal to the plasma membrane. We therefore performed molecular modeling of these 4 mutations to obtain new insights into the structure of a poorly understood region of this unique receptor. Aim: To identify structures or conformations engaged in the stability of the integrin and which are important for maturation and expression. Results: Of the 4 novel selected mutations, 3 concerned the calf-2 domain of αIIb - Gly792Glu (G823E, nomenclature with leader sequence), Leu924Gln (L955Q) and Thr953Lys (T984K) and one the EGF-3 domain of β3 Gly540Asp (G566D). All of these mutations affected highly conserved amino acids and were predicted to be damaging by in silico analysis (SIFT, Polyphen). None influenced glycosylation or mRNA splicing. They were present either in a homozygous form (β3 G540D) or were heterozygous in association with an identified and proven null mutation. Three were associated with type I GT (<5% αIIbβ3), while the αIIbG792E mutation occurred in a patient with type II GT (with 10% residual αIIbβ3) whose much reduced but partial transport to the surface was confirmed following expression of the recombinant integrin in CHO cells (with pro-αIIb predominating in the cytoplasm). The structural implications of these amino acid substitutions was assessed using PyMol Molecular Graphics System version 1.3 (www.pymol.org) based on the crystallographic data of αIIbβ3 in the bent non-activated state (3fcs PDB file). Amino acids were visualized in the rotamer form showing side change orientations incorporated from the Dunbrack Backbone library with the maximum probability. We first determined that the αIIb calf-2 domain has a β barrel-like structure largely composed of hydrophobic amino acids whose side chains orientate towards the inner cavity. Interestingly, L924Q and T953K substitutions occur at or adjacent to a conserved motif consisting of five polar amino acids central to the β barrel protected from H2O molecules and involved in H-bond interactions. This particular motif, specific to calf-2, may introduce rigidity close to the membrane. Both L924Q and T953K disrupt the β barrel motif and promote flexibility. G792E is situated between the calf-1 and calf-2 domains in an unstructured connecting loop between two adjacent β sheets. Its replacement by the larger negatively charged Glu introduces steric encumbrance and results in an increase of the angle formed by the two calf domains, probably leading to the straightening of the second distal part of the long arm of αIIb. The β3 G540D substitution is found in the EGF3 domain of β3 that occurs at the axe of the cysteine-rich domain of the β3 arm, facing the αIIb calf-1 and calf-2 domains in the intact integrin. This substitution with the introduction of a charged and larger amino acid results in a weaker link between the two β sheets of EGF-3 and a loss of H-bonds. The result is an increased fragility within the β3 arm structure notably at the site of two stacked aromatic amino acids (H539 and W553) with a moving apart of the β sheets. Conclusions: We show that 4 novel missense mutations in the extracellular membrane-proximal domains of αIIb and β3 cause conformational changes in domains that control the overall structure of the newly formed integrin. They show how the structure of both domains is under tight quality control and that precisely defined conformations are indispensable for αIIbβ3 maturation. Disclosures No relevant conflicts of interest to declare.

44-amino-acid E5 transforming protein of bovine papillomavirus requires a hydrophobic core and specific carboxyl-terminal amino acids

1988 ◽  
Vol 8 (10) ◽  
pp. 4071-4078
Author(s):  
B H Horwitz ◽  
A L Burkhardt ◽  
R Schlegel ◽  
D DiMaio
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Saturation Mutagenesis ◽  
Amino Acid Substitutions ◽  
Bovine Papillomavirus ◽  
Missense Mutations ◽  
Focus Formation ◽  
E5 Protein ◽  
Transforming Activity ◽  
Carboxyl Terminal

The 44-amino-acid E5 protein of bovine papillomavirus type 1 is the shortest known protein with transforming activity. To identify the specific amino acids required for in vitro focus formation in mouse C127 cells, we used oligonucleotide-directed saturation mutagenesis to construct an extensive collection of mutants with missense mutations in the E5 gene. Characterization of mutants with amino acid substitutions in the hydrophobic middle third of the E5 protein indicated that efficient transformation requires a stretch of hydrophobic amino acids but not a specific amino acid sequence in this portion of the protein. Many amino acids in the carboxyl-terminal third of the protein can also undergo substitution without impairment of focus-forming activity, but the amino acids at seven positions, including two cysteine residues that mediate dimer formation, appear essential for efficient transforming activity. These essential amino acids are the most well conserved among related fibropapillomaviruses. The small size of the E5 protein, its lack of similarity to other transforming proteins, and its ability to tolerate many amino acid substitutions implies that it transforms cells via a novel mechanism.

scholarly journals Molecular phylogeny and missense mutations of envelope proteins across coronaviruses

2020 ◽  
Author(s):  
Sk Sarif Hassan ◽  
Pabitra Pal Choudhury ◽  
Bidyut Roy
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Phylogeny ◽  
Envelope Protein ◽  
Envelope Proteins ◽  
Parental Origin ◽  
Missense Mutations ◽  
E Proteins ◽  
Complete Genomes

Envelope protein is one of the structural viroporins (76–109 amino acids) present in the coronavirus. Sixteen sequentially different E proteins were observed from a total of 4917 available complete genomes as on 18th June, 2020 in the NCBI database. The missense mutations over the envelope protein across various coronaviruses of the $\beta$-genus were analyzed to know the immediate parental origin of the envelope protein of SARS-CoV2. The evolutionary origin is also endorsed by the phylogenetic analysis of the envelope proteins comparing sequence homology as well as amino acid conservations.

scholarly journals Purification of feline lysosomal α-mannosidase, determination of its cDNA sequence and identification of a mutation causing α-mannosidosis in Persian cats

1997 ◽  
Vol 328 (3) ◽  
pp. 863-870 ◽  
Author(s):  
Thomas BERG ◽  
K. Ole TOLLERSRUD ◽  
U. Steven WALKLEY ◽  
Donald SIEGEL ◽  
Øivind NILSSEN
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Reverse Transcriptase ◽  
Cdna Sequence ◽  
Molecular Heterogeneity ◽  
Lysosomal Storage ◽  
Reverse Transcriptase Pcr ◽  
Pcr Products

α-Mannosidosis is a lysosomal storage disorder that is caused by the deficiency of lysosomal α-mannosidase. Feline α-mannosidosis is a well-characterized animal model used for studying pathological and therapeutic aspects of lysosomal storage disorders. We here report the purification of feline liver lysosomal α-mannosidase and determination of its cDNA sequence. The active enzyme consisted of three polypeptides, with molecular masses of 72, 41 and 12 kDa, joined by non-covalent forces. The cDNA sequence of feline lysosomal α-mannosidase was determined from reverse transcriptase PCR products obtained from skin fibroblast mRNA. The deduced amino acid sequence contained the N-terminal sequences of the 72 and 41 kDa peptides. This indicated that the enzyme is synthesized as a single-chain precursor with a putative signal peptide of 50 amino acids followed by a polypeptide chain of 957 amino acids, which is cleaved into the three polypeptides of the mature enzyme. The deduced amino acid sequence was 81.1 and 83.2% identical with the human and bovine lysosomal α-mannosidases sequences respectively. A 4 bp deletion was identified in an α-mannosidosis-affected Persian cat by DNA sequencing of reverse transcriptase PCR products. The deletion resulted in a frame shift from codon 583 and premature termination at codon 645. No lysosomal α-mannosidase activity could be detected in the liver of this cat. A domestic long-haired cat expressing a milder α-mannosidosis phenotype than the Persian cat had a lysosomal α-mannosidase activity of 2% of normal. This domestic long-haired cat did not possess the 4 bp deletion, proving molecular heterogeneity for feline α-mannosidosis.

scholarly journals Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge

2019 ◽  
Vol 40 (9) ◽  
pp. 1392-1399 ◽  
Author(s):  
Castrense Savojardo ◽  
Maria Petrosino ◽  
Giulia Babbi ◽  
Samuele Bovo ◽  
Carles Corbi‐Verge ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Stability ◽  
Single Amino Acid ◽  
Amino Acid Substitutions ◽  
Stability Change

scholarly journals Analyses of Molecular Characteristics and Enzymatic Activities of Ovine HSD17B3

Animals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 2876
Author(s):  
Mohammad Sayful Islam ◽  
Junsuke Uwada ◽  
Junki Hayashi ◽  
Kei-ichiro Kikuya ◽  
Yuki Muranishi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Molecular Mechanisms ◽  
Sex Differentiation ◽  
Mammalian Species ◽  
Enzymatic Activities ◽  
Molecular Characteristics ◽  
Missense Mutations ◽  
Reading Frame ◽  
Type 3

17β-hydroxysteroid dehydrogenase type 3 (HSD17B3) converts androstenedione (A4) into testosterone (T), which regulates sex steroid production. Because various mutations of the HSD17B3 gene cause disorder of sex differentiation (DSD) in multiple mammalian species, it is very important to reveal the molecular characteristics of this gene in various species. Here, we revealed the open reading frame of the ovine HSD17B3 gene. Enzymatic activities of ovine HSD17B3 and HSD17B1 for converting A4 to T were detected using ovine androgen receptor-mediated transactivation in reporter assays. Although HSD17B3 also converted estrone to estradiol, this activity was much weaker than those of HSD17B1. Although ovine HSD17B3 has an amino acid sequence that is conserved compared with other mammalian species, it possesses two amino acid substitutions that are consistent with the reported variants of human HSD17B3. Substitutions of these amino acids in ovine HSD17B3 for those in human did not affect the enzymatic activities. However, enzymatic activities declined upon missense mutations of the HSD17B3 gene associated with 46,XY DSD, affecting amino acids that are conserved between these two species. The present study provides basic information and tools to investigate the molecular mechanisms behind DSD not only in ovine, but also in various mammalian species.

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