Homology modeling and global computational mutagenesis of human myosin VIIa

Usher syndrome type 1B (USH1B) is a genetic disorder caused by mutations in the unconventional Myosin VIIa (MYO7A) protein. USH1B is characterized by hearing loss due to abnormalities in the inner ear and vision loss due to retinitis pigmentosa. Here, we present the model of human MYO7A homodimer, built using homology modeling, and refined using 5 ns molecular dynamics in water. Global computational mutagenesis was applied to evaluate the effect of missense mutations that are critical for maintaining protein structure and stability of MYO7A in inherited eye disease. We found that 43.26% (77 out of 178 in HGMD) and 41.9% (221 out of 528 in ClinVar) of the disease-related missense mutations were associated with higher protein structure destabilizing effects. Overall, most mutations destabilizing the MYO7A protein were found to associate with USH1 and USH1B. Particularly, motor domain and MyTH4 domains were found to be most susceptible to mutations causing the USH1B phenotype. Our work contributes to the understanding of inherited disease from the atomic level of protein structure and analysis of the impact of genetic mutations on protein stability and genotype-to-phenotype relationships in human disease.

Download Full-text

Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios

Cancer Informatics ◽

10.4137/cin.s618 ◽

2008 ◽

Vol 6 ◽

pp. CIN.S618 ◽

Cited By ~ 37

Author(s):

Rachel Karchin ◽

Mukesh Agarwal ◽

Andrej Sali ◽

Fergus Couch ◽

Mary S. Beattie

Keyword(s):

Genetic Testing ◽

Protein Structure ◽

Tumor Suppressor ◽

Likelihood Ratio ◽

Cancer Susceptibility ◽

Suppressor Gene ◽

Medical Genetics ◽

Missense Mutations ◽

Likelihood Ratios ◽

The Impact

Background Missense (amino-acid changing) variants found in cancer predisposition genes often create difficulties when clinically interpreting genetic testing results. Although bioinformatics has developed approaches to predicting the impact of these variants, many of these approaches have not been readily applicable in the clinical setting. Bioinformatics approaches for predicting the impact of these variants have not yet found their footing in clinical practice because 1) interpreting the medical relevance of predictive scores is difficult; 2) the relationship between bioinformatics “predictors” (sequence conservation, protein structure) and cancer susceptibility is not understood. Methodology/Principal Findings We present a computational method that produces a probabilistic likelihood ratio predictive of whether a missense variant impairs protein function. We apply the method to a tumor suppressor gene, BRCA2, whose loss of function is important to cancer susceptibility. Protein likelihood ratios are computed for 229 unclassified variants found in individuals from high-risk breast/ovarian cancer families. We map the variants onto a protein structure model, and suggest that a cluster of predicted deleterious variants in the BRCA2 OB1 domain may destabilize BRCA2 and a protein binding partner, the small acidic protein DSS1. We compare our predictions with variant “re-classifications” provided by Myriad Genetics, a biotechnology company that holds the patent on BRCA2 genetic testing in the U.S., and with classifications made by an established medical genetics model [ 1 ]. Our approach uses bioinformatics data that is independent of these genetics-based classifications and yet shows significant agreement with them. Preliminary results indicate that our method is less likely to make false positive errors than other bioinformatics methods, which were designed to predict the impact of missense mutations in general. Conclusions/Significance Missense mutations are the most common disease-producing genetic variants. We present a fast, scalable bioinformatics method that integrates information about protein sequence, conservation, and structure in a likelihood ratio that can be integrated with medical genetics likelihood ratios. The protein likelihood ratio, together with medical genetics likelihood ratios, can be used by clinicians and counselors to communicate the relevance of a VUS to the individual who has that VUS. The approach described here is generalizable to regions of any tumor suppressor gene that have been structurally determined by X-ray crystallography or for which a protein homology model can be built.

Download Full-text

A comparative study on the extraction effects of common agents on collagen-based binders in mural paintings

Heritage Science ◽

10.1186/s40494-021-00519-y ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Jianghao Du ◽

Zhanyun Zhu ◽

Junchang Yang ◽

Jia Wang ◽

Xiaotong Jiang

Keyword(s):

Protein Structure ◽

Comparative Study ◽

Protein Extraction ◽

Guanidine Hydrochloride ◽

Polyacrylamide Gel Electrophoresis ◽

Sodium Dodecyl ◽

Extraction Process ◽

Ultraviolet Absorption Spectrum ◽

Mural Paintings ◽

The Impact

AbstractIn this paper, a comparative study was conducted on the extraction effects of six agents for collagen-based mural painting binders. These agents were used to extract the residual proteins in the non-aged and thermal aged samples. The protein extraction efficiencies of different extracting agents were quantitatively determined by bicinchoninic acid (BCA) method, and then processed by multivariate analysis of variance (MANOVA). The impact of the extraction process on the protein structure was characterized by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), ultraviolet absorption spectrum (UV) and circular dichroism (CD). The results showed that, for both non-aged and aged samples, the extraction efficiency of 2 M guanidine hydrochloride (GuHCl) was significantly higher than the other five agents, with less damage to the protein structure during the extraction process.

Download Full-text

Codon harmonization reduces amino acid misincorporation in bacterially expressed P. falciparum proteins and improves their immunogenicity

AMB Express ◽

10.1186/s13568-019-0890-6 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Neeraja Punde ◽

Jennifer Kooken ◽

Dagmar Leary ◽

Patricia M. Legler ◽

Evelina Angov

Keyword(s):

Protein Structure ◽

Amino Acid ◽

Codon Usage ◽

Dna Sequences ◽

Structural Integrity ◽

Host Cells ◽

Loss Of Function ◽

Species Specific ◽

And Function ◽

The Impact

Abstract Codon usage frequency influences protein structure and function. The frequency with which codons are used potentially impacts primary, secondary and tertiary protein structure. Poor expression, loss of function, insolubility, or truncation can result from species-specific differences in codon usage. “Codon harmonization” more closely aligns native codon usage frequencies with those of the expression host particularly within putative inter-domain segments where slower rates of translation may play a role in protein folding. Heterologous expression of Plasmodium falciparum genes in Escherichia coli has been a challenge due to their AT-rich codon bias and the highly repetitive DNA sequences. Here, codon harmonization was applied to the malarial antigen, CelTOS (Cell-traversal protein for ookinetes and sporozoites). CelTOS is a highly conserved P. falciparum protein involved in cellular traversal through mosquito and vertebrate host cells. It reversibly refolds after thermal denaturation making it a desirable malarial vaccine candidate. Protein expressed in E. coli from a codon harmonized sequence of P. falciparum CelTOS (CH-PfCelTOS) was compared with protein expressed from the native codon sequence (N-PfCelTOS) to assess the impact of codon usage on protein expression levels, solubility, yield, stability, structural integrity, recognition with CelTOS-specific mAbs and immunogenicity in mice. While the translated proteins were expected to be identical, the translated products produced from the codon-harmonized sequence differed in helical content and showed a smaller distribution of polypeptides in mass spectra indicating lower heterogeneity of the codon harmonized version and fewer amino acid misincorporations. Substitutions of hydrophobic-to-hydrophobic amino acid were observed more commonly than any other. CH-PfCelTOS induced significantly higher antibody levels compared with N-PfCelTOS; however, no significant differences in either IFN-γ or IL-4 cellular responses were detected between the two antigens.

Download Full-text

The effects of nano-curcumin as a nutritional strategy on clinical and inflammatory factors in children with cystic fibrosis: the study protocol for a randomized controlled trial

Trials ◽

10.1186/s13063-021-05224-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Saeedeh Talebi ◽

Mahammad Safarian ◽

Mahmood Reza Jaafari ◽

Seyed Javad Sayedi ◽

Zahra Abbasi ◽

...

Keyword(s):

Cystic Fibrosis ◽

Controlled Trial ◽

Genetic Disorder ◽

The Body ◽

Inflammatory Factors ◽

Secondary Outcome ◽

Nasopharyngeal Swab ◽

Nutritional Strategy ◽

Cftr Protein ◽

The Impact

Abstract Background Cystic fibrosis (CF) is a genetic disorder, which is caused by the CFTR protein defects. Along with CFTR dysfunction, inflammation plays a key role in the disease outcomes. Inflammation may develop due to the internal dysfunction of the CFTR protein or external factors. Curcumin affects the CFTR protein function primarily as a corrector and potentiator and secondary as an anti-inflammatory and antimicrobial agent. The present study aims to assess the impact of nano-curcumin on clinical and inflammatory markers in children with CF. Methods This prospective, double blind control trial will be conducted at the Akbar Children’s Hospital in Mashhad, Iran. Children with CF will be enrolled based on the eligibility criteria. Placebo and curcumin with the maximum dose of 80 mg considering the body surface of the patients will be administrated for 3 months. The primary outcome is to evaluate inflammation based on serum interleukin-6, interleukin-10, and hs-CRP, stool calprotectin, and neutrophil count of nasopharyngeal swab. The secondary outcome involved clinical assessment via spirometry, anthropometrics, and quality of life. They will be assessed before and after 3 months. Discussion Due to the multifarious effects of curcumin on CF disease, it could be proposed as a nutritional strategy in the treatment of cystic fibrosis. Trial registration Iranian Registry of Clinical Trials IRCT20200705048018N1. Registered on July 10, 2020.

Download Full-text

The Impact of Vision Loss on Allocentric Spatial Coding

Frontiers in Neuroscience ◽

10.3389/fnins.2020.00565 ◽

2020 ◽

Vol 14 ◽

Author(s):

Chiara Martolini ◽

Giulia Cappagli ◽

Antonella Luparia ◽

Sabrina Signorini ◽

Monica Gori

Keyword(s):

Vision Loss ◽

Spatial Coding ◽

The Impact

Download Full-text

Getting a grip on the resilience to blur: The impact of simulated vision loss on a visually guided combat sports interaction

Psychology of Sport and Exercise ◽

10.1016/j.psychsport.2021.101941 ◽

2021 ◽

pp. 101941

Author(s):

Kai Krabben ◽

David Mann ◽

Arnt van Helden ◽

Youri Kalisvaart ◽

Daniel Fortin-Guichard ◽

...

Keyword(s):

Vision Loss ◽

Combat Sports ◽

Visually Guided ◽

The Impact

Download Full-text

Impacts of Usher Syndrome Type IB Mutations on Human Myosin VIIa Motor Function†

Biochemistry ◽

10.1021/bi8007142 ◽

2008 ◽

Vol 47 (36) ◽

pp. 9505-9513 ◽

Cited By ~ 10

Author(s):

Shinya Watanabe ◽

Nobuhisa Umeki ◽

Reiko Ikebe ◽

Mitsuo Ikebe

Keyword(s):

Motor Function ◽

Usher Syndrome ◽

Syndrome Type ◽

Myosin Viia ◽

Usher Syndrome Type

Download Full-text

Identification of 31 novel mutations in the F8 gene in Spanish hemophilia A patients: structural analysis of 20 missense mutations suggests new intermolecular binding sites

Blood ◽

10.1182/blood-2007-08-108068 ◽

2008 ◽

Vol 111 (7) ◽

pp. 3468-3478 ◽

Cited By ~ 10

Author(s):

Adoración Venceslá ◽

María Ángeles Corral-Rodríguez ◽

Manel Baena ◽

Mónica Cornet ◽

Montserrat Domènech ◽

...

Keyword(s):

Hemophilia A ◽

Low Density Lipoprotein ◽

Scavenger Receptor ◽

Density Lipoprotein ◽

Missense Mutations ◽

Factor X ◽

Novel Mutations ◽

Large Deletions ◽

Function Relationship ◽

The Impact

Abstract Hemophilia A (HA) is an X-linked bleeding disorder caused by a wide variety of mutations in the factor 8 (F8) gene, leading to absent or deficient factor VIII (FVIII). We analyzed the F8 gene of 267 unrelated Spanish patients with HA. After excluding patients with the common intron-1 and intron-22 inversions and large deletions, we detected 137 individuals with small mutations, 31 of which had not been reported previously. Eleven of these were nonsense, frameshift, and splicing mutations, whereas 20 were missense changes. We assessed the impact of the 20 substitutions based on currently available information about FV and FVIII structure and function relationship, including previously reported results of replacements at these and topologically equivalent positions. Although most changes are likely to cause gross structural perturbations and concomitant cofactor instability, p.Ala375Ser is predicted to affect cofactor activation. Finally, 3 further mutations (p.Pro64Arg, p.Gly494Val, and p.Asp2267Gly) appear to affect cofactor interactions with its carrier protein, von Willebrand factor, with the scavenger receptor low-density lipoprotein receptor–related protein (LRP), and/or with the substrate of the FVIIIapi•FIXa (Xase) complex, factor X. Characterization of these novel mutations is important for adequate genetic counseling in HA families, but also contributes to a better understanding of FVIII structure-function relationship.

Download Full-text