auc.cz/summerschool2013
People
SPEAKERS
FRANK RÜHLI
UNIVERSITY OF ZURICH
Paleopathology: Scientific examination of historic human remains
JANNETTE CAREY
PRINCETON UNIVERSITY
Allostery and Ligand-Binding
RÜDIGER ETTRICH
ACADEMY OF SCIENCES OF THE CZECH REPUBLIC, INSB GCRC
Was binding of free aminoacids an early innovation in the evolution of allostery?
Interpretation of thermodynamic ligand-binding data through the lens of molecular dynamics has led to a structural and energetic description of the molecular mechanism of allostery for the hexameric E. coli arginine repressor, the master feedback regulator of transcription in L-arginine metabolism, which displays strong negative cooperativity of L-arginine binding. A controversial prediction of the famous allostery model of Monod, Wyman, and Changeux is that constraints imposed on protein subunits by multimerization are relaxed by ligand binding, but with conservation of symmetry in partially-liganded states. Molecular dynamics simulations reveal that conserved Arg and Asp sidechains in each L-arginine binding pocket promote rotational oscillation of apoArgR trimers by engagement and release of salt bridges. Binding of exogenous L-arginine displaces resident Arg residues and arrests oscillation, shifting the equilibrium quaternary ensemble and promoting subunit motions that generate an entropic driving force while maintaining symmetry in partially-liganded states. Computational simulations supported by experimental data indicate that partially-liganded states can be structurally symmetric despite their conceptual asymmetry. The symmetric relaxed state is visualized as a multimer with all subunits anchored near the center, and with motions transferred to the periphery like a bouquet of balloons in strong wind. Thus, even during sequential filling of binding sites, symmetry can be maintained by exploiting the dynamics of the assembly and the distributed nature of its cohesive energy. The mechanism suggests the possibility that binding of free amino acids was an early innovation in the evolution of allostery.
JAN VALDMAN
VSB TU OSTRAVA
Numerical solutions of boundary value problems
We introduce examples of boundary value problems (BVPs) in physics, such as heat equation, elasticity or nonlinear obstacle problem. Then, we present the finite element method (FEM) as a powerful engineering tool for solving BVPs, its basic implementations in one and two space dimensions. It will be shown that the discretization using FEM leads to large systems of linear equations that can be solved by iterative methods of numerical linear algebra. There will be numerous computations in Matlab.
JOST LUDWIG
UNIVERSITY OF BONN
Ion channels and transporters
Cells and intracellular compartments are separated from their surroundings by membranes. In order to keep cell homeostasis intact and also for signal transduction, substances like nutrients or ions have to cross the cell membrane in a regulated manner. To achieve this, cells possess a large variety of proteins that mediate membrane transport. Transport can be passive, i.e. following the electrochemical gradient of the transported substance, or active, i.e. against this gradient. Examples for primary active (directly powered by an energy source), secondary active transport (co- or antiport of substances with their gradient to power the transport of another substance against its gradient) and passive transport through uniporters will be given. Ion channels and transporters comprise the largest group of membrane proteins. Their functional and structural features will be discussed in the second part of the lecture. The main focus will be on potassium (K) channels and - transporters. Previously it was thought that they represent structurally very different classes of proteins. However, since the determination of the first K channel structure in 1998, new models were developed for K transporters that indicated structural similarities between transporters and channels. More recently, these models were validated for two K transporters through their crystal structures. These results, that strengthen the hypothesis that ion channels and transporters share the same evolutionary origin, will be discussed.
JOSEF LAZAR
ACADEMY OF SCIENCES OF THE CZECH REPUBLIC, INSB GCRC
Genetics of human behavior
What can animal models, genetics, and cutting edge imaging techniques techniques tell us about who we are.
BABAK MINOFAR
ACADEMY OF SCIENCES OF THE CZECH REPUBLIC, INSB GCRC
Structure and dynamics of biomolecules in aqueous and non-aqueous solutions
Biomolecules can be solvated in both aqueous and non-aqueous media such as organic solvents and ionic liquids, leading either to conformational changes in their structure, or changes in their enzymatic activity. Using enzymes in aqueous solution of organic solvents and ionic liquids bring benefits forindustries as majority of substrates are insoluble in water and organic media can improve solubility. Although organic solvents and ionic liquids can improve the solubility of such non-soluble compounds, solutions containing organic solvents can not be used at all concentrations for enzymatic reactions thus limiting the usage of organic solvents in industrial applications. Non-aqueous solutions are not only changing the native structure of enzymes or their catalytic activity, but they may lead even to denaturation of biomolecules. In order to understand the solvation structure of biomolecules in non-aqueous media and ionic liquids surface structure and bulk properties of such media must be studied both experimentally and theoretically. As theoretical method, classical molecular dynamics simulations have been used to study solvation of biomolecules in aqueous solutions of organic solvents and ionic liquids. Due to special properties of ionic liquids such as low vapor pressure, high thermal stability, electrochemical stability and low volatility, they can serve as better solvents than usual organic solvents. Non-aqueous media may have different effect of the catalytic reaction such as lowering the energy of activated complex or stabilization of enzyme in solution. Also using solution of organic solvents can improve the solubility of some reactant and stabilize the structure of biomolecules both by hydrophobic interactions and hydrogen bonding. In our previous studies systematic activity by screening of haloalkane dehalogenases in the presence of organic solvents showed different activation and inhibition effects on enzymes occurs. Molecular dynamics simulations revealed that that organic solvent molecules can enter to the access tunnels and active sites of enzymes while no competitive inhibition was observed^1 . Moreover, we investigated the effect of non-denaturing concentrations ofdifferent organic solvents on the structure of haloalkane dehalogenases DhaA, LinB, and DbjA by molecular dynamics (MD) simulations and we showed that the orientation of organic solvent molecules on the protein surface clearly depends on hydrophobicity and hydrogen bonding of organic solvent which are responsible for thermal and structural stabilization of haloalkane dehalogenases inorganic solvents^2 .
In this talk the structure and dynamics of biomolecules such peptides, proteins and enzymes in non-aqueous media such as pure and aqueous solutions of protic ionic and aprotic liquid which is studied by means of classical molecular dynamics (MD)simulations will be presented.
DAVID ŘEHA
ACADEMY OF SCIENCES OF THE CZECH REPUBLIC, INSB GCRC
Biological Applications of QM/MM Calculations
During the lecture the two most common approaches to calculate energy of molecules used for computational biology will be introduced; quantum mechanics (QM) and Molecular mechanics (MM). The advantages and disadvantages of both approaches will be compared and demonstrated on the examples of typical applications used for computational biology. The most common MM applications where the advantages of MM (speed and efficiency, possibility to model system with more than 100000 atoms) can be applied are MD and MC simulations and molecular docking. Disadvantages of MM approach (need for parameterization, no explicit polarization and impossibility to model chemical reactions) can be tackled by QM methods. The most common applications for QM methods are calculation of electronic properties (atomic charge derivation), spectra, the reaction paths and vibrational analysis. Disadvantage of QM approach is computational demandingness (max 100 atoms can be included) making pure QM methods impractical for biological systems. The combinations of both approaches, hybrid QM/MM solves this problem. The region of the interest in biomolecule (active site) is calculated by QM methods, the rest is calculated by MM methods. The different kind of embedding (mechanical, electrostatic and polarizable) as well as different approaches to calculated final energy (additive or subtractive) will be introduced. The biological application of QM/MM calculations will be shown on the examples of the system studied in our laboratory. 1. The first example is the calculation of the ligand binding energy for the study of the mechanisms of NADH:quinone oxidation reduction reaction in flavoprotein WrbA. During the enzymatic reaction, the NADH is oxidized to NAD+ and quinone is reduced to hydroquionone. The reaction proceeds via FMN acting as an enzyme cofactor. The QM/MM calculations were used to estimate relative binding energies of the substrates of the WrbA protein. The results of calculations supports the experimental evidence of the hopping mechanisms, where in the first step, the NADH is oxidized to NAD+ by FMN and in the second step (after the NAD+ leaves to active site), the quinone is reduced to hydro-quinone by FMNH2. 2. The other example is QM/MM study of the reaction barrier of choristmate to prophenate reaction in chorismate mutase. Here we have introduced the polarizable embedding to QM/MM calculations and demonstrated the importance of polarization. 3. The final example is introduction of polarized molecular docking (based on QM/MM) in order to study the binding affinity of progesterone, propranolol and warfarin to human α1-acid glycoprotein. The ligands were docked to the protein using fully polarized molecular docking (based on QM/MM). The relative binding strength of the ligands corresponds to the experimental evidence.
VITALI BIALEVICH
ACADEMY OF SCIENCES OF THE CZECH REPUBLIC, INSB GCRC
Restriction-modification complex EcoR124I
EcoR124I is multi-subunit enzyme from Type IC R-M systems to which attributed such activities as methyltransferase, ATPase and endonuclease combination of which maintains integrity of host genome and protect bacterial cell from phage attacks. Pentameric complex EcoR124I is composed of three distinct subunits: HsdS recognizes EcoR124I specific sequence on DNA (GAAn_6 RTCG, where R is either purine) and binds to it; two HsdM subunits together with one HsdS subunit form methyltransferase or MTase compex which is able to exist in solution independently and to fulfil methylation function using /S/-adenosyl methyonine as donor of methyl groups; two HsdR subunits are required for ATPase and endonuclease activities in R_2 M_2 S_1 complex, while R_1 M_2 S_1 complex translocates but is not able to cleave DNA. HsdR subunits translocate dsDNA bidirectionally toward holoenzyme anchored on its recognition sequence extruding long DNA loops and consuming 1 ATP per 1 base pair (bp). Cleavage event occurs in random manner distantly from recognition site when further translocation is impeded by DNA topology or by collision with another translocating enzyme.
SUPERVISORS
JANNETTE CAREY
PRINCETON UNIVERSITY
RÜDIGER ETTRICH
ACADEMY OF SCIENCES OF THE CZECH REPUBLIC, INSB GCRC
JOST LUDWIG
UNIVERSITY OF BONN
JOSEF LAZAR
ACADEMY OF SCIENCES OF THE CZECH REPUBLIC, INSB GCRC