The purpose of this quick guide is to help new modelers who have little or no background in comparative modeling yet are keen to produce high-resolution protein 3D structures for their study by following systematic good modeling practices, using affordable personal computers or online computational resources. Through the available experimental 3D-structure repositories, the modeler should be able to access and use the atomic coordinates for building homology models. We also aim to provide the modeler with a rationale behind making a simple list of atomic coordinates suitable for computational analysis abiding to principles of physics (e.g., molecular mechanics). Keeping that objective in mind, these quick tips cover the process of homology modeling and some postmodeling computations such as molecular docking and molecular dynamics (MD). A brief section was left for modeling nonprotein molecules, and a short case study of homology modeling is discussed.

• MeSH
• algoritmy MeSH
• aminokyseliny chemie   MeSH
• biologické modely MeSH
• databáze proteinů MeSH
• internet MeSH
• ionty MeSH
• koncentrace vodíkových iontů MeSH
• ligandy MeSH
• počítačová simulace MeSH
• posttranslační úpravy proteinů MeSH
• proteiny chemie   MeSH
• rozpouštědla MeSH
• sbalování proteinů MeSH
• simulace molekulární dynamiky MeSH
• simulace molekulového dockingu MeSH
• software MeSH
• strojové učení MeSH
• strukturní homologie proteinů MeSH
• voda MeSH
• výpočetní biologie metody   MeSH
• zobrazování trojrozměrné metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• aminokyseliny MeSH
• ionty MeSH
• ligandy MeSH
• proteiny MeSH
• rozpouštědla MeSH
• voda MeSH

Beside of the protein crystallography or NMR, another attractive option in protein structure analysis has recently appeared: computer modeling of the protein structure based on homology and similarity with proteins of already known structures. We have used the combination of computer modeling with spectroscopic techniques, such as steady-state or time-resolved fluorescence spectroscopy, and with molecular biology techniques. This method could provide useful structural information in the cases where crystal or NMR structure is not available. Molecular modeling of the ATP site within the H4-H5-loop revealed eight amino acids residues, namely besides the previously reported amino acids Asp443, Lys480, Lys501, Gly502 and Arg544, also Glu446, Phe475 and Gln482, which form the complete ATP recognition site. Moreover, we have proved that a hydrogen bond between Arg423 and Glu472 supports the connection of two opposite halves of the ATP-binding pocket. Similarly, the conserved residue Pro489 is important for the proper interaction of the third and fourth beta-strands, which both contain residues that take part in the ATP-binding. Alternatively, molecular dynamics simulation combined with dynamic fluorescence spectroscopy revealed that 14-3-3 zeta C-terminal stretch is directly involved in the interaction of 14-3-3 protein with the ligand. Phosphorylation at Thr232 induces a conformational change of the C-terminus, which is presumably responsible for observed inhibition of binding abilities. Phosphorylation at Thr232 induces more extended conformation of 14-3-3zeta C-terminal stretch and changes its interaction with the rest of the 14-3-3 molecule. This could explain negative regulatory effect of phosphorylation at Thr232 on 14-3-3 binding properties.

• MeSH
• adenosintrifosfát chemie   metabolismus   MeSH
• alkoholoxidoreduktasy MeSH
• DNA vazebné proteiny fyziologie   MeSH
• fluorescenční spektrometrie metody   MeSH
• fosfoproteiny fyziologie   MeSH
• fosforylace MeSH
• konformace proteinů * MeSH
• konzervovaná sekvence MeSH
• molekulární modely * MeSH
• počítačová simulace * MeSH
• proteiny 14-3-3 chemie   metabolismus   MeSH
• sekvence aminokyselin MeSH
• sekvenční homologie aminokyselin MeSH
• sodíko-draslíková ATPasa chemie   fyziologie   MeSH
• threonin fyziologie   MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• adenosintrifosfát MeSH
• alkoholoxidoreduktasy MeSH
• C-terminal binding protein MeSH Prohlížeč
• DNA vazebné proteiny MeSH
• fosfoproteiny MeSH
• proteiny 14-3-3 MeSH
• sodíko-draslíková ATPasa MeSH
• threonin MeSH

Beside of the protein crystals, another attractive option in protein structure analysis has recently appeared: computer modeling of the protein structure based on homology and similarity with proteins of already known structures. We used the combination of computer modeling with spectroscopic techniques, such as steady-state or time-resolved fluorescence spectroscopy or Raman spectroscopy, and with molecular biology techniques. This method could achieve reliable results comparable with resolution obtained from crystal structures. Molecular modeling of the ATP site within the H4-H5-loop revealed eight amino acids residues, namely besides the previously reported amino acids Asp443, Lys480, Lys501, Gly502 and Arg544, also Glu446, Phe475 and Gln482, which form the complete ATP recognition site. Moreover, we proved that a hydrogen bond between Arg423 and Glu472 supported the connection of two opposite halves of the ATP-binding pocket. Similarly, the conserved residue Pro489 is important for the proper interaction of the third and fourth-strands, which both contain residues that take part in the ATP-binding (Ref. 34).

• MeSH
• adenosintrifosfát metabolismus   MeSH
• fluorescenční spektrometrie MeSH
• konformace proteinů * MeSH
• počítačová simulace * MeSH
• Ramanova spektroskopie MeSH
• sodíko-draslíková ATPasa metabolismus   MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• adenosintrifosfát MeSH
• sodíko-draslíková ATPasa MeSH

Side-chain rotamer prediction is one of the most critical late stages in protein 3D structure building. Highly advanced and specialized algorithms (e.g., FASPR, RASP, SCWRL4, and SCWRL4v) optimize this process by use of rotamer libraries, combinatorial searches, and scoring functions. We seek to identify the sources of key rotamer errors as a basis for correcting and improving the accuracy of protein modeling going forward. In order to evaluate the aforementioned programs, we process 2496 high-quality single-chained all-atom filtered 30% homology protein 3D structures and use discretized rotamer analysis to compare original with calculated structures. Among 513,024 filtered residue records, increased amino acid residue-dependent rotamer errors─associated in particular with polar and charged amino acid residues (ARG, LYS, and GLN)─clearly correlate with increased amino acid residue solvent accessibility and an increased residue tendency toward the adoption of non-canonical off rotamers which modeling programs struggle to predict accurately. Understanding the impact of solvent accessibility now appears key to improved side-chain prediction accuracies.

• MeSH
• algoritmy MeSH
• aminokyseliny * chemie   MeSH
• konformace proteinů MeSH
• proteiny * chemie   MeSH
• rozpouštědla MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• aminokyseliny * MeSH
• proteiny * MeSH
• rozpouštědla MeSH

SUMMARY: The SBILib Python library provides an integrated platform for the analysis of macromolecular structures and interactions. It combines simple 3D file parsing and workup methods with more advanced analytical tools. SBILib includes modules for macromolecular interactions, loops, super-secondary structures, and biological sequences, as well as wrappers for external tools with which to integrate their results and facilitate the comparative analysis of protein structures and their complexes. The library can handle macromolecular complexes formed by proteins and/or nucleic acid molecules (i.e. DNA and RNA). It is uniquely capable of parsing and calculating protein super-secondary structure and loop geometry. We have compiled a list of example scenarios which SBILib may be applied to and provided access to these within the library. AVAILABILITY AND IMPLEMENTATION: SBILib is made available on Github at https://github.com/structuralbioinformatics/SBILib.

• MeSH
• makromolekulární látky MeSH
• molekulární struktura MeSH
• proteiny MeSH
• RNA * MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• makromolekulární látky MeSH
• proteiny MeSH
• RNA * MeSH

The transition dipole coupling model allows to vary systematically many parameters, such as chromophore geometries and transition dipoles. We used it to explore conditions favorable to chirality enhancement observed in many experiments on protein amyloidal precipitates. Stacking of β-sheet planes has been identified as a particularly powerful mechanism of the enhancement.

• Klíčová slova
• Raman optical activity, circular dichroism, enhancement of optical activity, protein spectra, transition dipole coupling,
• MeSH
• molekulární modely MeSH
• multiproteinové komplexy chemie   MeSH
• optická otáčivost * MeSH
• stereoizomerie MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• multiproteinové komplexy 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

Recent advances in protein 3D structure prediction using deep learning have focused on the importance of amino acid residue-residue connections (i.e., pairwise atomic contacts) for accuracy at the expense of mechanistic interpretability. Therefore, we decided to perform a series of analyses based on an alternative framework of residue-residue connections making primary use of the TOP2018 dataset. This framework of residue-residue connections is derived from amino acid residue pairing models both historic and new, all based on genetic principles complemented by relevant biophysical principles. Of these pairing models, three new models (named the GU, Transmuted and Shift pairing models) exhibit the highest observed-over-expected ratios and highest correlations in statistical analyses with various intra- and inter-chain datasets, in comparison to the remaining models. In addition, these new pairing models are universally frequent across different connection ranges, secondary structure connections, and protein sizes. Accordingly, following further statistical and other analyses described herein, we have come to a major conclusion that all three pairing models together could represent the basis of a universal proteomic code (second genetic code) sufficient, in and of itself, to "encode" for both protein folding mechanisms and protein-protein interactions.

• Klíčová slova
• Contact map, Protein 3D structure, Protein folding, Protein-protein interactions, Proteomic code, Sense-antisense,
• MeSH
• aminokyseliny * chemie   genetika   MeSH
• databáze proteinů MeSH
• lidé MeSH
• molekulární modely * MeSH
• proteiny * chemie   genetika   metabolismus   MeSH
• proteomika * MeSH
• sbalování proteinů * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• aminokyseliny * MeSH
• proteiny * MeSH

INTRODUCTION: Sepsis is the main cause of morbidity and mortality in intensive care units and its early diagnosis is not straightforward. Many studies have evaluated the usefulness of various markers of infection, including C-reactive protein (CRP), which is the most accessible and widely used. CRP is of weak diagnostic value because of its low specificity; a better understanding of patterns of CRP levels associated with a particular form of infection may improve its usefulness as a sepsis marker. In the present article, we apply multilevel modeling techniques and mixed linear models to CRP-related data to assess the time course of CRP blood levels in association with clinical outcome in children with different septic conditions. METHODS: We performed a retrospective analysis of 99 patients with systemic inflammatory response syndrome, sepsis, or septic shock who were admitted to the Pediatric Critical Care Unit at the University Hospital, Brno. CRP blood levels were monitored for 10 days following the onset of the septic condition. The effect of different septic conditions and of the surgical or nonsurgical diagnosis on CRP blood levels was statistically analyzed using mixed linear models with a multilevel modeling approach. RESULTS: A significant effect of septic condition and diagnosis on the course of CRP levels was identified. In patients who did not progress to septic shock, CRP blood levels decreased rapidly after reaching peak values - in contrast to the values in patients with septic shock in whom CRP protein levels decreased slowly. Moreover, CRP levels in patients with a surgical diagnosis were higher than in patients with a nonsurgical condition. The magnitude of this additional elevation in surgical patients did not depend on the septic condition. CONCLUSION: Understanding the pattern of change in levels of CRP associated with a particular condition may improve its diagnostic and prognostic value in children with sepsis.

• MeSH
• analýza přežití MeSH
• biologické markery krev   MeSH
• C-reaktivní protein metabolismus   MeSH
• dítě MeSH
• kojenec MeSH
• komorbidita MeSH
• lidé MeSH
• lineární modely MeSH
• mladiství MeSH
• novorozenec MeSH
• předškolní dítě MeSH
• rány a poranění epidemiologie   MeSH
• retrospektivní studie MeSH
• sepse krev   epidemiologie   MeSH
• Check Tag
• dítě MeSH
• kojenec MeSH
• lidé MeSH
• mladiství MeSH
• mužské pohlaví MeSH
• novorozenec MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika epidemiologie   MeSH
• Názvy látek
• biologické markery MeSH
• C-reaktivní protein MeSH

A simple molecular model for the thermodynamic behavior of non-polar solutes in water and in aqueous solutions of protein denaturants is presented. Three contributions are considered: (i) combinatorial arising from the mixing process, (ii) interactional characterizing the molecular interactions occurring in the mixture and (iii) a contribution originating from the structural changes occurring in the first shell of water molecules around the solute. The latter is modeled assuming that water molecules in contact with the solute are involved in a chemical equilibrium between two states. The model describes well the temperature and denaturant concentration dependences of the Gibbs energies of solution and transfer for benzene, toluene and alkanes in water and aqueous solutions of urea and guanidine hydrochloride. Model parameters are physically meaningful, allowing a discussion of the molecular interactions involved. A preferential solvation of the solute by the denaturant is found. However, the non-polar solute-denaturant interaction is not specific, i.e. leading to a distinct chemical entity. Urea and guanidine hydrochloride are non-polar solubilizing agents because their interactions with the solute are less unfavorable than those between water and the solute.

• MeSH
• chemické modely MeSH
• denaturace proteinů * MeSH
• molekulární modely MeSH
• roztoky * MeSH
• sbalování proteinů MeSH
• termodynamika MeSH
• voda MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• roztoky * MeSH
• voda MeSH