Změnit instituci
Pokročilé nano a mikrotechnologie Pokročilé materiály Strukturní biologie Gen. a prot. rostlin. systémů Molekulární medicína Výzkum mozku a lidské mysli Molekulární vet. medicína

Výzkumná skupina Jaroslava Koči

Vedoucí výzkumné skupiny
Researcher ID
Telefon: +420 54949 4947, +420 54949 2685, +420 54949 2685

Research areas

  • Structure and dynamics of proteins, nucleic acids, saccharides, and their complexes in relationship to their biological function
  • Mechanistic studies on enzymatic reactions
  • Chemoinformatics and structural bioinformatics
  • Structure and dynamics of supramolecular complexes

Main objectives

  • To study the therapeutical and bioanalytical aspects of recognition and adhesion phenomena in host-pathogen interactions
  • To develop new methodologies for investigating the structure, interactions, and dynamics of biomolecules
  • New tools for structural bioinformatics and chemoinformatics
  • Development of soft matter models and understanding of self-assembled  bimolecular systems

Content of research

Computational chemistry helps to interpret experimental observations or to get a new information about systems where experimental approaches are not applicable or difficult to apply. It is widely employed in, for example, design and studies on new molecules with a possible biological impact.

Structure and Dynamics of Biomolecules

rsl_i_smallWe use a wide spectrum of state-of-the-art computational techniques to study structure and dynamics of short peptides, proteins, enzymes, and short nucleic fragments. Our main attempt is to understand how these biomolecules are assembled in space and how their structure is related to their function. We use a molecular docking to predict unknown structures of complexes between proteins and small molecules. Interactions are studied by several approaches ranging from very precise quantum chemical calculations to methods employing molecular mechanics.

Enzymatic Reactions

muth_active_site_white_smallThe understanding of reaction mechanisms is essential step in rational design of enzyme inhibitors that might act as drugs. We employ hybrid quantum mechanics (QM) / molecular mechanics (MM) approach to find the most probable reaction pathways. Various techniques to explore complicated potential (free) energy surfaces are used. They range from single/double coordinate energy scans to advanced techniques employing free energy calculations and Car-Parrinello dynamics. Developed techniques are used to study nucleases, glycotransferases and glycohydrolase enzymes.

Supramolecular Chemistry

rotax_smallStructure, stability and reactivity of supramolecular systems are studied by molecular modeling techniques, including both quantum and molecular mechanics approaches. Key molecules in our projects are glycoluril oligomers such as cucurbit[n]urils and bambus[n]urils. We study their interactions with various organic and inorganic guests. Our main attention is focused on reliable description of forces leading to complex assembly, which might be used in rational host modifications providing desired properties.

Coarse Grained Simulations

cg_pathw28We study cellular uptake of nanoparticles and virus capsids. These processes are crucial for drug delivery, toxicity, and nanomedicine. We investigate conditions of passive endocytosis of ligand-coated particles of various sizes, shapes, and coverage across a zero-tension, receptor-rich, phospholipid membrane. We also develop new coarse grained models for studying self-assembly of rod like molecules (peptides, carbon nanotubes, etc.). Using these models we determine crucial parameters that lead to different aggregated morphologies including barrels, fibrils, ribbons, bilayers and other oligomers.

Chemoinformatics and Structural Bioinformatics

chibi_heigh171Nowadays, a large amount of information about biomolecules (i.e. sequence of DNA, structure of proteins) and about small molecules (drug-like molecules, ligands, etc.) is available. Main goal of bioinformatics and chemoinformatics research is a processing of these data, which can provide information very useful in pharmacy, medicine, biotechnology etc. Our laboratory is focusing on advanced analyses of protein 3D structures, processing data from next generation sequencing and predicting of physico-chemical properties of organic molecules.



Computational studies of protein-carbohydrate interactions

  • Prediction of ligand position by molecular docking
  • Molecular dynamics simulations, methods for binding free energy prediction
  • High throughput virtual screening for lectin inhibitor design
  • High level QM methods to quantify the role of dispersion energy and CH-π interactions
  • In silico protein engineering of lectin mutants with improved affinity/selectivity
  • Thermodynamic integration and other methods for binding free energy prediction

QM/MM studies of reaction mechanisms of endonucleases and glycosyltransferases

  • QM/MM methods to study reaction mechanism of glycosyltransferases
  • QM/MM methods to study reaction mechanisms of endonucleases
  • Free energy calculations to identify reaction pathways in enzymatic reactions of endonucleases
  • Reactive force-field molecular dynamics to study reaction mechanism of glycosyltransferases

Supramolecular chemistry of cucurbiturils and bambusurils

  • Free energy calculations based on potential of mean force methods to reproduce results from experimental NMR studies

Coarse grained simulations

  • Assembly of peptides in solution
  • Interaction of peptides with membranes
  • Interaction of nanopartticles with membranes

Cheminformatics and structural bioinformatics

  • Empirical methods for fast calculation of partial atomic charges
  • Development of pKa predicting QSPR models based on atomic charges
  • Finding, comparing and characterization of protein structural motifs

Software development

seznam / vizitky

Jméno a pozice



prof. RNDr. Jaroslav Koča, DrSc.
Vědecký ředitel
+420 54949 4947, +420 54949 2685, +420 54949 2685
RNDr. Petr Kulhánek, Ph.D.
Výzkumný pracovník
+420 54949 5459
doc. RNDr. Radka Svobodová Vařeková, Ph.D.
Výzkumný pracovník
+420 54949 4860
Mgr. Stanislav Kozmon, Ph.D.
Výzkumný pracovník - postdoc
+420 54949 5108
RNDr. Lukáš Pravda
PhD student
+420 54949 6568
RNDr. Stanislav Geidl
PhD student
+420 54949 2521
Mgr. Ivo Kabelka
PhD student
+420 54949 2524
Mgr. Miroslav Jurásek
PhD student
+420 54949 2524
Ing. Ondřej Hradil
Koordinátor výzkumné infrastruktury
+420 776 253 638, +420 54949 3918
Mgr. Ing. Crina-Maria Ionescu, Ph.D.
Výzkumný pracovník - postdoc
+420 54949 6384
Mgr. Martin Prokop, Ph.D.
Výzkumný pracovník
+420 54949 6662
Mgr. Zuzana Novotná Jiroušková
PhD student
RNDr. Tomáš Raček
PhD student
+420 54949 2521
RNDr. David Sehnal, Ph.D.
PhD student
+420 54949 8127
Mgr. Bc. Lukáš Sukeník
PhD student
+420 54949 2524
Mgr. Jakub Štěpán
PhD student
+420 54949 2446
Ing. Tomáš Trnka
PhD student
+420 54949 2524
Deepti Mishra, Ph.D.
Výzkumný pracovník - postdoc
+420 54949 6011
Francesco Luca Falginella
PhD student
+420 54949 8140
prof. MVDr. RNDr. Petr Hořín, CSc.
Mgr. Jan Oppelt
PhD student
+420 54949 8964
Mgr. Veronika Bendová
RNDr. Josef Bodor, CSc.
Mgr. Tomáš Bouchal
PhD student
+420 54949 6568
Mgr. Václav Hejret
Mgr. Vladimír Horský
PhD student
+420 54949 2521
Mgr. Zdeněk Kříž, Ph.D.
Výzkumný pracovník
+420 54949 5343
Mgr. Radek Matuška
PhD student
Mgr. et Mgr. Adam Midlik
doc. RNDr. Karel Berka, Ph.D.
Tarakaramji Moturu
PhD student
Mgr. Veronika Navrátilová
Bc. Ondřej Balcárek
Ravi José Tristao Ramos
Mgr. Pavel Janoš
PhD student
+420 54949 2524
Ing. Jan Hutař


Skupina Výpočetní chemie (rok 2014).



  • BERKA, K; SEHNAL, D; BAZGIER, V; PRAVDA, L; SVOBODOVA-VAREKOVA, R; OTYEPKA, M; KOCA, J, 2017:Mole 2.5-Tool for Detection and Analysis of Macromolecular Pores and Channels. BIOPHYSICAL JOURNAL 112 (3), p. 292A - 293A.
  • PRAVDA, L; SEHNAL, D; VAREKOVA, RS; KOCA, J, 2017:Effective on-Demand Mining of Structural Databases. BIOPHYSICAL JOURNAL 112 (3), p. 348A - 348A.
  • VAREKOVA, RS; HORSKY, V; SEHNAL, D; BENDOVA, V; PRAVDA, L; KOCA, J, 2017:Quo Vadis, Biomacromolecular Structure Quality. BIOPHYSICAL JOURNAL 112 (3), p. 346A - 347A.


  • AMARO, M; SACHL, R; AYDOGAN, G; MIKHALYOV, I; VACHA, R; HOF, M, 2016:The role of ganglioside GM1 and sphingomyelin in the oligomerisation of beta-amyloid at physiological conditions: a single molecule study. FEBS JOURNAL 283 , p. 71 - 71.
  • AMARO, M; SACHL, R; AYDOGAN, G; MIKHALYOV, II; VACHA, R; HOF, M, 2016:GM(1) Ganglioside Inhibits beta-Amyloid Oligomerization Induced by Sphingomyelin. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 55 (32), p. 9411 - 9415.
  • BRANNA, P; CERNOCHOVA, J; ROUCHAL, M; KULHANEK, P; BABINSKY, M; MAREK, R; NECAS, M; KURITKA, I; VICHA, R, 2016:Cooperative Binding of Cucurbit[n]urils and beta-Cyclodextrin to Heteroditopic Imidazolium-Based Guests. JOURNAL OF ORGANIC CHEMISTRY 81 (20), p. 9595 - 9604.
  • JANOS, P; TRNKA, T; KOZMON, S; TVAROSKA, I; KOCA, J, 2016:Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12 (12), p. 6062 - 6076.
  • MIKULASEK, K; JARON, KS; KULHANEK, P; BITTOVA, M; HAVLIS, J, 2016:Sequence-dependent separation of trinucleotides by ion-interaction reversed-phase liquid chromatography A structure-retention study assisted by soft-modelling and molecular dynamics. JOURNAL OF CHROMATOGRAPHY A 1469 , p. 88 - 95.
  • PHULWALE, BV; MISHRA, SK; NECAS, M; MAZAL, C, 2016:Phenanthrylene-butadiynylene and Phenanthrylene-thienylene Macrocycles: Synthesis, Structure, and Properties. JOURNAL OF ORGANIC CHEMISTRY 81 (15), p. 6244 - 6252.
  • RACEK, T; PAZURIKOVA, J; VAREKOVA, RS; GEIDL, S; KRENEK, A; FALGINELLA, FL; HORSKY, V; HEJRET, V; KOCA, J, 2016:NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. JOURNAL OF CHEMINFORMATICS 8


  • GEIDL, S; BOUCHAL, T; RAČEK, T; SVOBODOVA VAREKOVA, R; HEJRET, V; KŘENEK, A; ABAGYAN, R; KOČA, J, 2015:High-quality and universal empirical atomic charges for chemoinformatics applications. JOURNAL OF CHEMINFORMATICS 7
  • GEIDL, S; VAREKOVA, RS; BENDOVA, V; PETRUSEK, L; IONESCU, CM; JURKA, Z; ABAGYAN, R; KOCA, J, 2015:How Does the Methodology of 3D Structure Preparation Influence the Quality of pK(a) Prediction?. JOURNAL OF CHEMICAL INFORMATION AND MODELING 55 (6), p. 1088 - 1097.
  • IONESCU, CM; SEHNAL, D; FALGINELLA, FL; PANT, P; PRAVDA, L; BOUCHAL, T; VAREKOVA, RS; GEIDL, S; KOCA, J, 2015:AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. JOURNAL OF CHEMINFORMATICS 7
  • ISLAM, B; STADLBAUER, P; KREPL, M; KOCA, J; NEIDLE, S; HAIDER, S; SPONER, J, 2015:Extended molecular dynamics of a c-kit promoter quadruplex. NUCLEIC ACIDS RESEARCH 43 (18), p. 8673 - 8693.
  • KABELKA, I; VACHA, R, 2015:Optimal conditions for opening of membrane pore by amphiphilic peptides. THE JOURNAL OF CHEMICAL PHYSICS 143 (24), p. 243115 - .
  • KOZMON, S; TVAROSKA, I, 2015:Molecular dynamic studies of amyloid-beta interactions with curcumin and Cu2+ ions. CHEMICAL PAPERS 69 (9), p. 1262 - 1276.
  • KUMARI, M; KOZMON, S; KUHANEK, P; STEPAN, J; TVAROSKA, I; KOCA, J, 2015:Exploring Reaction Pathways for O-GlcNAc Transferase Catalysis. A String Method Study. JOURNAL OF PHYSICAL CHEMISTRY B 119 (12), p. 4371 - 4381.
  • MISHRA, SK; CALABRO, G; LOEFFLER, HH; MICHEL, J; KOCA, J, 2015:Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11 (7), p. 3333 - 3345.
  • SEHNAL, D; VAREKOVA, RS; PRAVDA, L; IONESCU, CM; GEIDL, S; HORSKY, V; JAISWAL, D; WIMMEROVA, M; KOCA, J, 2015:ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. NUCLEIC ACIDS RESEARCH 43 (D1), p. D369 - D375.
  • SCHUBERTOVA, V; MARTINEZ-VERACOECHEA, FJ; VACHA, R, 2015:Influence of ligand distribution on uptake efficiency. SOFT MATTER 11 (14), p. 2726 - 2730.
  • STADLBAUER, P; KUHROVA, P; BANAS, P; KOCA, J; BUSSI, G; TRANTIREK, L; OTYEPKA, M; SPONER, J, 2015:Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. NUCLEIC ACIDS RESEARCH 43 (20), p. 9626 - 9644.
  • TRNKA, T; KOZMON, S; TVAROSKA, I; KOCA, J, 2015:Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2. PLOS COMPUTATIONAL BIOLOGY 11 (4)


  • GKIONIS, K; KRUSE, H; PLATTS, JA; MLADEK, A; KOCA, J; SPONER, J, 2014:Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 10 (3), p. 1326 - 1340.
  • KRIZ, Z; ADAM, J; MRAZKOVA, J; ZOTOS, P; CHATZIPAVLOU, T; WIMMEROVA, M; KOCA, J, 2014:Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 28 (9), p. 951 - 960.
  • NOVOTNY, J; YURENKO, YP; KULHANEK, P; MAREK, R, 2014:Tailoring the properties of quadruplex nucleobases for biological and nanomaterial applications. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 16 (29), p. 15241 - 15248.
  • VACHA, R; FRENKEL, D, 2014:Simulations Suggest Possible Novel Membrane Pore Structure. LANGMUIR 30 (5), p. 1304 - 1310.
  • VACHA, R; FRENKEL, D, 2014:Stability of Bicelles: A Simulation Study. LANGMUIR 30 (15), p. 4229 - 4235.
  • VACHA, R; LINSE, S; LUND, M, 2014:Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 136 (33), p. 11776 - 11782.


  • IONESCU, CM; GEIDL, S; VAREKOVA, RS; KOCA, J, 2013:Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. JOURNAL OF CHEMICAL INFORMATION AND MODELING 53 (10), p. 2548 - 2558.
  • KRIZ, Z; KLUSAK, J; KRISTOFIKOVA, Z; KOCA, J, 2013:How Ionic Strength Affects the Conformational Behavior of Human and Rat Beta Amyloids - A Computational Study. PLOS ONE 8 (5)
  • SEHNAL, D; VAREKOVAA, RS; BERKA, K; PRAVDA, L; NAVRATILOVA, V; BANAS, P; IONESCU, CM; OTYEPKA, M; KOCA, J, 2013:MOLE 2.0: advanced approach for analysis of biomacromolecular channels. JOURNAL OF CHEMINFORMATICS 5
  • SHI, QX; BERGQUIST, KE; HUO, RP; LI, JL; LUND, M; VACHA, R; SUNDIN, A; BUTKUS, E; ORENTAS, E; WARNMARK, K, 2013:Composition- and Size-Controlled Cyclic Self-Assembly by Solvent- and C-60-Responsive Self-Sorting. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 135 (40), p. 15263 - 15268.
  • STADLBAUER, P; KREPL, M; CHEATHAM, TE; KOCA, J; SPONER, J, 2013:Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. NUCLEIC ACIDS RESEARCH 41 (14), p. 7128 - 7143.
  • STANDARA, S; KULHANEK, P; MAREK, R; STRAKA, M, 2013:Xe-129 NMR chemical shift in Xe@C-60 calculated at experimental conditions: Essential role of the relativity, dynamics, and explicit solvent. JOURNAL OF COMPUTATIONAL CHEMISTRY 34 (22), p. 1890 - 1898.
  • VORACOVA, I; VANEK, J; PASULKA, J; STRELCOVA, Z; LUBAL, P; HERMANN, P, 2013:Dissociation kinetics study of copper(II) complexes of DO3A, DOTA and its monosubstituted derivatives. POLYHEDRON 61 , p. 99 - 104.


  • CERNOCHOVA, J; BRANNA, P; ROUCHAL, M; KULHANEK, P; KURITKA, I; VICHA, R, 2012:Determination of Intrinsic Binding Modes by Mass Spectrometry: Gas-Phase Behavior of Adamantylated Bisimidazolium Guests Complexed to Cucurbiturils. CHEMISTRY-A EUROPEAN JOURNAL 18 (43), p. 13633 - 13637.
  • GUERINEAU, M; KRIZ, Z; KOZAKOVA, L; BEDNAROVA, K; JANOS, P; PALECEK, J, 2012:Analysis of the Nse3/MAGE-Binding Domain of the Nse4/EID Family Proteins. PLOS ONE 7 (4)
  • IONESCU, CM; VAREKOVA, RS; PREHN, JHM; HUBER, HJ; KOCA, J, 2012:Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation. PLOS COMPUTATIONAL BIOLOGY 8 (6)
  • KRISTOFIKOVA, Z; KRIZ, Z; RIPOVA, D; KOCA, J, 2012:Interactions of Amyloid beta Peptide 1-40 and Cerebrosterol. NEUROCHEMICAL RESEARCH 37 (3), p. 604 - 613.
  • MISHRA, S; ADAMOVA, L; ADAM, J; WIMMEROVA, M; KOCA, J, 2012:Comparison of Docking Software to Predict Saccharide Binding to Proteins Combination with In silico Protein Engineering. GLYCOBIOLOGY 22 (11), p. 1648 - 1649.
  • MISHRA, SK; ADAM, J; WIMMEROVA, M; KOCA, J, 2012:In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding. JOURNAL OF CHEMICAL INFORMATION AND MODELING 52 (5), p. 1250 - 1261.
  • SEHNAL, D; VAREKOVA, RS; HUBER, HJ; GEIDL, S; IONESCU, CM; WIMMEROVA, M; KOCA, J, 2012:SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. JOURNAL OF CHEMICAL INFORMATION AND MODELING 52 (2), p. 343 - 359.
  • VAZDAR, M; PLUHAROVA, E; MASON, PE; VACHA, R; JUNGWIRTH, P, 2012:Ions at Hydrophobic Aqueous Interfaces: Molecular Dynamics with Effective Polarization. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 3 (15), p. 2087 - 2091.
  • WIMMEROVA, M; KOZMON, S; NECASOVA, I; MISHRA, SK; KOMAREK, J; KOCA, J, 2012:Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods. PLOS ONE 7 (10)


  • KOZMON, S; MATUSKA, R; SPIWOK, V; KOCA, J, 2011:Three-Dimensional Potential Energy Surface of Selected Carbohydrates' CH/pi Dispersion Interactions Calculated by High-Level Quantum Mechanical Methods. CHEMISTRY-A EUROPEAN JOURNAL 17 (20), p. 5680 - 5690.
  • VACHA, R; MARTINEZ-VERACOECHEA, FJ; FRENKEL, D, 2011:Receptor-Mediated Endocytosis of Nanoparticles of Various Shapes. NANO LETTERS 11 (12), p. 5391 - 5395.
  • VAREKOVA, RS; GEIDL, S; IONESCU, CM; SKREHOTA, O; KUDERA, M; SEHNAL, D; BOUCHAL, T; ABAGYAN, R; HUBER, HJ; KOCA, J, 2011:Predicting pK(a) Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. JOURNAL OF CHEMICAL INFORMATION AND MODELING 51 (8), p. 1795 - 1806.


  • MISHRA, NK; KRIZ, Z; WIMMEROVA, M; KOCA, J, 2010:Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations. CARBOHYDRATE RESEARCH 345 (10), p. 1432 - 1441.


  • WIMMEROVA, M; MISHRA, NK; POKORNA, M; KOCA, J, 2009:Importance of oligomerisation on Pseudomonas aeruginosa Lectin-II binding affinity. In silico and in vitro mutagenesis. JOURNAL OF MOLECULAR MODELING 15 (6), p. 673 - 679.


  • Synergies of life and material sciences to create a new future (286154), FP7 - Capacities - Research Potential, 2011 - 2014
  • Research of acetylcholinesterase reactivation by methods of computation chemistry (OVMASUN200901), Ministry of Defence - Development of attained operational capabilities of the Czech Armed Forces, 2009 - 2012
  • Molecular and structural biology of selected antitumor drugs. From mechanistic studies to chemotheraphy of tumors (GD301/09/H004), Czech Science Foundation - Doctor Grants, 2009 - 2013
  • Podpora mezinárodní a mezisektorové spolupráce ve výzkumu a vývoji v oblasti věd o živé přírodě (CZ.1.07/2.4.00/17.0042), MEYS - OP Education for Competiteveness, 2011 - 2014


The group operates with a research infrastructure composed of computational clusters with about 1000 processor cores and the possibility of sharing National Academic Supercomputer Centre resources.

1. Partial atomic charges – a clue to predict chemical and biological behaviour of biomacromolecules

Supervisor: prof. RNDr. Jaroslav Koča, DrSc.


Nowadays, large amount of structural data about biomacromolecules is available and the number of resolved structures is growing rapidly. This information provides us a great opportunity to analyse the data and to reach a key biological information. Partial atomic charges belong to very promising molecular characteristics. They describe the distribution of electron density in a molecule, and, therefore, they provide clues regarding the chemical and biological behaviour of molecules. Thanks to advanced computational approaches, they can became available also for large and extra-large biomacromolecules. As they belong to biomacromolecular chemical characteristics, they can consequently be very helpful in revealing biological implications. For example, they can serve for a prediction of point mutations effect, for understanding allostery and other biomacromolecular activation mechanisms, sometimes processes that are very difficult to access by experimental approaches.
The thesis will focus on two challenges. First is development a methodology to calculate atomic charges in biomacromolecular systems in a reasonable time and with a reasonable accuracy, and second is application of atomic charges on revealing selected biological problems where such biomacromolecules are involved.

2. Protein sensitivity of membrane curvature

Supervisor: RNDr. Robert Vácha, PhD.


The control of biological membrane shape and composition is vital to eukaryotic life. The shape is so specific that it allows us to recognize various organelles in the cell. Despite a continuous exchange of material, organelles maintain a precise combination and organization of membrane lipids, which is crucial for their function and the recruitment of many peripheral proteins. Membrane shape thus enables the cell to organize proteins and their functions in space and time, without which serious diseases can occur. Moreover, membrane curvature and lipid content can be specific to cancer cells, bacteria, and enveloped virus coatings, which could be utilized for selective targeting. The aim of this project is to unravel the relationship between the protein sequence and the preferred membrane. This will lay the foundations for the design of new protein motifs sensitive to membranes with a specific curvature and composition on enveloped viruses, organelles and cells. Student will master tools of computer simulations, in particular molecular dynamics technique, and methods to calculate free energies. Moreover, he/she will learn advantages and disadvantages of various protein and membrane parameterizations including all-atom and coarse-grained models.

3. Engineering the glycans of stem cells to have required bioactivity – a computational study combined with an experiment

Supervisor:  prof. RNDr. Jaroslav Koča, DrSc.
Consultant: Ing. Igor Tvaroška, DrSc.


Investigations throughout the end of the 20th century revealed that cell migration is coordinated by chemoattractants present within endothelial beds. The cell migration is encoded by a series of overlapping steps, and tissue-specific migration is controlled by a discrete combination of various receptors present on circulating cells. The first step of the cascade, tethering contact of cells on the endothelium, is governed by interactions of selectins (E-, P-, and L-selectin) with their ligands. Selectin ligands are specialized carbohydrate determinants, consisting of sialofucosylations containing an alpha(2,3)-linked sialic acid substitutions and an alpha(1,3)-linked fucose modification displayed as the tetrasaccharide sialyl Lewis X (sLex) that are exhibited on the glycoform CD44. However, in some human mesenchymal stem cells, the terminal alpha(2,3)-sialyllactosamine moieties are lacking alpha(1,3)-fucosylation at N-acetylglucosamine to have the complete sLex determinant and, therefore, are lacking E-selectin ligand. The enzyme responsible for the alpha(1,3)-fucosylation is fucosyltransferase VI (FucTVI). The Ph.D. study will attempt to shed some light on the role of alpha(1,3)-fucosylation on a function of selectin ligands.

4. Influence of membrane properties on peptide conformations

Supervisor: doc. RNDr. Robert Vácha, PhD.


Peptide and protein conformations are influenced by composition of phospholipid membrane, which they are interacting with. This is particularly important for antimicrobial and neurodegenerative peptides (such as Abeta peptide related to Alzheimer’s disease), which can disrupt cellular membrane by formation of toxic membrane pores. The lipid composition of the membrane can enhance or prevent the peptide aggregation and/or pore formation and thus determine the fate of the cell. Despite the importance, we do not understand the relation except few recent examples (e.g. DOI: 10.1002/anie.201603178). The aim of this project is to unravel the relationship between the membrane composition and peptide conformations. This information could lead to a new diet preventing the Alzheimer’s disease or to a rational design of new antimicrobial peptides. Student will master tools of computer simulations, in particular molecular dynamics technique, and methods to calculate free energies. Moreover, he/she will learn advantages and disadvantages of various protein and membrane parameterizations including all-atom and coarse-grained models.



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