Leandar Litov

Multigap RPC for PET: development and optimisation of the detector design

Transforming the resistive plate chambers from charged-particle into gamma-quanta detectors opens the way towards their application as a basic element of a hybrid imaging system, which combines positron emission tomography (PET) with magnetic resonance imaging (MRI) in a single device and provides non- and minimally- invasive quantitative methods for diagnostics. To this end, we performed detailed investigations encompassing the whole chain from the annihilation of the positron in the body, through the conversion of the created photons into electrons and to the optimization of the electron yield in the gas. GEANT4 based simulations of the efficiency of the RPC photon detectors with different converter materials and geometry were conducted for optimization of the detector design. The results justify the selection of a sandwich-type gas-insulator-converter design, with Bi or Pb as converter materials.

Computational study of solution behavior of magainin 2 monomers

Antimicrobial peptides (AMPs) play crucial role as mediators of the primary host defense against microbial invasion. They are considered a promising alternative to antibiotics for multidrug resistant bacterial strains. For complete understanding of the antimicrobial defense mechanism, a detailed knowledge of the dynamics of peptide-membrane interactions, including atomistic studies on AMPs geometry and both peptide and membrane structural changes during the whole process is a prerequisite. We aim at clarifying the conformation dynamics of small linear AMPs in solution as a first step of in silico protocol for establishing a correspondence between certain amino-acid sequence motifs, secondary-structure elements, conformational dynamics in solution and the intensity and mode of interaction with the bacterial membrane. To this end, we use molecular dynamics simulations augmented by well-tempered metadynamics to study the free-energy landscape of two AMPs with close primary structure and different antibacterial activity – the native magainin 2 (MG2) and an analog (MG2m, with substitutions F5Y and F16W) in aqueous solution. We observe that upon solvation, the initial α-helical structures change differently. The native form remains structured, with three shorter α-helical motifs, connected by random coils, while the synthetic analog tends predominantly to a disordered conformation. Our results indicate the importance of the side-chains at positions 5 and 16 for maintaining the solvated peptide conformation. They also provide a modeling background for recent experimental observations, relating the higher α-helical content in solution (peptide pre-folding) in the case of small linear AMPs to a lower antibacterial activity.

Are there folding pathways in the functional stages of intrinsically disordered proteins

We proceed from the description of protein folding by means of molecular dynamics (MD) simulations with all-atom force fields, with folding pathways interpreted in terms of soliton structures, to identify possible systematic dynamical patterns of self-organisation that govern protein folding process.We perform in silico investigations of the conformational transformations of three different proteins – MYC protein (an α-helical protein), amylin and indolicidin (IDPs with different length and binding dynamics). We discuss the emergence of soliton-mediated secondary motifs, in the case of IDPs – in the context of their functional activity. We hypothesize that soliton-like quasi-ordered conformations appear as an important intermediate stage in this process.

In Silico Studies on the Stability of Human Interferon-Gamma Mutants

ABSTRACT Human interferon-gamma (hIFNγ) is a key cytokine in the realisation of cellular immunity. It accomplishes its biological activity upon binding to a specific cell receptor thus inducing the JAK/STAT1 signal transduction pathway. Two putative NLS sequences were pointed out to assist in the translocation of STAT1 into the nucleus. In order to employ mutational analysis for study the biological significance of the polybasic sequence Lys86-Lys87-Lys88 belonging to the upstream putative NLS, hIFNγ mutants with preserved structure and intact binding affinity to cell receptor need to be selected. To this end in silico studies of molecular stability of hIFNγ mutants was performed. The potential conformational changes in the structure of the mutant proteins were investigated employing molecular dynamics simulations. The free energy surface of Lys86 backbone torsion angles space in hIFNγ wild type and mutants was analyzed using metadynamic model. The obtained in silico results were verified by construction of selected mutant recombinant hIFNy proteins, which were analysed for biological activity. To judge for the secondary structure of the mutants the affinity to the cell receptor was investigated. High correlation between results of the molecular dynamics simulations and biological data was obtained.

Computer simulations of human interferon gamma mutated forms

In the general framework of the computer‐aided drug design, the method of molecular‐dynamics simulations is applied for investigation of the human interferon‐gamma (hIFN‐γ) binding to its two known ligands (its extracellular receptor and the heparin‐derived oligosaccharides). A study of 100 mutated hIFN‐γ forms is presented, the mutations encompassing residues 86–88. The structural changes are investigated by comparing the lengths of the α‐helices, in which these residues are included, in the native hIFN‐γ molecule and in the mutated forms. The most intriguing cases are examined in detail.

Sampling in In Silico Biomolecular Studies: Single-Stage Experiments vs Multiscale Approaches

In silico studies of biological molecules face the problem of sampling quality due to the systems size (in atom numbers), the time scale of the investigated processes and the admissible computational time step. Advances in hardware alone are incapable of resolving this problem and the efforts are oriented towards sampling techniques enhancements, multilevel system representations and development of multistage and multiscale methods through synergistic protocols from complementary approaches. We combine a mean field approach with all atom molecular dynamics (MD), to develop a multistage algorithm that can model protein folding and dynamics over very long time periods with atomic-level precision. We compare the quality of conformation-space sampling for villin headpiece (PDB ID 2F4K) with a 125 \(\upmu \)s long folding simulation performed on the dedicated supercomputer ANTON.

Computational Modelling of the Full Length hIFN-\(\gamma \) Homodimer

Human interferon gamma (hIFN-\(\gamma \)) is an important signalling molecule, which plays a key role in the formation and modulation of immune response. The controversial conclusions concerning the function of hIFN-\(\gamma \) C-termini as well as the lack of structural information about this domain motivated us to perform molecular dynamics simulations in order to model the structure of the hIFN-\(\gamma \) C-terminal part. The simulations were carried out with the CHARMM22 force field, starting from a fully extended conformation of the C-termini. They showed unambiguously that the C-termini tend to approach the globular part of the protein, so that the whole hIFN-\(\gamma \) molecule adopts a more compact conformation. The energetic favourability of the more compact conformations of the whole cytokine was also confirmed by means of free energy perturbation simulations.

On the Use of Large Intel Xeon Phi Clusters for GEANT4-Based Simulations

Abstract GEANT4 is the basic software for fast and precise simulation of particle interactions with matter. Along the way towards enabling the execution of GEANT4 based simulations on hybrid High Performance Computing (HPC) architectures with large clusters of Intel Xeon Phi co-processors, we study the performance of this software suit on the supercomputer system Avitohol@BAS, Some practical scripts are collected in the supplementary material shown in the appendix.

His-FLAG Tag as a Fusion Partner of Glycosylated Human Interferon-Gamma and Its Mutant: Gain or Loss?

In order to obtain glycosylated human interferon-gamma (hIFNγ) and its highly prone to aggregation mutant K88Q, a secretory expression in insect cells was employed. To facilitate recombinant proteins purification, detection, and stability the baculovirus expression vectors were constructed to bear N-terminal His6-FLAG tag. Although the obtained proteins were glycosylated, we found that their biological activity was 100 times lower than expected. Our attempts to recover the biological properties of both proteins by tag removal failed due to enterokinase resistance of the tag. Surprisingly, the tag was easily cleaved when the proteins were expressed in E. coli cells and the tag-free proteins showed fully restored activity. To shed light on this phenomenon we performed molecular dynamics simulations. The latter showed that the tags interact with the receptor binding domains and the flexible C-termini of the fusion proteins thus suppressing their complex formation with the hIFNγ receptor. We hypothesize that in the case of glycosylated proteins the tag/C-terminal interaction positions the FLAG peptide in close proximity to the glycans thus sterically impeding the enterokinase access to its recognition site.

Molecular Dynamics Study of the Solution Behaviour of Antimicrobial Peptide Indolicidin

Understanding the mechanism of action of antimicrobial peptides (AMPs) on bacterial cells requires detailed knowledge of how AMPs interact with bacterial membranes. Our hypothesis is that the peptides do not interact with the membrane as monomers, but rather form clusters, that collectively approach the cell and attack the membrane. In this paper we investigate the behavior of the antimicrobial peptide indolicidin in solution, prior to their interaction with the bacterial membrane, by means of coarse grain molecular dynamics simulations (CG-MD). We show that indolicidin in particular and, probably, charged linear AMPs in general tend to aggregate in solution, forming globular amphipathic clusters with a central hydrophobic core. The dependence of the clusters size on the peptide concentration and on the temperature is studied, as well as the influence of the finite size of the simulation box. Our results manifest the investigation of the AMPs behavior in solution prior to membrane impact as an indispensable element in revealing the mechanism of their antimicrobial activity.