scholarly journals Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shih-Chi Luo ◽  
Hsin-Yi Yeh ◽  
Wei-Hsuan Lan ◽  
Yi-Min Wu ◽  
Cheng-Han Yang ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Structural Analysis ◽  
Md Simulation ◽  
Structural Basis ◽  
High Fidelity ◽  
Dna Dynamics ◽  
Genomic Integrity ◽  
Mismatched Dna ◽  
Dna Backbone ◽  
Loop 2

AbstractBoth high-fidelity and mismatch-tolerant recombination, catalyzed by RAD51 and DMC1 recombinases, respectively, are indispensable for genomic integrity. Here, we use cryo-EM, MD simulation and functional analysis to elucidate the structural basis for the mismatch tolerance of DMC1. Structural analysis of DMC1 presynaptic and postsynaptic complexes suggested that the lineage-specific Loop 1 Gln244 (Met243 in RAD51) may help stabilize DNA backbone, whereas Loop 2 Pro274 and Gly275 (Val273/Asp274 in RAD51) may provide an open “triplet gate” for mismatch tolerance. In support, DMC1-Q244M displayed marked increase in DNA dynamics, leading to unobservable DNA map. MD simulation showed highly dispersive mismatched DNA ensemble in RAD51 but well-converged DNA in DMC1 and RAD51-V273P/D274G. Replacing Loop 1 or Loop 2 residues in DMC1 with RAD51 counterparts enhanced DMC1 fidelity, while reciprocal mutations in RAD51 attenuated its fidelity. Our results show that three Loop 1/Loop 2 residues jointly enact contrasting fidelities of DNA recombinases.

scholarly journals Structural analysis of the human SYCE2–TEX12 complex provides molecular insights into synaptonemal complex assembly

Open Biology ◽  
2012 ◽  
Vol 2 (7) ◽  
pp. 120099 ◽  
Author(s):  
Owen R. Davies ◽  
Joseph D. Maman ◽  
Luca Pellegrini
Keyword(s):  
Structural Analysis ◽  
Synaptonemal Complex ◽  
Recurrent Miscarriage ◽  
Central Element ◽  
Biological Data ◽  
Structural Basis ◽  
Structural Framework ◽  
Chromosome Synapsis ◽  
Heterotypic Interactions ◽  
Physical Features

The successful completion of meiosis is essential for all sexually reproducing organisms. The synaptonemal complex (SC) is a large proteinaceous structure that holds together homologous chromosomes during meiosis, providing the structural framework for meiotic recombination and crossover formation. Errors in SC formation are associated with infertility, recurrent miscarriage and aneuploidy. The current lack of molecular information about the dynamic process of SC assembly severely restricts our understanding of its function in meiosis. Here, we provide the first biochemical and structural analysis of an SC protein component and propose a structural basis for its function in SC assembly. We show that human SC proteins SYCE2 and TEX12 form a highly stable, constitutive complex, and define the regions responsible for their homotypic and heterotypic interactions. Biophysical analysis reveals that the SYCE2–TEX12 complex is an equimolar hetero-octamer, formed from the association of an SYCE2 tetramer and two TEX12 dimers. Electron microscopy shows that biochemically reconstituted SYCE2–TEX12 complexes assemble spontaneously into filamentous structures that resemble the known physical features of the SC central element (CE). Our findings can be combined with existing biological data in a model of chromosome synapsis driven by growth of SYCE2–TEX12 higher-order structures within the CE of the SC.

High Fidelity Structural Analysis for Undergrad Structural Engineering Students

2018 ◽  
Author(s):  
Aaron Freidenberg ◽  
Jakob C. Bruhl ◽  
Christopher H. Conley ◽  
Charles L. Randow
Keyword(s):  
Structural Analysis ◽  
Structural Engineering ◽  
Engineering Students ◽  
High Fidelity

scholarly journals Structural and functional analysis of extracellular loop 2 of the Na+/H+ exchanger

2009 ◽  
Vol 1788 (12) ◽  
pp. 2481-2488 ◽  
Author(s):  
Brian L. Lee ◽  
Xiuju Li ◽  
Yongsheng Liu ◽  
Brian D. Sykes ◽  
Larry Fliegel
Keyword(s):  
Functional Analysis ◽  
Extracellular Loop ◽  
Loop 2

scholarly journals Structural Analysis of Respirasomes in Electron Transfer Pathway of Acidithiobacillus ferrooxidans: A Computer-Aided Molecular Designing Study

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Mahesh Chandra Patra ◽  
Sukanta Kumar Pradhan ◽  
Surya Narayan Rath ◽  
Jitendra Maharana
Keyword(s):  
Electron Transfer ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Acidithiobacillus Ferrooxidans ◽  
Md Simulation ◽  
Protein Docking ◽  
Metabolic Energy ◽  
Structural Basis ◽  
Electron Transfer Pathway ◽  
Hydrophobic Amino Acids

Acidithiobacillus ferrooxidans obtains its metabolic energy by reducing extracellular ferrous iron with either downhill or uphill electron transfer pathway. The downhill electron transfer pathway has been substantially explored in recent years to underpin the mechanism of iron respiration but, there exists a wide gap in our present understanding on how these proteins are organized as a supercomplex and what sort of atomic level interactions governs their stability in the iron respiratory chain. In the present study, we aimed at unraveling the structural basis of supermolecular association of respirasomes using protein threading, protein-protein docking, and molecular dynamics (MD) simulation protocols. Our results revealed that Phe312 of outer membrane cytochrome c plays a crucial role in diffusing electrons from heme C group to Asp73 of rusticyanin. In line with the previous experimental results, His143 of rusticyanin was found to have a stable interaction with Glu121 of periplasmic cytochrome c4. Cytochrome c4 interacts with subunit B of cytochrome c oxidase through Lys146 and Thr148 of the conserved hydrophobic/aromatic motif 145-WKWTFSY-151 to attain stability during simulation. Phe468 of cytochrome c oxidase was found indispensable for stabilizing heme aa3 during MD simulation. Taken together, we conclude that the molecular interactions of charged and hydrophobic amino acids present on the surface of each respirasome form a hypothetical electron wire in the iron respiratory supercomplex of A. ferrooxidans.

scholarly journals Crystal Structures of Two Coronavirus ADP-Ribose-1″-Monophosphatases and Their Complexes with ADP-Ribose: a Systematic Structural Analysis of the Viral ADRP Domain

2008 ◽  
Vol 83 (2) ◽  
pp. 1083-1092 ◽  
Author(s):  
Yuanyuan Xu ◽  
Le Cong ◽  
Cheng Chen ◽  
Lei Wei ◽  
Qi Zhao ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Crystal Structures ◽  
Structural Information ◽  
Large Family ◽  
Binding Pocket ◽  
Structural Basis ◽  
Active Site Residues ◽  
Replication Process ◽  
Functional Studies ◽  
Group I

ABSTRACT The coronaviruses are a large family of plus-strand RNA viruses that cause a wide variety of diseases both in humans and in other organisms. The coronaviruses are composed of three main lineages and have a complex organization of nonstructural proteins (nsp's). In the coronavirus, nsp3 resides a domain with the macroH2A-like fold and ADP-ribose-1"-monophosphatase (ADRP) activity, which is proposed to play a regulatory role in the replication process. However, the significance of this domain for the coronaviruses is still poorly understood due to the lack of structural information from different lineages. We have determined the crystal structures of two viral ADRP domains, from the group I human coronavirus 229E and the group III avian infectious bronchitis virus, as well as their respective complexes with ADP-ribose. The structures were individually solved to elucidate the structural similarities and differences of the ADRP domains among various coronavirus species. The active-site residues responsible for mediating ADRP activity were found to be highly conserved in terms of both sequence alignment and structural superposition, whereas the substrate binding pocket exhibited variations in structure but not in sequence. Together with data from a previous analysis of the ADRP domain from the group II severe acute respiratory syndrome coronavirus and from other related functional studies of ADRP domains, a systematic structural analysis of the coronavirus ADRP domains was realized for the first time to provide a structural basis for the function of this domain in the coronavirus replication process.

scholarly journals The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 5053
Author(s):  
Alina K. Bakunova ◽  
Alena Yu. Nikolaeva ◽  
Tatiana V. Rakitina ◽  
Tatiana Y. Isaikina ◽  
Maria G. Khrenova ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Structural Analysis ◽  
Active Site ◽  
Active Sites ◽  
Structural Basis ◽  
Active Site Residues ◽  
Type Iv ◽  
Fold Type ◽  
Arginine Residues

Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.

scholarly journals Structural basis for assembly of TRAPPII complex and specific activation of GTPase Ypt31/32

2021 ◽  
Author(s):  
Chenchen Mi ◽  
Li Zhang ◽  
Shan Sun ◽  
Guoqiang Huang ◽  
Guangcan Shao ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Bound States ◽  
Structural Basis ◽  
Guanine Nucleotide ◽  
Nucleotide Exchange ◽  
Nucleotide Binding Domain ◽  
Closed Conformation ◽  
Guanine Nucleotide Exchange ◽  
Nucleotide Exchange Factor ◽  
Protein Particle

Transport protein particle (TRAPP) complexes belong to the multiprotein tethering complex and have three forms- TRAPPI, TRAPPII and TRAPPIII, which share a core of six TRAPPI proteins. TRAPPII facilitates intra-Golgi and endosome-to-Golgi transports by activating GTPase Ypt31/Ypt32 as the guanine nucleotide exchange factor (GEF) in yeast. Here we present cryo-EM structures of yeast TRAPPII in apo and Ypt32-bound states. All the structures show a dimeric architecture assembled by two triangle shaped monomers, while the monomer in the apo structure exhibits both open and closed conformations, and the monomer in the Ypt32-bound form only captures the closed conformation. Located in the interior of the monomer, Ypt32 binds with both TRAPPI and Trs120 via its nucleotide binding domain and binds with Trs31 of TRAPPI via its hypervariable domain. Combined with functional analysis, the structures provide insights into the assembly of TRAPPII and the mechanism of the specific activation of Ypt31/Ypt32 by TRAPPII.

High-Fidelity Structural Analysis of a 10 MW Offshore Floating Wind Turbine Rotor Blade

2020 ◽  
Author(s):  
Reza Yaghmaie ◽  
Onur Bilgen
Keyword(s):  
Structural Analysis ◽  
Wind Turbine ◽  
Turbine Blade ◽  
Rotor Blade ◽  
Turbine Rotor ◽  
High Fidelity ◽  
Turbine Rotor Blade ◽  
Offshore Floating Wind Turbine ◽  
Fidelity Model ◽  
Wind Turbine Rotor

Abstract This paper presents a comparison of low- and high-fidelity structural analyses of a 10 MW offshore floating wind turbine rotor blade. For low-fidelity analysis, BeamDyn as a part of the OpenFAST toolset is used. For high-fidelity analysis, the Toolkit for the Analysis of Composite Structures (TACS) finite element method is used. First, several numerical examples with reference solutions from the literature are investigated to compare the accuracy and efficiency of the low- and high-fidelity structural models. Next, the DTU 10 MW reference wind turbine blade is analyzed using both the low- and high-fidelity methods. The bending response of the blade is analyzed. The results show that the high-fidelity model agrees with low-fidelity results and reference solutions. The high-fidelity model represents the deformations more accurately than the low-fidelity model and therefore is appropriate for structural analysis of complex wind turbine blade shapes.

Sign in / Sign up

Export Citation Format

Share Document