Date :

 16 November, 2012

Place :

  The auditorium on 1st floor, Institute of Physics, Academia Sinica, Taipei

 National Center for Theoretical Sciences (Critical Phenomena and Complex Systems focus group)

 Institute of Physics, Academia Sinica (Taipei)

 Miss Chia-Chi Liu (Secretary, Physics Division, NCTS)
 Tel:(886)-2-33665566; Fax:(886)-2-33665565; E-mail: ccliu@phys.ntu.edu.tw

Speakers :

Prof. Cheng-Hung Chang

Institute of Physics, National Chiao-Tung University, Hsinchu, Taiwan

E-mail: chchang@mail.nctu.edu.tw

The entropic forces of polymer translocation

  Entropic force is crucial for polymer translocation through nano-pores or channels. To extract the pure entropic contribution during polymer tug-of-war and recoiling, we carry out a Langevin dynamics simulation. The corresponding entropic forces are measured by an optical tweezer via Jarzynski equality and, additionally, determined theoretically by a recursion formula. These two approaches are more general than Freed-Edward’s diffusion equation and provide highly coincident force values beyond the precision estimated by Muthukumar’s formalism. We further derive a general formula, to estimate the entropic forces for different channel widths, channel stiffness, polymer persistence lengths, excluded volume strength, and temperature. As examples, we use this formula to quantify the entropic contribution in several recent DNA translocation experiments.

Prof. Wen-Tau Juan

Institute of Physics, Academia Sinica, Taipei

 E-amil: wtjuan@phys.sinica.edu.tw

Relaxation of DNA on a supported cationic lipid membrane

Prof. Yeong-Shin Lin

Institute of Bioinformatics and Systems Biology, National Chiao-Tung University, Hsinchu, Taiwan

E-mail: ganghu@bnu.edu.cn

The 3D structure and evolutionary rate of proteins

  Translational selection, including gene expression, protein abundance, and codon usage bias, has been suggested as the single dominant determinant of protein evolutionary rate in yeast. Here, we show that protein structure is also an important determinant. Buried residues, which are responsible for maintaining protein structure or are located on a stable interaction surface between 2 subunits, are usually under stronger evolutionary constraints than solvent-exposed residues. Our partial correlation analysis shows that, when whole proteins are included, the variance of evolutionary rate explained by the proportion of solvent-exposed residues (P(exposed)) can reach two-thirds of that explained by translational selection, indicating that P(exposed) is the most important determinant of protein evolutionary rate next only to translational selection. Our result suggests that proteins with many residues under selective constraint (e.g., maintaining structure or intermolecular interaction) tend to evolve slowly, supporting the "fitness (functional) density" hypothesis.

Prof. Hisashi Okumura

Research Center for Computational Science, Institute for Molecular Science, Okazaki, Japan

E-mail: hokumura@ims.ac.jp

Helix-strand replica-exchange molecular dynamics method and its application

  Biomolecules such as proteins have complicated free energy surfaces with many local minima. Conventional molecular dynamics (MD) and Monte Carlo (MC) simulations tend to get trapped in these local-minimum states. One of the powerful techniques to avoid this difficulty is the replica-exchange method. We propose a new type of the Hamiltonian replica-exchange method, which is referred to as helix-strand replica-exchange molecular dynamics method. In this method umbrella potential which enhances α-helix or b-strand conformation is exchanged. We apply this method to a design peptide and compare the results with those obtained by usual replica-exchange method.

Prof. Satoru G. Itoh

Research Center for Computational Science, Institute for Molecular Science, Okazaki, Japan

E-mail: itoh@ims.ac.jp

 Coulomb replica-exchange method and its applications
  Effective samplings in the conformational space are necessary to predict the native structures of proteins. The replica-exchange method (REM) is one of the most well-known methods among the generalized-ensemble algorithms which realize effective samplings in the conformational space for biomolecular systems. However, REM has a difficulty for large systems that many replicas are needed to realize such effective samplings. In other words, huge amount of computer time is required in the replica-exchange method for the large systems.
In order to overcome this difficulty, we proposed a new replica-exchange method, which we refer to as the Coulomb replica-exchange method (CREM), recently. In this CREM, electrostatic charges are exchanged among replicas although the temperatures are exchanged in conventional replica-exchange method. By exchanging the electrostatic charges, the free-energy barrier come from the electrostatic interactions are reduced. Moreover, the number of replicas can be decreased by exchanging the electrostatic charges of solute atoms only. Consequently, the CREM simulations realize effective samplings in the conformational space with small number of replicas. I will show the effectiveness of this method in my talk.

Dr. Shang-Te Danny Hsu

Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan

E-mail: sthsu@gate.sinica.edu.tw

Probing complex protein structures and dynamics along their folding pathways

  How protein molecules attain their native and functional conformation has been an outstanding question for biophysics for decades. While theoretical calculations and experimental observations are beginning to converge for small globular proteins, much remains elusive with regard to the mechanism by which proteins of complex folding topologies fold into defined three-dimensional structures. Recently, several proteins have been found to be able to thread themselves to form topological knots, such as trefoil knot, Gordian knot and Stevendore knot. These knotted proteins have drawn a great deal of interests in the field of protein folding. Despite the complexity of these topologically knotted structures, most of these knotted proteins can fold spontaneously and efficiently without the help from molecular chaperones whose job is to help folding and avoid misfolding of other proteins. In this talk, I shall discuss out experimental findings of some of these knotted proteins, including human ubiquitin C-terminal hydrolyase (UCH-L1), which is implicated in Parkinson’s disease, and challenges involved in defining the presence of loosely knotted structures of a knotted protein in its chemically denatured state.

Prof. Lee-Wei Yang

Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu, Taiwan

E-mail: lwyang@life.nthu.edu.tw

Protein-Ligand interactions treated as perturbations of protein intrinsic dynamics – Reconsider Induced-Fit Phenomenon

  Intrinsic fluctuations and ligand-induced conformational changes in proteins are functionally essential to support all forms of life in the molecular level. In this study, we formulate a set of linear response theories, both time-dependent and –independent, which describe ligand-triggered conformational changes of proteins. The triggering forces (or, external perturbations) excite relevant global modes, which proteins have intrinsic tendency to move along, resulting in conformational changes that are jointly contributed by these excited modes. Using these theories, we are able to derive time constants of molecular responses (ranging from hundreds of femtoseconds to a few tens of picoseconds) which agree with those characterized by UV Resonance Raman (UVRR) spectrometry. I will also talk about possible applications of the theory including the mechanism study of -1 frameshifting of the prokaryotic ribosome.

Prof. Chi-Lun Lee

Department of Physics, National Central University, Chungli, Taiwan

E-mail: chilun@ncu.edu.tw

Charge interactions in macroionic systems