scholarly journals Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling

2020 ◽  
Author(s):  
Junichi Higo ◽  
Takeshi Kawabata ◽  
Ayumi Kusaka ◽  
Kota Kasahara ◽  
Narutoshi Kamiya ◽  
...  
Keyword(s):  
Complex Structure ◽  
Three Dimensional ◽  
Interaction Mechanism ◽  
Salt Bridge ◽  
High Density ◽  
Receptor Protein ◽  
Stable Complex ◽  
Conformational Sampling ◽  
Stable Clusters ◽  
Phosphorylated Peptide

ABSTRACTEnhanced conformational sampling, a genetic-algorithm-guided multi-dimensional virtual-system coupled molecular dynamics, can provide equilibrated conformational distributions of a receptor protein and a flexible ligand at room temperature. The distributions provide not only the most stable but also semi-stable complex structures, and propose a ligand–receptor binding process. This method was applied to a system consisting of a receptor protein, 14-3-3ε, and a flexible peptide, phosphorylated Myeloid leukemia factor 1 (pMLF1). The results present comprehensive binding pathways of pMLF1 to 14-3-3ε. We identified four thermodynamically stable clusters of MLF1 on the 14-3-3ε surface, and free-energy barriers among some clusters. The most stable cluster includes two high-density spots connected by a narrow corridor. When pMLF1 passes the corridor, a salt-bridge relay (switching) related to the phosphorylated residue of pMLF1 occurs. Conformations in one high-density spots are similar to the experimentally determined complex structure. Three-dimensional distributions of residues in the intermolecular interface rationally explain the binding-constant changes resultant from alanine–mutation experiment for the residues. We performed a simulation of non-phosphorylated peptide and 14-3-3ε, which demonstrated that the complex structure was unstable, suggesting that phosphorylation of the peptide is crucially important for binding to 14-3-3ε.

Swirl Flow Investigations on the Enhancement of Heat Transfer Processes in Cyclone Cooling Ducts

2012 ◽  
Author(s):  
Florian Wassermann ◽  
Sven Grundmann ◽  
Michael Kloss ◽  
Heinz-Peter Schiffer
Keyword(s):  
Heat Transfer ◽  
Mass Transfer ◽  
Complex Structure ◽  
Three Dimensional ◽  
Swirl Flow ◽  
Flow Structures ◽  
Stable Complex ◽  
Reynolds Analogy ◽  
Transfer Processes ◽  
Cooling Ducts

Cyclone cooling is a promising method to enhance heat-transfer processes in future internal turbine-blade leading-edge cooling-ducts. The basic component of such cooling channels is the swirl generator, which induces a swirling movement of the coolant. The angular momentum generates stable, complex and three-dimensional flow structures of helical shape with alternating axial flow directions. Full three-dimensional and three-component velocity measurements using magnetic resonance velocimetry (3D3C-MRV) were conducted, with the aim to understand the complex structure of pipe flows with strong swirl. In order to mimic the effect of different installation concepts of the cyclone-cooling ducts an idealized bend-duct swirl-tube configuration with variable exit orifices has been investigated. Pronounced helical flow structures and distinct velocity zones could be found in this swirl flow. One substantial result is the identification of stationary helix-shaped streaks of high axial velocity in the direct vicinity of the wall. These findings are in good agreement with mass-transfer measurements that also show helix-shaped structures with increased mass transfer at the inner surface of the tube. According to the Reynolds analogy between heat and mass transfer, augmented heat-transfer processes in these areas are to be expected.

scholarly journals Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling

2020 ◽  
Vol 60 (10) ◽  
pp. 4867-4880
Author(s):  
Junichi Higo ◽  
Takeshi Kawabata ◽  
Ayumi Kusaka ◽  
Kota Kasahara ◽  
Narutoshi Kamiya ◽  
...  
Keyword(s):  
Molecular Interaction ◽  
Interaction Mechanism ◽  
Conformational Sampling ◽  
Phosphorylated Peptide

scholarly journals Discrimination among Rhinovirus Serotypes for a Variant ICAM-1 Receptor Molecule

2004 ◽  
Vol 78 (18) ◽  
pp. 10034-10044 ◽  
Author(s):  
Chuan Xiao ◽  
Tobias J. Tuthill ◽  
Carol M. Bator Kelly ◽  
Lisa J. Challinor ◽  
Paul R. Chipman ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Salt Bridge ◽  
Human Rhinovirus ◽  
Intercellular Adhesion Molecule ◽  
Stable Complex ◽  
Intercellular Adhesion Molecule 1 ◽  
Binding Characteristics ◽  
X Ray Crystallography ◽  
Density Maps ◽  
Charge Interaction

ABSTRACT Intercellular adhesion molecule 1 (ICAM-1) is the cellular receptor for the major group of human rhinovirus serotypes, including human rhinovirus 14 (HRV14) and HRV16. A naturally occurring variant of ICAM-1, ICAM-1Kilifi, has altered binding characteristics with respect to different HRV serotypes. HRV14 binds to ICAM-1 only transiently at physiological temperatures but forms a stable complex with ICAM-1Kilifi. Conversely, HRV16 forms a stable complex with ICAM-1 but does not bind to ICAM-1Kilifi. The three-dimensional structures of HRV14 and HRV16, complexed with ICAM-1, and the structure of HRV14, complexed with ICAM-1Kilifi, have been determined by cryoelectron microscopy (cryoEM) image reconstruction to a resolution of approximately 10 Å. Structures determined by X-ray crystallography of both viruses and of ICAM-1 were fitted into the cryoEM density maps. The interfaces between the viruses and receptors contain extensive ionic networks. However, the interactions between the viruses and ICAM-1Kilifi contain one less salt bridge than between the viruses and ICAM-1. As HRV16 has fewer overall interactions with ICAM-1 than HRV14, the absence of this charge interaction has a greater impact on the binding of ICAM-1Kilifi to HRV16 than to HRV14.

scholarly journals Predicting Protein Interactions by Brownian Dynamics Simulations

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Xuan-Yu Meng ◽  
Yu Xu ◽  
Hong-Xing Zhang ◽  
Mihaly Mezei ◽  
Meng Cui
Keyword(s):  
Protein Interactions ◽  
Brownian Dynamics ◽  
Protein Complexes ◽  
Complex Structure ◽  
Protein Docking ◽  
Receptor Protein ◽  
Conformational Sampling ◽  
Test Set ◽  
Docking Approach ◽  
Dynamics Simulations

We present a newly adapted Brownian-Dynamics (BD)-based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. In order to reduce the computational costs for energy evaluations, a shell-based grid force field was developed to represent the receptor protein and solvation effects. The performance of this BD protein docking approach has been evaluated on a test set of 24 crystal protein complexes. Reproduction of experimental structures in the test set indicates the adequate conformational sampling and accurate scoring of this BD protein docking approach. Furthermore, we have developed an approach to account for the flexibility of proteins, which has been successfully applied to reproduce the experimental complex structure from the structure of two unbounded proteins. These results indicate that this adapted BD protein docking approach can be useful for the prediction of protein-protein interactions.

Flavin radicals, conformational sampling and robust design principles in interprotein electron transfer: the trimethylamine dehydrogenase-electron-transferring flavoprotein complex

2004 ◽  
Vol 71 ◽  
pp. 1-14
Author(s):  
David Leys ◽  
Jaswir Basran ◽  
François Talfournier ◽  
Kamaldeep K. Chohan ◽  
Andrew W. Munro ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Kinetic Studies ◽  
Molecular Assembly ◽  
Conformational Sampling ◽  
Trimethylamine Dehydrogenase ◽  
Key Residues ◽  
Electron Transferring Flavoprotein ◽  
Electron Transfer Complex

TMADH (trimethylamine dehydrogenase) is a complex iron-sulphur flavoprotein that forms a soluble electron-transfer complex with ETF (electron-transferring flavoprotein). The mechanism of electron transfer between TMADH and ETF has been studied using stopped-flow kinetic and mutagenesis methods, and more recently by X-ray crystallography. Potentiometric methods have also been used to identify key residues involved in the stabilization of the flavin radical semiquinone species in ETF. These studies have demonstrated a key role for 'conformational sampling' in the electron-transfer complex, facilitated by two-site contact of ETF with TMADH. Exploration of three-dimensional space in the complex allows the FAD of ETF to find conformations compatible with enhanced electronic coupling with the 4Fe-4S centre of TMADH. This mechanism of electron transfer provides for a more robust and accessible design principle for interprotein electron transfer compared with simpler models that invoke the collision of redox partners followed by electron transfer. The structure of the TMADH-ETF complex confirms the role of key residues in electron transfer and molecular assembly, originally suggested from detailed kinetic studies in wild-type and mutant complexes, and from molecular modelling.

scholarly journals In Silico Molecular Docking and Interaction Analysis of Traditional Chinese Medicines Against SARS-CoV-2 Receptor

2021 ◽  
Vol 16 (5) ◽  
pp. 1934578X2110150
Author(s):  
Gang Li ◽  
Wei Zhou ◽  
Xiurong Zhao ◽  
Ying Xie
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Interaction Analysis ◽  
Herbal Remedies ◽  
Receptor Protein ◽  
Stable Complex ◽  
Traditional Chinese Medicines ◽  
Ligand Interaction ◽  
Chinese Medicines ◽  
In Silico Molecular Docking

The novel coronavirus, 2019-nCoV, has led to a major pandemic in 2020 and is responsible for more than 2.9 million officially recorded deaths worldwide. As well as synthetic anti-viral drugs, there is also a need to explore natural herbal remedies. The Traditional Chinese Medicines (TCMs) system has been used for thousands of years for the prevention, diagnosis, and treatment of several chronic diseases. In this paper, we performed an in silico molecular docking and interaction analysis of TCMs against SARS-CoV-2 receptor RNA-dependent RNA polymerase (RdRp). We obtained the 5 most effective plant compounds which had a better binding affinity towards the target receptor protein. These compounds areforsythoside A, rutin, ginkgolide C, icariside II, and nolinospiroside E. The top-ranked compound, based on docking score, was nolinospiroside, a glycoside found in Ophiopogon japonicas that has antioxidant properties. Protein-ligand interaction analysis discerned that nolinospiroside formed a strong bond between ARG 349 of the protein receptor and the carboxylate group of the ligand, forming a stable complex. Hence, nolinospiroside could be deployed as a lead compound against SARS-CoV-2 infection that can be further investigated for its potential benefits in curbing the viral infection.

scholarly journals D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2622
Author(s):  
Romina Oliva ◽  
Abdul Rajjak Shaikh ◽  
Andrea Petta ◽  
Anna Vangone ◽  
Luigi Cavallo
Keyword(s):  
Three Dimensional ◽  
Salt Bridge ◽  
Structural Effect ◽  
Host Cells ◽  
Heptad Repeat ◽  
Genomic Sequences ◽  
Strong Interactions ◽  
Virus Infectivity ◽  
S Protein ◽  
Global Threat

The crown of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constituted by its spike (S) glycoprotein. S protein mediates the SARS-CoV-2 entry into the host cells. The “fusion core” of the heptad repeat 1 (HR1) on S plays a crucial role in the virus infectivity, as it is part of a key membrane fusion architecture. While SARS-CoV-2 was becoming a global threat, scientists have been accumulating data on the virus at an impressive pace, both in terms of genomic sequences and of three-dimensional structures. On 15 February 2021, from the SARS-CoV-2 genomic sequences in the GISAID resource, we collected 415,673 complete S protein sequences and identified all the mutations occurring in the HR1 fusion core. This is a 21-residue segment, which, in the post-fusion conformation of the protein, gives many strong interactions with the heptad repeat 2, bringing viral and cellular membranes in proximity for fusion. We investigated the frequency and structural effect of novel mutations accumulated over time in such a crucial region for the virus infectivity. Three mutations were quite frequent, occurring in over 0.1% of the total sequences. These were S929T, D936Y, and S949F, all in the N-terminal half of the HR1 fusion core segment and particularly spread in Europe and USA. The most frequent of them, D936Y, was present in 17% of sequences from Finland and 12% of sequences from Sweden. In the post-fusion conformation of the unmutated S protein, D936 is involved in an inter-monomer salt bridge with R1185. We investigated the effect of the D936Y mutation on the pre-fusion and post-fusion state of the protein by using molecular dynamics, showing how it especially affects the latter one.

Ab Initio Determination of a New Complex Structure (55 Non-Hydrogen Atoms) from Synchrotron Powder Data: An Uncommon Nickel Succinate, Ni7(C4H4O4)4(OH)6(H2O)3•7H2O

2004 ◽  
Vol 443-444 ◽  
pp. 333-336
Author(s):  
N. Guillou ◽  
C. Livage ◽  
W. van Beek ◽  
G. Férey
Keyword(s):  
Ab Initio ◽  
Complex Structure ◽  
Three Dimensional ◽  
Free Water ◽  
Hydrogen Atoms ◽  
Monoclinic System ◽  
Synchrotron Powder Diffraction ◽  
Chloride Hexahydrate ◽  
Autogenous Pressure

Ni7(C4H4O4)4(OH)6(H2O)3. 7H2O, a new layered nickel(II) succinate, was prepared hydrothermally (180°C, 48 h, autogenous pressure) from a 1:1.5:4.1:120 mixture of nickel (II) chloride hexahydrate, succinic acid, potassium hydroxide and water. It crystallizes in the monoclinic system (space group P21/c, Z = 4) with the following parameters a = 7.8597(1) Å, b = 18.8154(3)Å, c = 23.4377(4) Å,ϐ = 92.0288(9)°, and V = 3463.9(2) Å3. Its structure, which contains 55 non-hydrogen atoms, was solved ab initio from synchrotron powder diffraction data. It can be described from hybrid organic-inorganic layers, constructed from nickel oxide corrugated chains. These chains are built up from NiO6hexameric units connected via a seventh octahedron. Half of the succinates decorate the chains, and the others connect them to form the layers. The three dimensional arrangement is ensured by hydrogen bonds directly between two adjacent layers and via free water molecules.

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