Introduction: Colorectal carcinoma is the third most common cancer worldwide. The usual immunophe... more Introduction: Colorectal carcinoma is the third most common cancer worldwide. The usual immunophenotype of colorectal adenocarcinoma is CDX2 positive, CK20 positive, and CK7 negative. Aberrant expression is reported in a variety of colorectal carcinomas but its relation to morphological variables and survival data is still unclear. Aim: The aim of this study was to investigate the correlation between the aberrant immunostaining of colorectal carcinoma and different clinicopathological characteristics. Materials and methods: Immunohistochemical expression of CK20, CK7, and CDX2 was evaluated in 71 cases of colorectal carcinoma. Statistical analysis was performed to identify correlations between the morphological characteristics and the immunoprofile of colorectal carcinoma. Results: Positive cytoplasmic and/or membranous signal for CK20 was observed in 66.2% of colorectal carcinomas. CK7 positive immunostaining was seen in 7% of the cases. In terms of combined expression of CK20 and ...
This Best Practice Guide provides information about Intel's Many Integrated Core (MIC) archit... more This Best Practice Guide provides information about Intel's Many Integrated Core (MIC) architecture and programming<br> models for the first generation Intel® Xeon Phi™ coprocessor named Knights Corner (KNC) in order<br> to enable programmers to achieve good performance out of their applications.<br> The guide covers a wide range of topics from the description of the hardware of the Intel® Xeon Phi™ coprocessor<br> through information about the basic programming models as well as information about porting programs up to<br> tools and strategies how to analyse and improve the performance of applications. Through the highly parallel architecture<br> and the use of high bandwidth memory, the MIC architecture allows higher performance than traditional<br> CPUs for many types of scientific applications. The guide was created based on the PRACE-3IP Intel® Xeon<br> Phi™ Best Practice Guide. New is the inclusion of information about applic...
Human interferon gamma is an important antiviral and im-munomodulating signaling molecule, which ... more Human interferon gamma is an important antiviral and im-munomodulating signaling molecule, which is also related to several au-toimmune deceases. The cytokine expresses its activity through a specicextracellular receptor, the Interferon gamma receptor. Understanding the process of ....
The increased emergence of antibiotic-resistant bacterial strains renders inefficient the existin... more The increased emergence of antibiotic-resistant bacterial strains renders inefficient the existing traditional antibiotics. The situation is enforced by a substantial decline in the development of new antibacterial agents. Therefore, in recent years considerable efforts are focused on the development of alternative therapies for the treatment of infectious diseases. The characteristics, the broad spectrum and largely nonspecific activity of the antimicrobial peptides (AMPs), qualify them as possible candidates for therapeutic alternatives and their potential against multi-drug resistant pathogen infections has attracted a lot of interest. AMPs come in nature in the form of multicomponent secretory fluids that exhibit certain biological activity. Additional complications arise when the studies are exploratory and probe desired interaction patterns at the stage of protein design, that is -- when the 3D structure of the peptide is not known, but only its amino acid sequence (primary st...
Human interferon gamma (hIFN-\(\gamma \)) is an important signalling molecule, which plays a key ... more 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.
The antimicrobial peptides (AMPs) are small water-soluble peptides, evolving from organisms of al... more The antimicrobial peptides (AMPs) are small water-soluble peptides, evolving from organisms of all types. Because of cytolytic abilities they are in position to kill a variety of bacteria and other cells. The AMPs mode of action includes a stage of association with the cell border structures bacterial envelope (wall and membranes) and penetration through them. Many peptides are prone to conformational changes depending on the environmental conditions and characteristics of protein folding and denaturation, in general and specifically concerning AMPs, are intriguing in no lesser extent. Undoubtedly, any perturbation in AMPs 3D structure will be reflected in their interaction with the membrane. Magainins are good example in this regard, because it is still not absolutely clear what is the exact secondary structure of magainins before accessing the membrane surface and how this structure is responsible for their action. For this reason, we investigated the secondary structure stability...
Problems in model studies of biological molecules and complexes result from the size of the syste... more Problems in model studies of biological molecules and complexes result from the size of the systems on the one hand (a large number of elements -- atoms or atomic complexes in the picometer range) and the time scale of the running processes-- from femtoseconds to hours and even days – on the other. Due to the nature of interactions in which biomolecules are involved (short as well as long-range interactions), simply increasing the computing power of modern supercomputers is not enough to solve them. Efforts are concentrated on the development of enhanced phase-space sampling methods or alternative (coarse-grained in one sense or another) representations of the studied systems, but foremost on expanding the boundaries of the existing modeling techniques through synergetic protocols of complementary approaches. The aim is to create multilevel multi-scale approaches to understanding biomolecular structure and dynamics ...
The key actors in the cell-cell interactions of the adaptive immune response are the major histoc... more The key actors in the cell-cell interactions of the adaptive immune response are the major histocompatibility complex (MHC) molecule and the T cell antigen receptor (TCR). The former (in humans also known as human leukocyte antigen - HLA) is found on antigen presenting cells and serves as extraction tool to bring antigens in the intercellular space for recognition by the T cells through the TCR. T cells are selected for recognition of certain pMHC complexes, but often alloreact with foreign HLA, presenting different allopeptides, sometimes subject to extensive polymorphism and with disparate peptide sequences. Understanding mechanisms behind this phenomenon is of great theoretical and practical importance. We study two MHC molecules with a single-aminioacid polymorphism to the original (alloreactive) complex (LC13 TCR in complex with HLA B*4405 bound to EEYLQAFTY - a self peptide from the ABCD3 protein) and significantly different binding affinities, resp. immunogenicity, in the co...
A protein is commonly visualised as a discrete piecewise linear curve, its backbone geometry bein... more A protein is commonly visualised as a discrete piecewise linear curve, its backbone geometry being characterised in terms of the extrinsically determined Ramachandran angles. However, in addition to the extrinsic geometry, the protein backbone has also two independent intrinsic geometric structures determined by the peptide planes, and the side chains and their relative orientations. We develop a novel methodology for analysis and 3D visualisation of protein structure, based on the construction of a series of orthonormal coordinate frames, along the protein side chains, and mapping the atoms positions onto a unit sphere. Thus, we obtain a consistent picture of side-chain covalent bonds spatial orientations, though from a different perspective --- that of an observer, who climbs up the side chains from one carbon atom to the next. We validate the method by studying the distribution of distal and proximal histidine, as well as of valine in the molecule of myoglobinin, on a statistical...
Antimicrobial peptides (AMPs) are an abundant and diverse group of molecules produced by many tis... more Antimicrobial peptides (AMPs) are an abundant and diverse group of molecules produced by many tissues and cell types in a variety of invertebrate, plant and animal species in contact with infectious microorganisms. They play a crucial role as mediators of the primary host defense against microbial invasion. The characteristics, the broad spectrum and largely nonspecific activity of the antimicrobial peptides qualify them as possible candidates for therapeutic alternatives against multi-resistant bacterial strains.
A protein is traditionally visualised as a piecewise linear discrete curve, and its geometry is c... more A protein is traditionally visualised as a piecewise linear discrete curve, and its geometry is conventionally characterised by the extrinsically determined Ramachandran angles. However, a protein backbone has also two independent intrinsic geometric structures, due to the peptide planes and the side chains. Here we adapt and develop modern 3D virtual reality techniques to scrutinize the atomic geometry along a protein backbone, in the vicinity of a peptide plane. For this we compare backbone geometry-based (extrinsic) and structure-based (intrinsic) coordinate systems, and as an example we inspect the trans and cis peptide planes. We reveal systematics in the way how a cis peptide plane deforms the neighbouring atomic geometry, and we develop a virtual reality based visual methodology that can identify the presence of a cis peptide plane from the arrangement of atoms in its vicinity. Our approach can easily detect exceptionally placed atoms in crystallographic structures. Thus it c...
In silico studies of biological molecules face the problem of sampling quality due to the systems... more 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.
Our objective is to reveal the molecular mechanism of the anti-inflammatory action of low-molecul... more Our objective is to reveal the molecular mechanism of the anti-inflammatory action of low-molecular-weight heparin (LMWH) based on its influence on the activity of two key cytokines, IFNγ and IL-6. The mechanism of heparin binding to IFNγ and IL-6 and the resulting inhibition of their activity were studied by means of extensive molecular-dynamics simulations. The effect of LMWH on IFNγ signalling inside stimulated WISH cells was investigated by measuring its antiproliferative activity and the translocation of phosphorylated STAT1 in the nucleus. We found that LMWH binds with high affinity to IFNγ and is able to fully inhibit the interaction with its cellular receptor. It also influences the biological activity of IL-6 by binding to either IL-6 or IL-6/IL-6Rα, thus preventing the formation of the IL-6/IL-6Rα/gp130 signalling complex. These findings shed light on the molecular mechanism of the anti-inflammatory action of LMWH and underpin its ability to influence favourably conditions...
GEANT4 is the basic software for fast and precise simulation of particle interactions with matter... more 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.
ABSTRACTTimely control of the cytokine release syndrome (CRS) at the severe stage of COVID-19 is ... more ABSTRACTTimely control of the cytokine release syndrome (CRS) at the severe stage of COVID-19 is key to improving the treatment success and reducing the mortality rate. The inhibition of the activity of the two key cytokines, IFNγ and IL-6, can significantly reduce or even reverse the development of the cytokine storm. The objective of our investigations is to reveal the anti-inflammatory potential of heparin for prevention and suppression of the development of CRS in acute COVID-19 patients.The effect of low-molecular-weight heparin (LMWH) on IFNγ signalling inside the stimulated WISH cells was investigated by measuring its antiproliferative activity and the translocation of phosphorylated STAT1 in the nucleus. The mechanism of heparin binding to IFNγ and IL-6 and therefore inhibition of their activity was studied by means of extensive molecular-dynamics simulations. We find that LMWH binds with high affinity to IFNγ and is able to inhibit fully the interaction with its cellular re...
Introduction: Colorectal carcinoma is the third most common cancer worldwide. The usual immunophe... more Introduction: Colorectal carcinoma is the third most common cancer worldwide. The usual immunophenotype of colorectal adenocarcinoma is CDX2 positive, CK20 positive, and CK7 negative. Aberrant expression is reported in a variety of colorectal carcinomas but its relation to morphological variables and survival data is still unclear. Aim: The aim of this study was to investigate the correlation between the aberrant immunostaining of colorectal carcinoma and different clinicopathological characteristics. Materials and methods: Immunohistochemical expression of CK20, CK7, and CDX2 was evaluated in 71 cases of colorectal carcinoma. Statistical analysis was performed to identify correlations between the morphological characteristics and the immunoprofile of colorectal carcinoma. Results: Positive cytoplasmic and/or membranous signal for CK20 was observed in 66.2% of colorectal carcinomas. CK7 positive immunostaining was seen in 7% of the cases. In terms of combined expression of CK20 and ...
This Best Practice Guide provides information about Intel's Many Integrated Core (MIC) archit... more This Best Practice Guide provides information about Intel's Many Integrated Core (MIC) architecture and programming<br> models for the first generation Intel® Xeon Phi™ coprocessor named Knights Corner (KNC) in order<br> to enable programmers to achieve good performance out of their applications.<br> The guide covers a wide range of topics from the description of the hardware of the Intel® Xeon Phi™ coprocessor<br> through information about the basic programming models as well as information about porting programs up to<br> tools and strategies how to analyse and improve the performance of applications. Through the highly parallel architecture<br> and the use of high bandwidth memory, the MIC architecture allows higher performance than traditional<br> CPUs for many types of scientific applications. The guide was created based on the PRACE-3IP Intel® Xeon<br> Phi™ Best Practice Guide. New is the inclusion of information about applic...
Human interferon gamma is an important antiviral and im-munomodulating signaling molecule, which ... more Human interferon gamma is an important antiviral and im-munomodulating signaling molecule, which is also related to several au-toimmune deceases. The cytokine expresses its activity through a specicextracellular receptor, the Interferon gamma receptor. Understanding the process of ....
The increased emergence of antibiotic-resistant bacterial strains renders inefficient the existin... more The increased emergence of antibiotic-resistant bacterial strains renders inefficient the existing traditional antibiotics. The situation is enforced by a substantial decline in the development of new antibacterial agents. Therefore, in recent years considerable efforts are focused on the development of alternative therapies for the treatment of infectious diseases. The characteristics, the broad spectrum and largely nonspecific activity of the antimicrobial peptides (AMPs), qualify them as possible candidates for therapeutic alternatives and their potential against multi-drug resistant pathogen infections has attracted a lot of interest. AMPs come in nature in the form of multicomponent secretory fluids that exhibit certain biological activity. Additional complications arise when the studies are exploratory and probe desired interaction patterns at the stage of protein design, that is -- when the 3D structure of the peptide is not known, but only its amino acid sequence (primary st...
Human interferon gamma (hIFN-\(\gamma \)) is an important signalling molecule, which plays a key ... more 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.
The antimicrobial peptides (AMPs) are small water-soluble peptides, evolving from organisms of al... more The antimicrobial peptides (AMPs) are small water-soluble peptides, evolving from organisms of all types. Because of cytolytic abilities they are in position to kill a variety of bacteria and other cells. The AMPs mode of action includes a stage of association with the cell border structures bacterial envelope (wall and membranes) and penetration through them. Many peptides are prone to conformational changes depending on the environmental conditions and characteristics of protein folding and denaturation, in general and specifically concerning AMPs, are intriguing in no lesser extent. Undoubtedly, any perturbation in AMPs 3D structure will be reflected in their interaction with the membrane. Magainins are good example in this regard, because it is still not absolutely clear what is the exact secondary structure of magainins before accessing the membrane surface and how this structure is responsible for their action. For this reason, we investigated the secondary structure stability...
Problems in model studies of biological molecules and complexes result from the size of the syste... more Problems in model studies of biological molecules and complexes result from the size of the systems on the one hand (a large number of elements -- atoms or atomic complexes in the picometer range) and the time scale of the running processes-- from femtoseconds to hours and even days – on the other. Due to the nature of interactions in which biomolecules are involved (short as well as long-range interactions), simply increasing the computing power of modern supercomputers is not enough to solve them. Efforts are concentrated on the development of enhanced phase-space sampling methods or alternative (coarse-grained in one sense or another) representations of the studied systems, but foremost on expanding the boundaries of the existing modeling techniques through synergetic protocols of complementary approaches. The aim is to create multilevel multi-scale approaches to understanding biomolecular structure and dynamics ...
The key actors in the cell-cell interactions of the adaptive immune response are the major histoc... more The key actors in the cell-cell interactions of the adaptive immune response are the major histocompatibility complex (MHC) molecule and the T cell antigen receptor (TCR). The former (in humans also known as human leukocyte antigen - HLA) is found on antigen presenting cells and serves as extraction tool to bring antigens in the intercellular space for recognition by the T cells through the TCR. T cells are selected for recognition of certain pMHC complexes, but often alloreact with foreign HLA, presenting different allopeptides, sometimes subject to extensive polymorphism and with disparate peptide sequences. Understanding mechanisms behind this phenomenon is of great theoretical and practical importance. We study two MHC molecules with a single-aminioacid polymorphism to the original (alloreactive) complex (LC13 TCR in complex with HLA B*4405 bound to EEYLQAFTY - a self peptide from the ABCD3 protein) and significantly different binding affinities, resp. immunogenicity, in the co...
A protein is commonly visualised as a discrete piecewise linear curve, its backbone geometry bein... more A protein is commonly visualised as a discrete piecewise linear curve, its backbone geometry being characterised in terms of the extrinsically determined Ramachandran angles. However, in addition to the extrinsic geometry, the protein backbone has also two independent intrinsic geometric structures determined by the peptide planes, and the side chains and their relative orientations. We develop a novel methodology for analysis and 3D visualisation of protein structure, based on the construction of a series of orthonormal coordinate frames, along the protein side chains, and mapping the atoms positions onto a unit sphere. Thus, we obtain a consistent picture of side-chain covalent bonds spatial orientations, though from a different perspective --- that of an observer, who climbs up the side chains from one carbon atom to the next. We validate the method by studying the distribution of distal and proximal histidine, as well as of valine in the molecule of myoglobinin, on a statistical...
Antimicrobial peptides (AMPs) are an abundant and diverse group of molecules produced by many tis... more Antimicrobial peptides (AMPs) are an abundant and diverse group of molecules produced by many tissues and cell types in a variety of invertebrate, plant and animal species in contact with infectious microorganisms. They play a crucial role as mediators of the primary host defense against microbial invasion. The characteristics, the broad spectrum and largely nonspecific activity of the antimicrobial peptides qualify them as possible candidates for therapeutic alternatives against multi-resistant bacterial strains.
A protein is traditionally visualised as a piecewise linear discrete curve, and its geometry is c... more A protein is traditionally visualised as a piecewise linear discrete curve, and its geometry is conventionally characterised by the extrinsically determined Ramachandran angles. However, a protein backbone has also two independent intrinsic geometric structures, due to the peptide planes and the side chains. Here we adapt and develop modern 3D virtual reality techniques to scrutinize the atomic geometry along a protein backbone, in the vicinity of a peptide plane. For this we compare backbone geometry-based (extrinsic) and structure-based (intrinsic) coordinate systems, and as an example we inspect the trans and cis peptide planes. We reveal systematics in the way how a cis peptide plane deforms the neighbouring atomic geometry, and we develop a virtual reality based visual methodology that can identify the presence of a cis peptide plane from the arrangement of atoms in its vicinity. Our approach can easily detect exceptionally placed atoms in crystallographic structures. Thus it c...
In silico studies of biological molecules face the problem of sampling quality due to the systems... more 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.
Our objective is to reveal the molecular mechanism of the anti-inflammatory action of low-molecul... more Our objective is to reveal the molecular mechanism of the anti-inflammatory action of low-molecular-weight heparin (LMWH) based on its influence on the activity of two key cytokines, IFNγ and IL-6. The mechanism of heparin binding to IFNγ and IL-6 and the resulting inhibition of their activity were studied by means of extensive molecular-dynamics simulations. The effect of LMWH on IFNγ signalling inside stimulated WISH cells was investigated by measuring its antiproliferative activity and the translocation of phosphorylated STAT1 in the nucleus. We found that LMWH binds with high affinity to IFNγ and is able to fully inhibit the interaction with its cellular receptor. It also influences the biological activity of IL-6 by binding to either IL-6 or IL-6/IL-6Rα, thus preventing the formation of the IL-6/IL-6Rα/gp130 signalling complex. These findings shed light on the molecular mechanism of the anti-inflammatory action of LMWH and underpin its ability to influence favourably conditions...
GEANT4 is the basic software for fast and precise simulation of particle interactions with matter... more 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.
ABSTRACTTimely control of the cytokine release syndrome (CRS) at the severe stage of COVID-19 is ... more ABSTRACTTimely control of the cytokine release syndrome (CRS) at the severe stage of COVID-19 is key to improving the treatment success and reducing the mortality rate. The inhibition of the activity of the two key cytokines, IFNγ and IL-6, can significantly reduce or even reverse the development of the cytokine storm. The objective of our investigations is to reveal the anti-inflammatory potential of heparin for prevention and suppression of the development of CRS in acute COVID-19 patients.The effect of low-molecular-weight heparin (LMWH) on IFNγ signalling inside the stimulated WISH cells was investigated by measuring its antiproliferative activity and the translocation of phosphorylated STAT1 in the nucleus. The mechanism of heparin binding to IFNγ and IL-6 and therefore inhibition of their activity was studied by means of extensive molecular-dynamics simulations. We find that LMWH binds with high affinity to IFNγ and is able to inhibit fully the interaction with its cellular re...
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Papers by Nevena Litova