scholarly journals Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds

ACS Omega ◽  
2021 ◽  
Author(s):  
Hiroshi Izumi ◽  
Laurence A. Nafie ◽  
Rina K. Dukor
Keyword(s):  
Conformational Variability ◽  
Multiple Mutation

scholarly journals On the use of 3J-coupling NMR data to derive structural information on proteins

2021 ◽  
Vol 75 (1) ◽  
pp. 39-70
Author(s):  
Lorna J. Smith ◽  
Wilfred F. van Gunsteren ◽  
Bartosz Stankiewicz ◽  
Niels Hansen
Keyword(s):  
Protein Structure ◽  
Structural Information ◽  
Protein Structure Determination ◽  
High Sensitivity ◽  
Time Averaging ◽  
Conformational Ensemble ◽  
Torsional Angle ◽  
Conformational Variability ◽  
Egg White Lysozyme ◽  
Coupling Time

AbstractValues of 3J-couplings as obtained from NMR experiments on proteins cannot easily be used to determine protein structure due to the difficulty of accounting for the high sensitivity of intermediate 3J-coupling values (4–8 Hz) to the averaging period that must cover the conformational variability of the torsional angle related to the 3J-coupling, and due to the difficulty of handling the multiple-valued character of the inverse Karplus relation between torsional angle and 3J-coupling. Both problems can be solved by using 3J-coupling time-averaging local-elevation restraining MD simulation. Application to the protein hen egg white lysozyme using 213 backbone and side-chain 3J-coupling restraints shows that a conformational ensemble compatible with the experimental data can be obtained using this technique, and that accounting for averaging and the ability of the algorithm to escape from local minima for the torsional angle induced by the Karplus relation, are essential for a comprehensive use of 3J-coupling data in protein structure determination.

scholarly journals The effect of attachment site mutations on strand exchange in bacteriophage lambda site-specific recombination.

Genetics ◽  
1989 ◽  
Vol 122 (4) ◽  
pp. 727-736
Author(s):  
C E Bauer ◽  
J F Gardner ◽  
R I Gumport ◽  
R A Weisberg
Keyword(s):  
Attachment Site ◽  
Strand Exchange ◽  
Segregation Pattern ◽  
Base Substitution ◽  
Base Pairs ◽  
Multiple Mutation ◽  
Attachment Sites ◽  
Dna Strands ◽  
Substitution Mutations ◽  
Overlap Region

Abstract Recombination of phage lambda attachment sites occurs by sequential exchange of the DNA strands at two specific locations. The first exchange produces a Holliday structure, and the second resolves it to recombinant products. Heterology for base substitution mutations in the region between the two strand exchange points (the overlap region) reduces recombination; some mutations inhibit the accumulation of Holliday structures, others inhibit their resolution to recombinant products. To see if heterology also alters the location of the strand exchange points, we determined the segregation pattern of three single and one multiple base pair substitution mutations of the overlap region in crosses with wild type sites. The mutations are known to differ in the severity of their recombination defect and in the stage of strand exchange they affect. The three single mutations behaved similarly: each segregated into both products of recombination, and the two products of a single crossover were frequently nonreciprocal in the overlap region. In contrast, the multiple mutation preferentially segregated into one of the two recombinant products, and the two products of a single crossover appeared to be fully reciprocal. The simplest explanation of the segregation pattern of the single mutations is that strand exchanges occur at the normal locations to produce recombinants with mismatched base pairs that are frequently repaired. The segregation pattern of the multiple mutation is consistent with the view that both strand exchanges usually occur to one side of the mutant site. We suggest that the segregation pattern of a particular mutation is determined by which stage of strand exchange it inhibits and by the severity of the inhibition.

scholarly journals Numerical simulation of conformational variability in biopolymer translocation through wide nanopores

2009 ◽  
Vol 2009 (06) ◽  
pp. P06009 ◽  
Author(s):  
Maria Fyta ◽  
Simone Melchionna ◽  
Massimo Bernaschi ◽  
Efthimios Kaxiras ◽  
Sauro Succi
Keyword(s):  
Numerical Simulation ◽  
Conformational Variability

scholarly journals Conformational variability in proteins bound to single-stranded DNA: a new benchmark for new docking perspectives

2021 ◽  
Author(s):  
Dominique MIAS-LUCQUIN ◽  
Isaure Chauvot de Beauchêne
Keyword(s):  
Protein Data Bank ◽  
Conformational Changes ◽  
Molecular Interactions ◽  
Protein Structures ◽  
Data Bank ◽  
Computational Docking ◽  
Ssdna Binding ◽  
Conformational Variability ◽  
High Flexibility ◽  
Docking Benchmark

We explored the Protein Data-Bank (PDB) to collect protein-ssDNA structures and create a multi-conformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA unbound structure is included. For the 143 groups identified as bound-unbound structures of the same protein , we studied the conformational changes in the protein induced by the ssDNA binding. Moreover, based on several bound or unbound protein structures in some groups, we also assessed the intrinsic conformational variability in either bound or unbound conditions, and compared it to the supposedly binding-induced modifications. This benchmark is, to our knowledge, the first attempt made to peruse available structures of protein – ssDNA interactions to such an extent, aiming to improve computational docking tools dedicated to this kind of molecular interactions.

Simulative Analysis of a Family of DNA Tetrahedrons Produced by Changing the Twisting Number of Each Double Helix

2021 ◽  
Vol 20 (05) ◽  
pp. 529-537
Author(s):  
Hui Bai ◽  
Jia Li ◽  
Heng Zhang ◽  
Shuya Liu
Keyword(s):  
Cross Correlation ◽  
Double Helix ◽  
Dynamics Simulation ◽  
Conformational Variability ◽  
Double Helices ◽  
Dna Tetrahedron ◽  
Entire Trajectory ◽  
Dna Double Helix ◽  
Twist Number ◽  
Insight Into

In this paper, three tetrahedral nanocages, composed of six DNA double helix edges with all having the twist number 1, 2 or 3, have been characterized using classical molecular dynamics simulation to measure the specific structural and conformational features produced by only changing the twisting number of each double helix. The simulation result indicates that three tetrahedral cages are relatively stable and are maintained along the entire trajectory. Each double helix is more inclined to behave as a whole in the 2TD and 3TD cages than in the 1TD cage according to the cross-correlation maps for three nanocages, and also their local motions are more easily induced by the conformational variability of the thymidine linkers due to the increased flexibility of each helix. Hence, the double helices become the important factors on the structural stability of total cages with the DNA twisting number, and also give the signification contributions to the sizes of these cages conferring the larger spaces of the 2TD and 3TD cages than the 1TD cage. Our result provides an insight into which roles the double helix edges play in assembling DNA polyhedron, and also contribute to improving the loading capacity of DNA tetrahedron in drug delivery.

Sign in / Sign up

Export Citation Format

Share Document