Predicting the Permeability of Macrocycles from Conformational Sampling – Limitations of Molecular Flexibility

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.

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The Study on Molecular Flexibility Treating and Near-Native Structure Screening in Protein-Protein Docking Approaches

ACTA BIOPHYSICA SINICA ◽

10.3724/sp.j.1260.2012.10065 ◽

2012 ◽

Vol 28 (1) ◽

pp. 15

Author(s):

Feng YANG ◽

Libin CAO ◽

Xinqi GONG ◽

Shan CHANG ◽

Weizu CHEN ◽

...

Keyword(s):

Protein Docking ◽

Native Structure ◽

Molecular Flexibility

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FSATOOL: A useful tool to do the conformational sampling and trajectory analysis work for biomolecules

Journal of Computational Chemistry ◽

10.1002/jcc.26083 ◽

2019 ◽

Vol 41 (2) ◽

pp. 156-164

Author(s):

Haomiao Zhang ◽

Qiankun Gong ◽

Haozhe Zhang ◽

Changjun Chen

Keyword(s):

Trajectory Analysis ◽

Conformational Sampling

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On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽

10.3390/polym13010099 ◽

2020 ◽

Vol 13 (1) ◽

pp. 99

Author(s):

Cristian Privat ◽

Sergio Madurga ◽

Francesc Mas ◽

Jaime Rubio-Martínez

Keyword(s):

Molecular Dynamics ◽

Amino Acids ◽

Md Simulations ◽

Point Of View ◽

Conformational Space ◽

Conformational Sampling ◽

Protonation State ◽

Constant Ph ◽

Biochemical Systems ◽

Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

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An automated protocol for modelling peptide substrates to proteases

BMC Bioinformatics ◽

10.1186/s12859-020-03931-6 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Rodrigo Ochoa ◽

Mikhail Magnitov ◽

Roman A. Laskowski ◽

Pilar Cossio ◽

Janet M. Thornton

Keyword(s):

Substrate Recognition ◽

Accessible Surface Area ◽

Conformational Sampling ◽

Structural Determinants ◽

Peptide Substrates ◽

The Family ◽

Protease Substrate ◽

Peptide Complexes ◽

Accessible Surface ◽

Automated Protocol

Abstract Background Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promiscuity which can also be essential. Databases compiling specificity matrices derived from experimental assays have provided valuable insights into protease substrate recognition. Despite this, there are still gaps in our knowledge of the structural determinants. Here, we compile a set of protease crystal structures with bound peptide-like ligands to create a protocol for modelling substrates bound to protease structures, and for studying observables associated to the binding recognition. Results As an application, we modelled a subset of protease–peptide complexes for which experimental cleavage data are available to compare with informational entropies obtained from protease–specificity matrices. The modelled complexes were subjected to conformational sampling using the Backrub method in Rosetta, and multiple observables from the simulations were calculated and compared per peptide position. We found that some of the calculated structural observables, such as the relative accessible surface area and the interaction energy, can help characterize a protease’s substrate recognition, giving insights for the potential prediction of novel substrates by combining additional approaches. Conclusion Overall, our approach provides a repository of protease structures with annotated data, and an open source computational protocol to reproduce the modelling and dynamic analysis of the protease–peptide complexes.

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The Dynamics of Subunit Rotation in a Eukaryotic Ribosome

Biophysica ◽

10.3390/biophysica1020016 ◽

2021 ◽

Vol 1 (2) ◽

pp. 204-221

Author(s):

Frederico Campos Freitas ◽

Gabriele Fuchs ◽

Ronaldo Junio de Oliveira ◽

Paul Charles Whitford

Keyword(s):

Free Energy ◽

Large Scale ◽

Small Subunit ◽

Free Energy Barrier ◽

Temperature Dependent ◽

Molecular Flexibility ◽

Subunit Rotation ◽

Biological Kinetics ◽

Rate Limiting ◽

Reversible Rotation

Protein synthesis by the ribosome is coordinated by an intricate series of large-scale conformational rearrangements. Structural studies can provide information about long-lived states, however biological kinetics are controlled by the intervening free-energy barriers. While there has been progress describing the energy landscapes of bacterial ribosomes, very little is known about the energetics of large-scale rearrangements in eukaryotic systems. To address this topic, we constructed an all-atom model with simplified energetics and performed simulations of subunit rotation in the yeast ribosome. In these simulations, the small subunit (SSU; ∼1 MDa) undergoes spontaneous and reversible rotation events (∼8∘). By enabling the simulation of this rearrangement under equilibrium conditions, these calculations provide initial insights into the molecular factors that control dynamics in eukaryotic ribosomes. Through this, we are able to identify specific inter-subunit interactions that have a pronounced influence on the rate-limiting free-energy barrier. We also show that, as a result of changes in molecular flexibility, the thermodynamic balance between the rotated and unrotated states is temperature-dependent. This effect may be interpreted in terms of differential molecular flexibility within the rotated and unrotated states. Together, these calculations provide a foundation, upon which the field may begin to dissect the energetics of these complex molecular machines.

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