Cezary Czaplewski

University of Gdansk | UG · Department of Theoretical Chemistry

The dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of...

In this paper we report the improvements and extensions of the UNRES server ( https://unres-server.chem.ug.edu.pl ) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UN...

We report major algorithmic improvements of the UNRES package for physics‐based coarse‐grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral an...

The UNited RESidue (UNRES) model of polypeptide chains was applied to study the association of 20 peptides with sizes ranging from 6 to 32 amino-acid residues. Twelve of those were potentially aggregating hexa- or heptapeptides excised from larger proteins, while the remaining eight contained potentially aggregating sequences, functionalized by att...

The SARS-CoV-2 virus, commonly known as COVID-19, first occurred in December 2019 in Wuhan, Hubei Province, China. Since then, it has become a tremendous threat to human health. With a pandemic threat, it is in the significant interest of the scientific world to establish its method of infection. In this manuscript, we combine knowledge of the infe...

One of the definitions of hydrophobic interactions is the aggregation of nonpolar particles in a polar solvent, such as water. While this phenomenon appears to be very simple, it is crucial for many complex processes, such as protein folding, to take place. In this work, the hydrophobic association of adamantane and hexane at various temperatures a...

Coarse-grained approaches, in which groups of atoms are represented by single interaction sites, are very important in biological and materials sciences because they enable us to cover the size- and time-scales by several orders of magnitude larger than those available all-atom simulations, while largely keeping the details of the systems studied....

The physics-based united-residue (UNRES) model of proteins (www.unres.pl) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations su...

Many proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental obs...

Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion...

We present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interface...

One of the possible applications of ionic liquids is to produce electricity from heat. The iron oxide nanoparticle is a potent electrical particle, which is expected to improve the heat's efficiency to electricity conversion, however, it is prone to aggregation and sedimentation, which hamper its application. One of the methods to enhance the nanop...

The UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-ass...

Motivation The majority of the proteins in living organisms occur as homo- or hetero-multimeric structures. While there are many tools to predict the structures of single-chain proteins or protein complexes with small ligands, peptide-protein and protein-protein docking is more challenging. In this work, we utilized multiplexed replica exchange MD...

The force-matching approach to coarse graining, in which the forces that act on site centers are fitted to the respective average forces computed from all-atom molecular dynamics simulations, provides a link between coarse-grained and all-atom molecular dynamics. In the existing implementations, radial site–site interaction potentials are assumed,...

The study provides a deep computational analysis of the thermodynamic and structural features associated with the hydration of xenon, Xe, and its pairwise hydrophobic interaction (i.e., the potential of mean force, PMF), over a large temperature range. Xe is described both as a Lennard-Jones particle, LJ-Xe, and as a Mie particle, Mie-Xe (pseudo ha...

The method for protein-structure prediction, which combines the physics-based coarse-grained UNRES force field with knowledge-based modeling, has been developed further and tested in the 13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP13). The method implements restraints from the consen...

In this chapter the scale-consistent approach to the derivation of coarse-grained force fields developed in our laboratory is presented, in which the effective energy function originates from the potential of mean force of the system under consideration and embeds atomistically detailed interactions in the resulting energy terms through use of Kubo...

We present the results for CAPRI Round 46, the third joint CASP‐CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo‐oligomers and 6 heterocomplexes. Eight of the homo‐oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank,...

We present the results for CAPRI Round 46, the 3rd joint CASP‐CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo‐oligomers and 6 hetero‐complexes. Eight of the homo‐oligomer targets and one hetero‐dimer comprised proteins that could be readily modeled using templates from the Protein Data Bank,...

Cysteine cathepsin C (CatC) is a ubiquitously expressed, lysosomal aminopeptidase involved in the activation of zymogens of immune-cell-associated serine proteinases (elastase, cathepsin G, proteinase 3, neutrophil serine proteinase 4, lymphocyte granzymes, and mast cell chymases). CatC is first synthetized as an inactive zymogen containing an intr...

With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance the accuracy of protein structure modeling. Here, we review the current state of the art in modeling protein structures with the assistance of experimentally determined chemic...

The physics-based UNRES coarse-grained force field for the simulations of protein structure and dynamics has been extended to treat membrane proteins. The lipid bilayer has been modeled by introducing a continuous nonpolar phase with the water-interface region of appropriate thickness. The potentials for average electrostatic and correlation intera...

The recent NEWCT-9P version of the coarse-grained UNRES force field for proteins, with scale-consistent formulas for the local and correlation terms, has been tested in the CASP13 experiment of the blind-prediction of protein structure, in the ab initio, contact-assisted, and data-assisted modes. Significant improvement of the performance has been...

The general theory of the construction of scale-consistent energy terms in the coarse-grained force fields presented in Paper I of this series has been applied to the revision of the UNRES force field for physics-based simulations of proteins. The potentials of mean force corresponding to backbone-local and backbone-correlation energy terms were ca...

The secondary structure of proteins results from both local and long-range interactions, the latter being primarily backbone hydrogen bonding. In this chapter, based on our recent work, we suggest that the striking regularity of secondary structure can be described, in a semi-analytical manner, in terms of Kubo cluster cumulants (corresponding to t...

Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort cal...

The Unified Coarse Grained Model of biological macromolecules (UCGM) that is being developed in our laboratory is a model designed to carry out large-scale simulations of biological macromolecules. The simplified chain representation used in the model allows to obtain 3-4 orders of magnitude extention of the time-scale of simulations, compared to t...

Knowledge-based methods are, at present, the most effective ones for the prediction of protein structures; however, their results heavily depend on the similarity of a target sequence to those of proteins with known structures. On the other hand, the physics-based methods, although still less accurate and more expensive to execute, are independent...

A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including...

Helicobacter pylori HP0377 is a thiol oxidoreductase, a member of the CcmG family involved in cytochrome biogenesis, as previously shown by in vitro experiments. In this report, we document that HP0377 also acts in vivo in the cytochrome assembly process in Bacillus subtilis, where it complements the lack of ResA. However, unlike other characterize...

A new approach to assisted protein-structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics simulations with the coarse-grained UNRES force field with restraints derived from knowledge-based models and distance distribution from small angle X-ray scattering (SAXS) measurements. The latter res...

Acid-base properties of 3-[2-(n-quinolinyl)benzoxazol-5-yl]alanine (n = 2,3,4,6,8 and 3-iso) were studied by means of absorption and fluorescence spectroscopy as well as theoretical calculations. It was found that basicity of heterocyclic derivatives in the ground and excited state depends on the position of the heteroatom in the substituent. Exper...

Molecular simulations restrained to single or multiple templates are commonly used in protein-structure modeling. However, the restraints introduce additional barriers, thus impairing the ergodicity of simulations, which can affect the quality of the resulting models. In this work, the effect of restraint types and simulation schemes on ergodicity...

Diphenylacetylene derivatives containing electron-donor (amino) and electron-acceptor (ester) groups in 2,2′ or 3,2′ positions in phenyl rings were synthesized to study the effects of intramolecular charge transfer and stiffening of the conformation by intramolecular hydrogen bond on the photophysical properties. Additionally, the derivatives with...

The p-xylylene monomers of parylene N, C and D have similar high polymerization reactivity. For effective copolymerization processes this fact is basically a drawback and for instance the copolymerization with styrene doesn’t go at all (Corley et al. J Pol Sc 13(68):137–156, [15]). Substitution of terminal hydrogen atoms by chlorine atoms reduces r...

Force fields are empirical energy functions that are designed to compute the properties of molecular systems at a relatively low cost, subject to the condition that there are no chemical changes in a system. A force field is a sum of various energy contributions which were developed and parameterized using small model systems. A long-sought goal in...

Ionic liquids (ILs) have attracted much attention for their unique physicochemical properties, which can be designed as needed by altering the ion combinations. Besides experimental work, numerous computational studies have been concerned with prediction of physical properties of ILs. The results of molecular dynamics simulations of ILs depend stro...

Recently, we developed a new approach to protein-structure prediction, which combines template-based modeling with the physics-based coarse-grained UNited RESidue (UNRES) force field. In this approach, restrained multiplexed replica exchange molecular dynamics (MREMD) simulations with UNRES, with the Cα-distance and virtual-bond-dihedral-angle rest...

Thurincin H is a small protein produced by Bacillus thuringiensis SF361 with gram-positive antimicrobial properties. The toxins produced by B. thuringiensis are widely used in the agriculture as, e.g., natural preservatives in dairy products. The structure of thurincin H possesses four covalent sulfur to α-carbon bonds that involve the cysteine sid...

Participating as the Cornell-Gdansk group, we have used our physics-based coarse-grained UNited RESidue (UNRES) force field to predict protein structure in the 11th Community Wide Exercise on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11). Our methodology involved extensive multiplexed replica exchange simulations o...

The 20S catalytic core of the human 26S proteasome can be secreted from cells, and high levels of extracellular 20S proteasome have been linked to many types of cancers and autoimmune diseases. Several diagnostic approaches have been developed that detect 20S proteasome activity in plasma, but these suffer from problems with efficiency and sensitiv...

Force fields are empirical energy functions that are designed to compute the properties of molecular systems at a relatively low cost, subject to the condition that there are no chemical changes in a system. A force field is a sum of various energy contributions which were developed and parameterized using small model systems. A long-sought goal in...

A series of symmetrically substituted diarylacetylenes and diaryl-1,3-butadiynes were prepared and studied with an emphasis on their spectral and photophysical properties. The photophysical characteristics of these compounds were studied in relation to their structures and the influence of solvent or temperature. The observed spectral and photophys...

A new approach to the calibration of the force fields is proposed, in which force-field parameters are obtained by maximum-likelihood fitting of the calculated conformational ensembles to the experimental ensembles of training system(s). The maximum-likelihood function is composed of logarithms of the Boltzmann probabilities of the experimental con...

A new approach to the prediction of protein structures, which uses distance- and backbone virtual-bond-dihedral-angle restraints derived from template-based models and simulations with the UNited RESidue (UNRES) force field, is proposed. The approach combines the accuracy and reliability of template-based methods for the segments of the target sequ...

A series of symmetrically substituted diphenylacetylene (DPA) derivatives possessing electron-donating (N,N-dimethylamino or metoxy) or electron-accepting (nitrile, ester or aldehyde) character have been prepared and studied with respect of their spectral and photophysical properties. The photophysical characteristic of these compounds have been st...

The 70 kDa Heat Shock Proteins (Hsp70) are a family of molecular chaperones involved in protein folding, aggregate prevention, and protein disaggregation. They consist of the substrate binding domain (SBD) that binds client substrates, and the nucleotide-binding domain (NBD), whose cycles of nucleotide hydrolysis and exchange underpin the activity...

Calibration is the final and critical stage of the design of the force fields for proteins and other biological macromolecules. For proteins, the usual goal of this procedure is to optimize the force-field parameters to reproduce the native structures of selected training proteins. However, the resulting force fields are usually not sufficiently pr...

The UNited RESidue (UNRES) model of polypeptide chains is a coarse-grained model in which each amino-acid residue is reduced to two interaction sites, namely a united peptide group (p) located halfway between the two neighboring α-carbon atoms (C(α)s), which serve only as geometrical points, and a united side chain (SC) attached to the respective C...

To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28WWdomain and six nonnatural variants,...

Pull–push molecules containing dimethylaniline and aromatic hydrocarbon linked by an acetylene unit were studied using spectroscopic methods and DFT theoretical calculations. Spectral and photophysical properties of N,N-dimethyl-4-(naphthalen-1-ylethynyl)aniline, N,N-dimethyl-4-(naphthalen-2-ylethynyl)aniline, 4-(athracen-9-ylethynyl)-N,N-dimethyla...

The present work theoretically investigates the mechanical properties of a novel silk-derived biopolymer as polymerized in-silico from sericin and elastin-like monomers. Molecular Dynamics simulations and Steered Molecular Dynamics were the principal computational methods employed, the latter of which applies an external force onto the system and t...

A unified coarse-grained model of three major classes of biological molecules—proteins, nucleic acids, and polysaccharides—has been developed. It is based on the observations that the repeated units of biopolymers (peptide groups, nucleic acid bases, sugar rings) are highly polar and their charge distributions can be represented crudely as point mu...

Even though most of the existing studies of gold nanoparticles indicate that they are safe to use, some researchers show that specific forms of nanoparticles (e.g. nanorods) are able to destroy the cell membrane and very small nanoparticles (below 37 nm in diameter) in high concentration have been deadly for mice. We used the Amber12 package to per...

The structures of the key classes of biological macromolecules: proteins, nucleic acids and polysaccharides can be dissected into very regular motifs, which are alpha-, beta, and double helices and sheets. In this communication we demonstrate that these regular patterns arise as a result of dipole-dipole interactions of the polar groups (peptide, n...

The UNited RESidue (UNRES) coarse-grained model of polypeptide chains, developed in our laboratory, enables us to carry out millisecond-scale molecular-dynamics simulations of large proteins effectively. It performs well in ab initio predictions of protein structure, as demonstrated in the last Community Wide Experiment on the Critical Assessment o...

Understanding the functioning of living cells requires knowledge of structure and long-time dynamics of proteins and other biological macromolecules, which information is not readily available from experiment. The development of distributed computing has opened new avenues for such studies. Further, reduction of the representation of polypeptide ch...

Significance With the example of the coarse-grained United Residue model of polypeptide chains, this paper demonstrates that the physics-based approach for protein-structure prediction can lead to exceptionally good results when correct domain packing is an issue, even for a highly homologous target. The reason for this is probably that emphasis is...

Acid–base properties of 3-[2-(2-pyridyl)benzoxazol-5-yl]alanine and 3-[2-(4-pyridyl)benzoxazol-5-yl]alanine as well as a model compound without heterocyclic substituent (3-[2-(4-methylphenyl)benzoxazol-5-yl]alanine) were studied by means of absorption and fluorescence spectroscopy as well as theoretical calculations. It was found that basicity of h...

In addition to wet laboratory experiments and theory, molecular simulations have emerged as the third methodology for studying molecular systems. Nowadays, they are indispensable for interpreting experimental results and understanding the molecular origin of biological processes. In this chapter, the techniques for simulating protein structure, dyn...

Molecular dynamics simulations in explicit water were carried out for two stacks, each composed of six 10-strand antiparallel β-sheets for two peptides corresponding to the diverging turn of two homologous Abl-SH3 domains. The first system, referred to as 10×6×MK contained the DLSFMKGE sequence from the Drosophila, while the second one, referred to...

Poly-para-xylylene based polymers, also known as parylenes, are polymers that can be deposited in thin film form at room temperature by chemical vapor deposition (CVD). In the CVD process the p-xylylene monomers obtained by pyrolysis of paracyclophane polymerize into long chain molecules. The initiation of polymerization requires dimerization of t...

Solvatochromic probes are often used in biophysical studies to obtain information about polarity of the microenvironment. As there is not much natural fluorophores with such properties, there is still need for new synthetic compounds such as 3-(2-benzoxazol-5-yl)alanine derivatives. Among this group of non-proteinogenic fluorescent amino acids espe...