Molecular dynamics (MD) simulations of uncoupling proteins (UCP), a class of transmembrane proteins relevant for proton transport across inner mitochondrial membranes, represent a complicated task due to the lack of available structural data. In this work, we use a combination of homology modelling and subsequent microsecond molecular dynamics simulations of UCP2 in the DOPC phospholipid bilayer, starting from the structure of the mitochondrial ATP/ADP carrier (ANT) as a template. We show that this protocol leads to a structure that is impermeable to water, in contrast to MD simulations of UCP2 structures based on the experimental NMR structure. We also show that ATP binding in the UCP2 cavity is tight in the homology modelled structure of UCP2 in agreement with experimental observations. Finally, we corroborate our results with conductance measurements in model membranes, which further suggest that the UCP2 structure modeled from ANT protein possesses additional key functional elements, such as a fatty acid-binding site at the R60 region of the protein, directly related to the proton transport mechanism across inner mitochondrial membranes.

• Klíčová slova
• conductance measurements in model membranes, long-chain fatty acid, membrane protein, proton transfer, purine nucleotide, uncoupling,
• MeSH
• adenosintrifosfát chemie   metabolismus   MeSH
• iontový transport MeSH
• konformace proteinů * MeSH
• mastné kyseliny chemie   metabolismus   MeSH
• membránové proteiny chemie   MeSH
• mitochondriální proteiny chemie   metabolismus   MeSH
• myši MeSH
• sekvence aminokyselin MeSH
• simulace molekulární dynamiky * MeSH
• stabilita proteinů MeSH
• uncoupling protein 2 chemie   metabolismus   MeSH
• vazba proteinů MeSH
• vztahy mezi strukturou a aktivitou MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• adenosintrifosfát MeSH
• mastné kyseliny MeSH
• membránové proteiny MeSH
• mitochondriální proteiny MeSH
• uncoupling protein 2 MeSH

The delineation of protein-lipid interfaces is essential for understanding the mechanisms of various membrane-associated processes crucial to plant development and growth, including signalling, trafficking, and membrane transport. Due to their highly dynamic nature, the precise characterization of lipid-protein interactions by experimental techniques is challenging. Molecular dynamics simulations provide a powerful computational alternative with a spatial-temporal resolution allowing the atomistic-level description. In this review, we aim to introduce plant scientists to molecular dynamics simulations. We describe different steps of performing molecular dynamics simulations and provide a broad survey of molecular dynamics studies investigating plant protein-lipid interfaces. Our aim is also to illustrate that combining molecular dynamics simulations with artificial intelligence-based protein structure determination opens up unprecedented possibilities for future investigations of dynamic plant protein-lipid interfaces.

• Klíčová slova
• Integral membrane protein, membrane, molecular dynamics simulations, peripheral membrane protein, protein–lipid interactions, structural modelling,
• MeSH
• rostlinné proteiny * metabolismus   chemie   MeSH
• rostliny metabolismus   MeSH
• simulace molekulární dynamiky * MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• rostlinné proteiny * MeSH

BACKGROUND: Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein behavior and to design proteins with modified properties. One of the most common approaches to these studies is to compare the protein structure with other molecules and to reveal similarities and differences in their polypeptide chains. RESULTS: We support the comparison process by proposing a new visualization technique that bridges the gap between traditionally used 1D and 3D representations. By introducing the information about mutual positions of protein chains into the 1D sequential representation the users are able to observe the spatial differences between the proteins without any occlusion commonly present in 3D view. Our representation is designed to serve namely for comparison of multiple proteins or a set of time steps of molecular dynamics simulation. CONCLUSIONS: The novel representation is demonstrated on two usage scenarios. The first scenario aims to compare a set of proteins from the family of cytochromes P450 where the position of the secondary structures has a significant impact on the substrate channeling. The second scenario focuses on the protein flexibility when by comparing a set of time steps our representation helps to reveal the most dynamically changing parts of the protein chain.

• Klíčová slova
• Molecular sequence analysis, Molecular structure and function, Molecular visualization,
• MeSH
• algoritmy MeSH
• molekulární modely MeSH
• proteiny chemie   MeSH
• sekundární struktura proteinů * MeSH
• sekvence aminokyselin MeSH
• sekvenční seřazení MeSH
• simulace molekulární dynamiky * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• proteiny MeSH

MOTIVATION: Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications. RESULTS: CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels and channels in static and dynamic structures. This version provides the users with many new functions, including advanced techniques for intuitive visual inspection of the spatiotemporal behavior of tunnels and channels. Novel integrated algorithms allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations. AVAILABILITY AND IMPLEMENTATION: CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• algoritmy MeSH
• konformace proteinů MeSH
• proteinové inženýrství MeSH
• proteiny chemie   MeSH
• simulace molekulární dynamiky * MeSH
• software MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• proteiny MeSH

Understanding of interactions between proteins and grafted hydrophilic polymer layers is crucial in the search for antifouling materials. Experimental techniques often use an external force that pushes a protein against the polymer-coated surface, which differs from the situation in living systems. The comparison of both setups using atomistic molecular dynamics simulations is provided in this work. Poly(ethylene oxide) (PEO) chains grafted onto graphene at different grafting densities interact with a fragment of C1q protein. At the lowest grafting density, contradictory outcomes are achieved, attributed to the restricted space of C1q near the grafted PEO layer. The most favorable interactions between C1q and the PEO layer are obtained for the medium grafting density. The secondary structure of C1q undergoes changes during its interactions with the PEO layer, including destabilization of β-sheets and formation of 310-helices. The orientation of C1q anchored to graphene also affects the interactions with the PEO layer.

• MeSH
• grafit chemie   MeSH
• hydrofobní a hydrofilní interakce MeSH
• polyethylenglykoly * chemie   MeSH
• sekundární struktura proteinů MeSH
• simulace molekulární dynamiky * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• grafit MeSH
• polyethylenglykoly * MeSH

Hydrogen-Deuterium exchange mass spectrometry's (HDX-MS) utility in identifying and characterizing protein-small molecule interaction sites has been established. The regions that are seen to be protected from exchange upon ligand binding indicate regions that may be interacting with the ligand, giving a qualitative understanding of the ligand binding pocket. However, quantitatively deriving an accurate high-resolution structure of the protein-ligand complex from the HDX-MS data remains a challenge, often limiting its use in applications such as small molecule drug design. Recent efforts have focused on the development of methods to quantitatively model Hydrogen-Deuterium exchange (HDX) data from computationally modeled structures to garner atomic level insights from peptide-level resolution HDX-MS. One such method, HDX ensemble reweighting (HDXer), employs maximum entropy reweighting of simulated HDX data to experimental HDX-MS to model structural ensembles. In this study, we implement and validate a workflow which quantitatively leverages HDX-MS data to accurately model protein-small molecule ligand interactions. To that end, we employ a strategy combining computational protein-ligand docking, molecular dynamics simulations, HDXer, and dimensional reduction and clustering approaches to extract high-resolution drug binding poses that most accurately conform with HDX-MS data. We apply this workflow to model the interaction of ERK2 and FosA with small molecule compounds and inhibitors they are known to bind. In five out of six of the protein-ligand pairs tested, the HDX derived protein-ligand complexes result in a ligand root-mean-square deviation (RMSD) within 2.5 Å of the known crystal structure ligand.

• Klíčová slova
• Computational Docking, ERK2, FosAKP, HDX-MS, HDXer, Hydrogen−Deuterium Exchange, Maximum Entropy Reweighting, Molecular Dynamics Simulations, Protein−Ligand Modeling, Protein−Small Molecule Interactions, Structure Based Drug Design,
• MeSH
• konformace proteinů MeSH
• ligandy MeSH
• proteiny chemie   metabolismus   MeSH
• simulace molekulární dynamiky * MeSH
• simulace molekulového dockingu MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• vodík/deuteriová výměna a hmotnostní spektrometrie * metody   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• ligandy MeSH
• proteiny MeSH

Understanding the RNA binding specificity of protein is of primary interest to decipher their function in the cell. Here, we review the methodology used to solve the structures of protein-RNA complexes using solution-state NMR spectroscopy: from sample preparation to structure calculation procedures. We also describe how molecular dynamics simulations can help providing additional information on the role of key amino acid side chains and of water molecules in protein-RNA recognition.

• Klíčová slova
• MD simulation, Protein–RNA interactions, Solution-state NMR, Structures,
• MeSH
• CELF proteiny chemie   metabolismus   MeSH
• interakční proteinové domény a motivy MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů, alfa-helix MeSH
• konformace proteinů, beta-řetězec MeSH
• lidé MeSH
• magnetická rezonanční spektroskopie metody   MeSH
• RNA chemie   genetika   metabolismus   MeSH
• sestřihové faktory chemie   metabolismus   MeSH
• simulace molekulární dynamiky * MeSH
• termodynamika MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• vodíková vazba MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• CELF proteiny MeSH
• RBFOX1 protein, human MeSH Prohlížeč
• RNA MeSH
• sestřihové faktory MeSH

Human stimulator of interferon genes (hSTING) is a signaling adaptor protein that triggers innate immune system by response to cytosolic DNA and second messenger cyclic dinucleotides (CDNs). Natural CDNs contain purine nucleobase with different phosphodiester linkage types (3'-3', 2'-2' or mixed 2'-3'-linkages) and exhibit different binding affinity towards hSTING, ranging from micromolar to nanomolar. High-affinity CDNs are considered as suitable candidates for treatment of chronic hepatitis B and cancer. We have used molecular dynamics simulations to investigate dynamical aspects of binding of natural CDNs (specifically, 2'-2'-cGAMP, 2'-3'-cGAMP, 3'-3'-cGAMP, 3'-3'-c-di-AMP, and 3'-3'-c-di-GMP) with hSTINGwt protein. Our results revealed that CDN/hSTINGwt interactions are controlled by the balance between fluctuations (conformational changes) in the CDN ligand and the protein dynamics. Binding of different CDNs induces different degrees of conformational/dynamics changes in hSTINGwt ligand binding cavity, especially in α1-helices, the so-called lid region and α2-tails. The ligand residence time in hSTINGwt protein pocket depends on different contribution of R232 and R238 residues interacting with oxygen atoms of phosphodiester groups in ligand, water distribution around interacting charged centers (in protein residues and ligand) and structural stability of closed conformation state of hSTINGwt protein. These findings may perhaps guide design of new compounds modulating hSTING activity.Communicated by Ramaswamy H. Sarma.

• Klíčová slova
• Human stimulator of interferon genes STING, Molecular Dynamics, cyclic dinucleotides CDNs,
• MeSH
• dinukleosidfosfáty * chemie   MeSH
• DNA MeSH
• lidé MeSH
• ligandy MeSH
• oligonukleotidy MeSH
• simulace molekulární dynamiky * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• dinukleosidfosfáty * MeSH
• DNA MeSH
• ligandy MeSH
• oligonukleotidy MeSH

The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this "missing link", we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1-45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found.

• Klíčová slova
• Spinacia oleracea, dynamic N-terminus, extrinsic photosynthetic protein, hydrogen bond dynamics, intrinsic disorder, solution structure,
• MeSH
• fotosystém II (proteinový komplex) chemie   genetika   metabolismus   MeSH
• krystalografie rentgenová MeSH
• magnetická rezonanční spektroskopie metody   MeSH
• rekombinantní proteiny chemie   metabolismus   MeSH
• rostlinné proteiny chemie   genetika   metabolismus   MeSH
• roztoky MeSH
• sekundární struktura proteinů * MeSH
• sekvence aminokyselin MeSH
• simulace molekulární dynamiky * MeSH
• Spinacia oleracea genetika   metabolismus   MeSH
• terciární struktura proteinů MeSH
• termodynamika MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• fotosystém II (proteinový komplex) MeSH
• rekombinantní proteiny MeSH
• rostlinné proteiny MeSH
• roztoky MeSH

Picornaviruses are small positive-sense single-stranded RNA viruses that include many important human pathogens. Within the host cell, they replicate at specific replication sites called replication organelles. To create this membrane platform, they hijack several host factors including the acyl-CoA-binding domain-containing protein-3 (ACBD3). Here, we present a structural characterization of the molecular complexes formed by the non-structural 3A proteins from two species of the Kobuvirus genus of the Picornaviridae family and the 3A-binding domain of the host ACBD3 protein. Specifically, we present a series of crystal structures as well as a molecular dynamics simulation of the 3A:ACBD3 complex at the membrane, which reveals that the viral 3A proteins act as molecular harnesses to enslave the ACBD3 protein leading to its stabilization at target membranes. Our data provide a structural rationale for understanding how these viral-host protein complexes assemble at the atomic level and identify new potential targets for antiviral therapies.

• Klíčová slova
• 3A, ACBD3, Aichivirus, GOLD, Kobuvirus, molecular dynamics simulations, structure,
• MeSH
• adaptorové proteiny signální transdukční chemie   genetika   metabolismus   MeSH
• aminokyselinové motivy MeSH
• buněčné linie MeSH
• exprese genu MeSH
• interakce hostitele a patogenu * MeSH
• interakční proteinové domény a motivy MeSH
• klonování DNA MeSH
• Kobuvirus genetika   metabolismus   MeSH
• konformace proteinů, alfa-helix MeSH
• konformace proteinů, beta-řetězec MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• membránové proteiny chemie   genetika   metabolismus   MeSH
• rekombinantní proteiny chemie   genetika   metabolismus   MeSH
• replikace viru genetika   MeSH
• simulace molekulární dynamiky MeSH
• stabilita proteinů MeSH
• unilamelární lipozómy chemie   MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• virové nestrukturální proteiny chemie   genetika   metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ACBD3 protein, human MeSH Prohlížeč
• adaptorové proteiny signální transdukční MeSH
• membránové proteiny MeSH
• rekombinantní proteiny MeSH
• unilamelární lipozómy MeSH
• virové nestrukturální proteiny MeSH