Individual human genomes frequently contain variants that have epistatic interactions

2020 ◽  
Author(s):  
Henry J Martell ◽  
Darren K Griffin ◽  
Mark N Wass
Keyword(s):  
Genetic Variation ◽  
Structural Data ◽  
Genome Project ◽  
Dimensional Structure ◽  
Protein Interfaces ◽  
Human Genomes ◽  
Synonymous Variant ◽  
And Function ◽  
The Relationship ◽  
Individual Human

AbstractThe availability of thousands of individual genomes provides many opportunities to understand genetic variation and the relationship to phenotype, particularly disease. However, this remains challenging as it is often difficult to identify if a non-synonymous variant alters protein structure and function. Many computational methods have been developed but they typically interpret individual variants in isolation, despite the possibility of variant-variant interactions. Here, we combine the genetic variation data present in the 1000 genome project with protein structural data to identify variant-variant interactions within individual human genomes. We find more than 4,000 combinations of variants that located close in 3D dimensional structure and more than 1,200 in protein-protein interfaces. Many variant combinations include amino acid changes that are compensatory such as maintaining charges or functional groups, thus supporting that these are coevolutionary events. This highlights the need for variant interpretation and precision medicine to consider the gestalt effects of variants.

scholarly journals Impact of genetic variation on three dimensional structure and function of proteins

PLoS ONE ◽  
2017 ◽  
Vol 12 (3) ◽  
pp. e0171355 ◽  
Author(s):  
Roshni Bhattacharya ◽  
Peter W. Rose ◽  
Stephen K. Burley ◽  
Andreas Prlić
Keyword(s):  
Genetic Variation ◽  
Three Dimensional ◽  
Structure And Function ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
And Function

Mapping of monoclonal antibodies specific to P64k: A common antigen of several isolates of Neisseria meningitidis

2001 ◽  
Vol 47 (2) ◽  
pp. 158-164 ◽  
Author(s):  
C Nazábal ◽  
T Carmenate ◽  
S Cruz ◽  
S González ◽  
R Silva ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Neisseria Meningitidis ◽  
Three Dimensional ◽  
Structural Data ◽  
Dimensional Structure ◽  
Bacterial Surface ◽  
A Minor ◽  
The Relationship ◽  
Cell Elisa ◽  
Competition Assays

P64k is a minor outer membrane protein from Neisseria meningitidis. This protein has been produced at high levels in Escherichia coli. We generated a group of monoclonal antibodies (mAbs) against recombinant P64k, which recognise four non-overlapping epitopes, as shown using competition assays with biotinylated mAbs. The P64k sequences involved in mAbs binding were mapped with synthetic overlapping peptides derived from the P64k protein, and located in the previously determined three-dimensional structure of the protein. These antibodies were also characterised by whole-cell ELISA and bactericidal tests against N. meningitidis. Only two of the recognised epitopes were exposed on the bacterial surface, and none of the mAbs showed bactericidal activity. The relationship between these results and the structural data on the epitopes bound by the mAbs is discussed.Key words: Neisseria meningitidis, P64k, monoclonal antibodies, epitope mapping.

scholarly journals Significant abundance of cis configurations of mutations in diploid human genomes

2017 ◽  
Author(s):  
Margret R. Hoehe ◽  
Ralf Herwig ◽  
Qing Mao ◽  
Brock A. Peters ◽  
Radoje Drmanac ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genome Project ◽  
Personal Genome ◽  
Functional Interpretation ◽  
Protein Coding ◽  
Specific Distribution ◽  
Gene Sets ◽  
Human Genomes ◽  
Significant Enrichment ◽  
Coding Variants

AbstractTo fully understand human genetic variation, one must assess the specific distribution of variants between the two chromosomal homologues of genes, and any functional units of interest, as the phase of variants can significantly impact gene function and phenotype. To this end, we have systematically analyzed 18,121 autosomal protein-coding genes in 1,092 statistically phased genomes from the 1000 Genomes Project, and an unprecedented number of 184 experimentally phased genomes from the Personal Genome Project. Here we show that mutations predicted to functionally alter the protein, and coding variants as a whole, are not randomly distributed between the two homologues of a gene, but do occur significantly more frequently in cis-than trans-configurations, with cis/trans ratios of ∼60:40. Significant cis-abundance was observed in virtually all individual genomes in all populations. Nearly all variable genes exhibited either cis, or trans configurations of protein-altering mutations in significant excess, allowing distinction of cis- and trans-abundant genes. These common patterns of phase were largely constituted by a shared, global set of phase-sensitive genes. We show significant enrichment of this global set with gene sets indicating its involvement in adaptation and evolution. Moreover, cis- and trans-abundant genes were found functionally distinguishable, and exhibited strikingly different distributional patterns of protein-altering mutations. This work establishes common patterns of phase as key characteristics of diploid human exomes and provides evidence for their potential functional significance. Thus, it highlights the importance of phase for the interpretation of protein-coding genetic variation, challenging the current conceptual and functional interpretation of autosomal genes.

scholarly journals Structural pharmacology of GABAА receptors

2021 ◽  
Vol 15 (4) ◽  
pp. 44-53
Author(s):  
Alexey V. Rossokhin ◽  
Irina N. Sharonova
Keyword(s):  
Electron Microscopy ◽  
Structural Data ◽  
Receptor Activation ◽  
Physiological Effects ◽  
Gamma Aminobutyric Acid ◽  
Inhibitory Neurotransmitter ◽  
Main Target ◽  
Modulatory Sites ◽  
And Function ◽  
The Relationship

Gamma-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the mammalian central nervous system (CNS), activating the inotropic type A receptors (GABAА receptors) to provide fast inhibition. GABAА receptors are the main target for various groups of drugs that are widely used in the treatment of CNS disorders. This review examines the relationship between the physiological effects of GABAА receptor activation and modulation by various substances (including medicinal compounds), the receptor's structure, and the interaction of these substances with specific modulatory sites. Recent advances in cryogenic electron microscopy have led to fundamental improvements in understanding the detailed organization and function of GABAА receptors. This review is based on both the latest structural data obtained from cryogenic electron microscopy and the results of biochemistry and electrophysiology studies, as well as molecular modelling.

scholarly journals Three-dimensional structure of the human breast cancer resistance protein (BCRP/ABCG2) in an inward-facing conformation

2015 ◽  
Vol 71 (8) ◽  
pp. 1725-1735 ◽  
Author(s):  
Mark F. Rosenberg ◽  
Zsolt Bikadi ◽  
Eszter Hazai ◽  
Tobias Starborg ◽  
Lawrence Kelley ◽  
...  
Keyword(s):  
Drug Disposition ◽  
Three Dimensional ◽  
Structural Data ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Cancer Resistance ◽  
Three Dimensional Structure ◽  
Binding Domains ◽  
Subtomogram Averaging ◽  
And Function

ABCG2 is an efflux drug transporter that plays an important role in drug resistance and drug disposition. In this study, the first three-dimensional structure of human full-length ABCG2 analysed by electron crystallography from two-dimensional crystals in the absence of nucleotides and transported substrates is reported at 2 nm resolution. In this state, ABCG2 forms a symmetric homodimer with a noncrystallographic twofold axis perpendicular to the two-dimensional crystal plane, as confirmed by subtomogram averaging. This configuration suggests an inward-facing configuration similar to murine ABCB1, with the nucleotide-binding domains (NBDs) widely separated from each other. In the three-dimensional map, densities representing the long cytoplasmic extensions from the transmembrane domains that connect the NBDs are clearly visible. The structural data have allowed the atomic model of ABCG2 to be refined, in which the two arms of the V-shaped ABCG2 homodimeric complex are in a more closed and narrower conformation. The structural data and the refined model of ABCG2 are compatible with the biochemical analysis of the previously published mutagenesis studies, providing novel insight into the structure and function of the transporter.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Structural Role of rRNAs on the Ribosomal Subunits from E. Coli by Scanning Transmission Electron Microscopy

1981 ◽  
Vol 39 ◽  
pp. 424-425
Author(s):  
M. Boublik ◽  
N. Robakis ◽  
J.S. Wall
Keyword(s):  
Three Dimensional ◽  
Uranyl Acetate ◽  
Dimensional Structure ◽  
Electron Microscopic ◽  
Ribosomal Subunits ◽  
E Coli ◽  
Freeze Dried ◽  
16S Rna ◽  
Scanning Transmission ◽  
And Function

The three-dimensional structure and function of biological supramolecular complexes are, in general, determined and stabilized by conformation and interactions of their macromolecular components. In the case of ribosomes, it has been suggested that one of the functions of ribosomal RNAs is to act as a scaffold maintaining the shape of the ribosomal subunits. In order to investigate this question, we have conducted a comparative TEM and STEM study of the structure of the small 30S subunit of E. coli and its 16S RNA.The conventional electron microscopic imaging of nucleic acids is performed by spreading them in the presence of protein or detergent; the particles are contrasted by electron dense solution (uranyl acetate) or by shadowing with metal (tungsten). By using the STEM on freeze-dried specimens we have avoided the shearing forces of the spreading, and minimized both the collapse of rRNA due to air drying and the loss of resolution due to staining or shadowing. Figure 1, is a conventional (TEM) electron micrograph of 30S E. coli subunits contrasted with uranyl acetate.

Scanning tunneling microscopy (STM) of DNA and RNA

1989 ◽  
Vol 47 ◽  
pp. 34-35
Author(s):  
Patricia G. Arscott ◽  
Gil Lee ◽  
Victor A. Bloomfield ◽  
D. Fennell Evans
Keyword(s):  
Molecular Structures ◽  
Inorganic Materials ◽  
Resolving Power ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Form And Function ◽  
Dna And Rna ◽  
Calf Thymus ◽  
And Function ◽  
The Relationship

STM is one of the most promising techniques available for visualizing the fine details of biomolecular structure. It has been used to map the surface topography of inorganic materials in atomic dimensions, and thus has the resolving power not only to determine the conformation of small molecules but to distinguish site-specific features within a molecule. That level of detail is of critical importance in understanding the relationship between form and function in biological systems. The size, shape, and accessibility of molecular structures can be determined much more accurately by STM than by electron microscopy since no staining, shadowing or labeling with heavy metals is required, and there is no exposure to damaging radiation by electrons. Crystallography and most other physical techniques do not give information about individual molecules.We have obtained striking images of DNA and RNA, using calf thymus DNA and two synthetic polynucleotides, poly(dG-me5dC)·poly(dG-me5dC) and poly(rA)·poly(rU).

Structure prediction of SPAK C-terminal domain and analysis of its binding to RFXV/I motifs by homology modelling, docking, and molecular dynamics simulation studies

2020 ◽  
Vol 16 ◽  
Author(s):  
Mubarak A. Alamri ◽  
Ahmed D. Alafnan ◽  
Obaid Afzal ◽  
Alhumaidi B. Alabbas ◽  
Safar M. Alqahtani
Keyword(s):  
Molecular Dynamic ◽  
Dynamic Stability ◽  
Md Simulation ◽  
Homology Modelling ◽  
Antihypertensive Agents ◽  
Structure And Function ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Terminal Domain ◽  
And Function

Background: The STE20/SPS1-related proline/alanine-rich kinase (SPAK) is a component of WNKSPAK/OSR1 signaling pathway that plays an essential role in blood pressure regulation. The function of SPAK is mediated by its highly conserved C-terminal domain (CTD) that interacts with RFXV/I motifs of upstream activators, WNK kinases, and downstream substrate, cation-chloride cotransporters. Objective: To determine and validate the three-dimensional structure of the CTD of SPAK and to study and analyze its interaction with the RFXV/I motifs. Methods: A homology model of SPAK CTD was generated and validated through multiple approaches. The model was based on utilizing the OSR1 protein kinase as a template. This model was subjected to 100 ns molecular dynamic (MD) simulation to evaluate its dynamic stability. The final equilibrated model was used to dock the RFQV-peptide derived from WNK4 into the primary pocket that was determined based on the homology sequence between human SPAK and OSR1 CTDs. The mechanism of interaction, conformational rearrangement and dynamic stability of the binding of RFQV-peptide to SPAK CTD were characterized by molecular docking and molecular dynamic simulation. Results: The MD simulation suggested that the binding of RFQV induces a large conformational change due to the distribution of salt bridge within the loop regions. These results may help in understanding the relation between the structure and function of SPAK CTD and to support drug design of potential SPAK kinase inhibitors as antihypertensive agents. Conclusion: This study provides deep insight into SPAK CTD structure and function relationship.

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