A5052827727- Protein Structure and Dynamics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Spectroscopy and Quantum Chemical Studies
- Mass Spectrometry Techniques and Applications
- Chemical Synthesis and Analysis
- DNA and Nucleic Acid Chemistry
- Analytical Chemistry and Chromatography
- Free Radicals and Antioxidants
- Chemical Reaction Mechanisms
- Glycosylation and Glycoproteins Research
- Bacteriophages and microbial interactions
- Advanced Chemical Physics Studies
- Lipid Membrane Structure and Behavior
- Photochemistry and Electron Transfer Studies
- Neuropeptides and Animal Physiology
- Advanced NMR Techniques and Applications
- Force Microscopy Techniques and Applications
- Computational Drug Discovery Methods
- Neuroendocrine regulation and behavior
- Molecular spectroscopy and chirality
- Biochemical and Structural Characterization
- Organic Chemistry Cycloaddition Reactions
- Analytical Chemistry and Sensors
- Chemical and Physical Properties in Aqueous Solutions
University of Gdańsk
2016-2025
Gdańsk University of Technology
2002-2024
Universidad de Sevilla
2021
University of Zagreb
2021
George Mason University
2021
Institute for Advanced Study
2021
University of Genoa
2021
University of Salerno
2021
Sapienza University of Rome
2021
UNSW Sydney
2021
Abstract We present the results for CAPRI Round 54, 5th joint CASP‐CAPRI protein assembly prediction challenge. The offered 37 targets, including 14 homodimers, 3 homo‐trimers, 13 heterodimers antibody–antigen complexes, and 7 large assemblies. On average ~70 CASP predictor groups, more than 20 automatics servers, submitted models each target. A total of 21 941 by these groups 15 scorer were evaluated using model quality measures DockQ score consolidating measures. performance was quantified...
Time-averaged restraints from nuclear magnetic resonance (NMR) measurements have been implemented in the UNRES coarse-grained model of polypeptide chains order to develop a tool for data-assisted modeling conformational ensembles multistate proteins, intrinsically disordered proteins (IDPs) and with regions (IDRs), many which are essential cell biology. A numerically stable variant molecular dynamics time-averaged has introduced, total energy is conserved sections trajectory microcanonical...
A two-stage procedure for the determination of a united-residue potential designed protein simulations is outlined. In first stage, long-range and local-interaction energy terms total polypeptide chain are determined by analyzing protein-crystal data averaging all-atom surfaces. second stage (described in accompanying article), relative weights optimized so as to locate native structures selected test proteins lowest structures. The goal work present study parameterize physically reasonable...
We report the application of Langevin dynamics to physics-based united-residue (UNRES) force field developed in our laboratory. Ten trajectories were run on seven proteins [PDB ID codes 1BDD (α; 46 residues), 1GAB 47 1LQ7 67 1CLB 75 1E0L (β; 28 and 1E0G (α+β; 48 1IGD 61 residues)] with UNRES parameterized by using recently method for obtaining a hierarchical structure energy landscape. All α-helical folded native-like structures, whereas yielded mostly nonnative folds although structures are...
A general method to derive site-site or united-residue potentials is presented. The basic principle of the separation degrees freedom a system into primary and secondary ones. describe features system, while ones are averaged over when calculating potential mean force, which hereafter referred as restricted free energy (RFE) function. RFE can be factored one-, two-, multibody terms, using cluster-cumulant expansion Kubo. These factors assigned functional forms corresponding lowest-order...
An approach based exclusively on finding the global minimum of an appropriate potential energy function has been used to predict unknown structures five globular proteins with sizes ranging from 89 140 amino acid residues. Comparison computed lowest-energy two them (HDEA and MarA) crystal structures, released by Protein Data Bank after predictions were made, shows that large fragments (61 residues) both predicted rms deviations 4.2 6.0 Å for C α atoms, HDEA MarA, respectively. This...
We report the modification and parametrization of united-residue (UNRES) force field for energy-based protein structure prediction folding simulations. tested approach on three training proteins separately: 1E0L (beta), 1GAB (alpha), 1E0G (alpha + beta). Heretofore, UNRES had been designed parametrized to locate native-like structures as global minima their effective potential energy surfaces, which largely neglected conformational entropy because decoys composed only lowest-energy...
Continuing our work on the determination of an off-lattice united-residue force field for protein-structure simulations, we determined and parameterized appropriate functional forms local-interaction terms, corresponding to rotation about virtual bonds (Utor), bending virtual-bond angles (Ub), energy different rotameric states side chains (Urot). These terms were by applying Boltzmann principle distributions torsional side-chain states, respectively, calculated from a data base 195...
By using principal component analysis (PCA) to examine the molecular dynamics (MD) of protein folding trajectories, generated with coarse-grained UNRES force field, for B-domain staphylococcal A and triple β-strand WW domain from formin binding 28 (FBP), we demonstrate how different free energy landscapes (FELs) pathways trajectories can be, even though they appear be very similar by visual inspection time dependence root-mean-square deviation (rmsd). Approaches determine minimal...
The alanine-based peptide Ac-XX(A) 7 OO-NH 2 , referred to as XAO (where X, A, and O denote diaminobutyric acid, alanine, ornithine, respectively), has recently been proposed possess a well defined polyproline II (P ) conformation at low temperatures. Based on the results of extensive NMR CD investigations combined with theoretical calculations, reported here, we present evidence that, contrary, this does not have any significant amount organized P structure but exists in an ensemble...
A unified coarse-grained model of three major classes biological molecules—proteins, nucleic acids, and polysaccharides—has been developed. It is based on the observations that repeated units biopolymers (peptide groups, acid bases, sugar rings) are highly polar their charge distributions can be represented crudely as point multipoles. The an extension united residue (UNRES) proteins developed previously in our laboratory. respective force fields defined potentials mean biomacromolecules...
We present the results for CAPRI Round 46, third joint CASP-CAPRI protein assembly prediction challenge. The comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight homo-oligomer one heterodimer proteins that could be readily modeled using templates from Protein Data Bank, often available full assembly. remaining 11 5 homodimers, 3 heterodimers, two higher-order assemblies. These were more difficult to model, as their mainly involved "ab-initio" docking...
Abstract We present the results for CAPRI Round 50, fourth joint CASP‐CAPRI protein assembly prediction challenge. The comprised a total of twelve targets, including six dimers, three trimers, and higher‐order oligomers. Four these were easy which good structural templates available either full assembly, or main interfaces (of oligomers). Eight difficult targets only distantly related found individual subunits. Twenty‐five groups eight automatic servers submitted ~1250 models per target....
Microbial communities are found throughout the biosphere, from human guts to glaciers, soil activated sludge. Understanding statistical properties of such diverse can pave way elucidate common mechanisms ...Multiple ecological forces act together shape composition microbial communities. Phyloecology approaches—which combine phylogenetic relationships between species with community ecology—have potential disentangle but often ...
Based on the dipole model of peptide groups developed in our earlier work [Liwo et al., Prot. Sci., 2, 1697 (1993)], a cumulant expansion average free energy system freely rotating peptide-group dipoles tethered to fixed α-carbon trace is derived. A graphical approach presented find all nonvanishing terms cumulants. In particular, analytical expressions for three- and four-body (correlation) averaged interaction potential united are These similar cooperative forces hydrogen bonding...
Recent improvements of a hierarchical ab initio or de novo approach for predicting both alpha and beta structures proteins are described. The united-residue energy function used in this procedure includes multibody interactions from cumulant expansion the free polypeptide chains, with their relative weights determined by Z-score optimization. critical initial stage involves search conformational space annealing (CSA) method, followed optimization an all-atom model. was assessed recent blind...
The implementation of molecular dynamics (MD) with our physics-based protein united-residue (UNRES) force field, described in the accompanying paper (Khalili et al. J. Phys. Chem. B 2005, 109, 13785), was extended to Langevin dynamics. equations motion are integrated by using a simplified stochastic velocity Verlet algorithm. To compare results those all-atom simulations implicit solvent which no explicit and friction forces present, we alternatively introduced Berendsen thermostat. Test on...
Recent improvements in the protein-structure prediction method developed our laboratory, based on thermodynamic hypothesis, are described. The conformational space is searched extensively at united-residue level by using physics-based UNRES energy function and annealing of global optimization. lowest-energy coarse-grained structures then converted to an all-atom representation energy-minimized with ECEPP/3 force field. procedure was assessed two recent blind tests prediction. During first...
The conformational space annealing (CSA) method for global optimization has been applied to the 10-55 fragment of B-domain staphylococcal protein A (protein A) and a 75-residue protein, apo calbindin D9K (PDB ID code 1CLB ), by using UNRES off-lattice united-residue force field. Although potential was not calibrated with these two proteins, native-like structures were found among low-energy conformations, without use threading or secondary-structure predictions. This is because CSA can find...
Based on the concept that hydrophobic interactions cause a polypeptide chain to adopt compact structure, method is proposed predict structure of protein. The procedure carried out in four stages: (1) use virtual-bond united-residue approximation with side chains represented by spheres search conformational space extensively using specially designed lead collapsed (2) conversion lowest-energy one real backbone, optimization hydrogen-bond network among backbone groups, (3) perturbation latter...
The Lagrange formalism was implemented to derive the equations of motion for physics-based united-residue (UNRES) force field developed in our laboratory. C(alpha)...C(alpha) and C(alpha)...SC (SC denoting a side-chain center) virtual-bond vectors were chosen as variables. velocity Verlet algorithm adopted integrate motion. Tests on unblocked Ala(10) polypeptide showed that is stable short periods time up step 1.467 fs; however, even with shorter 0.489 fs, some drift total energy occurs...