Accepted Posters

Category 'B'- Biophysics '

Poster B01

Comparative analysis of computational models of two-enzyme systems in presence of a competitive inhibitor in case of isolated and complex interactions between enzymes

Armen Takgyozyan- Yerevan State University

Aram Gevorgyan (Yerevan State University, Biophysics); Emil Gevorgyan (Yerevan State University, Biophysics); Valeri Arakelyan (Yerevan State University, Physics);

Short Abstract: Two models were created by STELLA package. In two-enzyme chain complex interaction of enzymes increases the products concentrations. It also causes sharp variations in change dynamics of products concentrations, which is the result of competition between enzymes. Complex interaction of enzymes does not affect change dynamics of inhibitor’s concentration.

Long Abstract: Click Here

Poster B02

Primary response of myoglobin studied by time-dependent Linear Response Theory (LRT)

Lee Yang- University of Tokyo

Akio Kitao (University of Tokyo, Institute of Molecular and Cellular Biosciences); Nobuhiro Gō (Japan Atomic Energy Agency, Neutron Biology Research Center);

Short Abstract: Induce-fit (or sequential/KNF) model, explaining ligand-induced conformational changes, is re-comprehended in the context of a linear response theory (LRT). Here we formulated a time-dependent LRT to address experimentally observed myoglobin primary response at a time scale from femto- to 10s picoseconds.

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Poster B03

Electron tomography and molecular modeling study of chemoreceptor organization

Xiongwu Wu- National Institutes of Health

Peijun Zhang (University of Pittsburgh, Structural Biology); Cezar Khursigara (NIH, NCI); Sriram Subramaniam (NIH, NCI); Bernard Brooks (NIH, NHLBI);

Short Abstract: Through cryo-electron tomography and map-constrained molecular dynamics simulations, we obtained the assembly structures of tsr organized in a two dimensional array. It is suggested that the position of the ligand binding domain and the HAMP domain play a pivotal role in mediating signal transduction across the cell membrane.

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Poster B04

Assisted crystallographic RNA model building: A directed rotameric approach for building the RNA backbone

Kevin Keating- Yale University

Anna Marie Pyle (Yale University & HHMI, Molecular Biophysics and Biochemistry);

Short Abstract: The backbone of RNA is critical for function, but studies of the backbone have long been hampered by the difficulty of accurately determining its structure. We have combined a reduced representation of RNA with an all-atom rotamer library to increase the ease and accuracy of crystallographic backbone structure determination.

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Poster B05

Conformational energies and entropies of peptides. Dependence on sequence type, and relation to peptide-protein binding.

Evrim Besray Ünal- Koc University

Burak Erman (Prof., Chemical and Biological Engineering); Attila Gürsoy (Assoc. Prof., Computer Engineering);

Short Abstract: A novel statistical thermodynamics approach is applied to the free peptide segments to classify them according to their entropies, conformational energies and heat capacities. Our approach employs the rotational isomeric states model. Low energy, low entropy and low heat capacity determined to be essential for a good candidate inhibitor peptide.

Long Abstract: Click Here

Poster B06

Structural Insights into Bacterial Signal Transduction

Martín Graña- Institut Pasteur Montevideo

Hugo Naya (Institut Pasteur Montevideo, Bioinformatics Unit); Pedro Alzari (Institut Pasteur, Structural Biochemistry Unit); Alejandro Buschiazzo (Institut Pasteur Montevideo, Protein Crystallography Unit);

Short Abstract: Signal transduction in prokaryotes is conducted primarily by two-component regulatory systems, basically a sensor histidine kinase and a response regulator. Several genomes revealed additional signal transduction modes, in particular Ser/Thr kinases. We provide structure/sequence insights on a His kinase family and a Ser/Thr kinase family, providing with candidate mutations.

Long Abstract: Click Here

Poster B07

Paying the entropic cost: peptides and proteins in a bind

Ora Schueler-Furman- The Hebrew University of Jerusalem

No additional authors

Short Abstract: Strategies for peptide-protein binding are identified by a computational structural analysis of peptide-protein complex structures. The protein uses a “prepaid strategy” where no significant conformational changes occur, thereby reducing entropy reduction to the peptide. The peptide forms exceptionally many contacts and hydrogen bonds, thus maximizing enthalpy gain.

Long Abstract: Click Here

Poster B08

Can we trust results from protein – ligand docking? Evaluation of the most commonly used docking programs on PDBbind database

Dariusz Plewczynski- University of Warsaw

Michal Lazniewski (University of Warsaw, ICM); Rafal Augustyniak (University of Warsaw, ICM); Krzysztof Ginalski (University of Warsaw, ICM);

Short Abstract: Molecular recognition plays a fundamental role in all biological processes and that is why great efforts have been made to understand and predict such kind of interactions.The purpose of our studies was to evaluate widely used docking tools on all protein-ligand complexes from PDBbind database (large set of 1300 complexes)

Long Abstract: Click Here

Poster B09

A graphical model approach for predicting free energies of association for protein-protein interactions under backbone and side-chain flexibility

Hetunandan Kamisetty- Carnegie Mellon University

Christopher J (Carnegie Mellon University, Computer Science Department); Chris Bailey-Kellogg (Dartmouth College, Computer Science);

Short Abstract: We present GOBLIN, the first graphical-model based approach for predictingbinding free energies for all-atom models of protein complexes.GOBLIN uses a rigorous approximation to the partitionfunction of the system that is fast and accurate. Our resultsindicate the utility of accounting for entropic contributions to the bindingfree energy.

Long Abstract: Click Here

Poster B10

Disordered flanks prevent peptide aggregation.

Sanne Abeln- FOM Institute for Atomic and Molecular Physics [AMOLF]

No additional authors

Short Abstract: We report a Monte Carlo study that aims to elucidate the role of disordered regions in proteins adjacent to binding motifs. Coarse-grained simulations show that small hydrophobic peptides without disordered flanks tend to aggregate under conditions where peptides embedded in unstructured peptide sequences remain soluble.

Long Abstract: Click Here

Accepted Posters

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