Date :

 12-13, 15 June 2009

Place :

 12-13 June: Room 312, Department of Physics, National Taiwan University, Taipei

 (14:00-18:00, 12 June: Room 406, Department of Physics, National Taiwan University, Taipei)

 15 June: 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

 Miss Chun-Ling Chang (Assistant of LSCP, Institute of Physics, Academia Sinica)

 Tel: +886-2-27898362; FAX: (886)-2-2782-2467; E-mail: labthpp@phys.sinica.edu.tw

The Taste of Taiwan Cuisine 2009:

http://www.taiwantaste.net/index.aspx

Speakers :

Dr. Hsin-Liang Chen

Institute of Biochemistry, Academia Sinica, TAIWAN

E-mail: d91222015@ntu.edu.tw

Studying the Fast Folding Kinetics of An Antifreeze Protein RD1 by A Photolabile Caging Strategy and Time-Resolved Photoacoustic Calorimetry on A Nanosecond Timescale

    In order to understand the intrinsic principle of protein folding, events of the folding process have to be systematically explored. In this work, the folding information of a small protein (RD1, about 7 kDa) including kinetic, enthalpy and volume change were reported by combining the photo-triggered caging-strategy and time-resolved photoacoustic calorimetry. In this strategy, the mutation with Ala-7 to Cys (designated RD1-A7C) was introduced for adding a photolabile cage group, 4-(bromomethyl)-6, 7-dimethoxycoumarin, to unfold the protein. The structural properties of the caged protein were analyzed by nuclear magnetic resonance spectroscopy (NMR) and circular dichroism spectroscopy (CD).  A pulse UV laser (~10^-9 s) was used to break the photolabile cage and two events were observed in the refolding of RD1-A7C toward its native state by using photoacoustic calorimetry (PAC).  The fast event, which has a folding time of 20 ns and a volume change of -9.7 mL/mol, was explained as the result of rapid hydrophobic collapse.  This event was followed by a conformational rearrangement, which has a folding time ~ 500 ns and small volume change (-1.4 mL/mol).

Prof. Jen-Yang Chen

Department of Microbiology, National Taiwan University, TAIWAN; National Institute of Cancer Research, NHRI, TAIWAN

E-mail: cjy@nhri.org.tw

Epstein-Barr Virus and Nasopharyngeal Carcinoma

Dr. Yun-Wen Chi

Department of Pediatrics, Love Saint Hospital, TAIWAN

E-mail: medicchi@yahoo.com.tw

Heavy Metals in Traditional Chinese Medicine

    Heavy metal intoxication of newborn infants fed with "Ba-Pao-Neu-Hwang-San" has been reported every year by many hospitals in Taiwan. In 1983, the National Laboratories of Foods and Drugs of the Department of Health, Executive Yuan, received one case report of a five month old female infant who died as a result of long term feeding with "Ba-Pao-Neu-Hwang-San". The drug was found to have contained lead 44,000 ppm. Although this unfortunate incident was propagated by most newspapers, the prescription of this ancient Chinese medicinal preparation is still widely accepted by ordinary people. Herbal medicine doctors prefer complex mineral drugs as did their ancestors thousands of years ago. About 15 years ago, we have collected 5 samples of "Ba-Pao-Neu-Hwang-San" from different manufacturers and measured the concentration of 16 heavy metals (including Cadmium, Mercury, Arsenic, Lead, Chromium, Manganese, Selenium, Germanium, Nickel, Calcium, Magnesium, Aluminum, Iron, Copper, Zinc, and Vanadmium) in these drugs with Inductively-Coupled Plasma Atomic Emission Spectrometry and Graphite Furnace Atomic Absorption Spectrometry. The result of our survey revealed that the first sample (from Tainan) contained mercury 52,800 ppm, the fourth (from Ping-tung) contained mercury 34,500 ppm, and the fifth (from Sin-chu) contained mercury 65,700 ppm. The mercurial contents of these samples were apparently too high to be a safe drug.

Prof. Feng Ding

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, USA

E-mail: fding@unc.edu

1. Multiscale Modeling of Proteins

    Rapid sampling of the conformation and sequence spaces is crucial for computational structure biology. We have developed multiple protein models to sample dynamics of various time and length scales with discrete molecular dynamics (DMD). We also developed the Medusa molecular modeling tool, which allows rapid sampling of the sequence space and evaluation of the associated free energy changes. Using DMD and/or Medusa, we are able to efficiently sample the sequence and conformations space of proteins. For example, using Medusa we are able to accurately predict the stability change of proteins upon mutations (http://eris.dokhlab.org). In collaboration with experimentalists, we have strategically designed destabilizing mutations of Galpha protein in yeast to study different degradations pathways via poly-ubiquitination and mono-ubiquitination. In another application, EGFP was broken into halves without fluorescence. Using DMD to sample the folding dynamics of each of halves and also the complex, we showed that a fluorogenic chromophore can self-catalytically form within an isolated N-terminal fragment of the EGFP. In vitro studies indicates that restoration of the split protein fluorescence can be driven by nucleic acid complementary interactions.

2. Discrete Molecular Dynamics Modeling of RNA

    RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. We developed a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, incorporating base-pairing and base-stacking interactions. We demonstrate correct folding of 150 structurally diverse, small RNA sequences. The majority of DMD-predicted 3D structures have <4 Å deviations from experimental structures. However, as the RNA sequence length increases, the available conformational space increase exponentially, which hinders the direct approach for RNA folding using DMD. We propose to incorporate structural constraints derived from biochemical experiments. We have developed an novel approach to incorporate distance constraints derived experiments and successfully applied on tRNA.

Prof. Nikolay V. Dokholyan

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, USA

E-mail: dokh@med.unc.edu

1. Multiscale Modeling and Design of Biological Molecules

    Some of the emerging goals in modern medicine are to uncover the molecular origins of human diseases, and ultimately contribute to the development of new therapeutic strategies to rationally abate disease. Of immediate interests are the roles of molecular structure and dynamics in certain cellular processes leading to human diseases and the ability to rationally manipulate these processes. Despite recent revolutionary advances in experimental methodologies, we are still limited in our ability to sample and decipher the structural and dynamic aspects of single molecules that are critical for their biological function. Thus, there is a crucial need for new and unorthodox techniques to uncover the fundamentals of molecular structure and interactions. We developed a multiscale approach which is based on tailoring simplified protein models to the systems of interest.  Such an approach allows significantly extending the length and time scales for studies of complex biological systems. I will describe several recent studies that signify the predictive power of simplified protein models within the hypothesis-driven modeling approach utilizing rapid Discrete Molecular Dynamics (DMD) simulations.

2. Mysteries of the Lou Gehrig's Disease

    Mutation-induced aggregation of the dimeric enzyme Cu, Zn superoxide dismutase (SOD1) has been implicated in the familial form of the amyotrophic lateral sclerosis (ALS) or Lou Gehrig’s disease, but the mechanism of aggregation is not known. We studied the folding thermodynamics and kinetics of SOD1 using a hybrid molecular dynamics approach. We found that the residues which contribute the most to SOD1 thermal stability are also crucial for apparent two-state folding kinetics. Surprisingly, we found that these residues are located on the surface of the protein and not in the hydrophobic core. Mutations in some of the identified residues are found in patients with the disease. We argue that the identified residues may play an important role in aggregation (Khare et al., "Folding of Cu, Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis" Journal of Molecular Biology, 334: 515–525 (2003)). 

    We further investigated in silico the sequence and structural determinants of SOD1 aggregation: (a) we identified sequence fragments in SOD1 that have a high aggregation propensity, using only the sequence of SOD1, and (b) we performed molecular dynamics simulations of the SOD1 dimer folding and misfolding. In both cases, we identified identical regions of the protein as having high propensity to form intermolecular interactions. These regions correspond to the N- and C-termini, and two cross-over loops and two β-strands in the Greek-key native fold of SOD1. Our results suggest that the high aggregation propensity of mutant SOD1 may result from a synergy of two factors: the presence of highly amyloidogenic sequence fragments (“hot-spots”), and the presence of these fragments in regions of the protein that are structurally most likely to form inter-molecular contacts under destabilizing conditions.  Therefore, we postulated that the balance between the self-association of aggregation-prone sequences and the specific structural context of these sequences in the native state determines the aggregation propensity of proteins (Khare, et al., "Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation" Proteins: Structure, Function, and Bioinformatics, 61: 617-632 (2005)).

    We further experimentally measured dissociation rate and equilibrium constants for human SOD1 dimer dissociation. We have also determined that loss of Zn is required for SOD1 aggregation. Using computation and experiments, we determined the rates of Zn loss and further SOD1 aggregation. Thus, we have identified a minimal aggregation sequence of SOD1 and measured the rate and equilibrium constants for each step of this sequence. Our findings suggest the role of mutations that are associated with familial ALS (Khare, et al., "The rate and equilibrium constants for a multi-step reaction sequence for the aggregation of superoxide dismutase in ALS" Proceedings of the National Academy of Sciences USA, 101: 15094-15099 (2004)).

Dr. Yao-Chen Hung

Institute of Physics, Academia Sinica, TAIWAN

E-mail: ychung@phys.sinica.edu.tw

Stochastic Resonance in p53 Regulatory Network

    We study the effect of noise on p53 regulatory network, the core of a cell's modulator for switching between survival and apoptosis. We find that the fluctuation, originating from stochastic expression of p53-responsive genes or randomness in other cellular components, introduces marked advantages for the system to sense external stimuli and sustain the function of switches. The performance of ordering between a stimulus and the system's response undergoes a maximum with the raise of noise level, indicating the occurrence of stochastic resonance. We discuss the biological significance of the phenomenon and possible experimental methods to test our results.

Dr. Wen-Jong Ma

Institute of Physics, Academia Sinica, TAIWAN

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

Molecular Dynamics Approach to Relaxation and Aggregation of Polymer Chains

Prof. Hisashi Okumura

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

E-mail: hokumura@ims.ac.jp

1. Temperature and Pressure Dependence of Alanine Dipeptide Studied by Multibaric-Multithermal Molecular Dynamics Simulations

    We applied the multibaric-multithermal molecular dynamics algorithm to an alanine dipeptide in explicit water [1].  This algorithm enables us to calculate the population of each state of biomolecules as functions of temperature and pressure.  We calculated the partial molar enthalpy difference and partial molar volume difference among each conformation of an alanine dipeptide for the first time.  We compare and discuss our simulational study and experimental data.

References
[1] H. Okumura and Y. Okamoto: J. Phys. Chem. B 112, 12038 (2008).

2. Partial Multicanonical Algorithm for Molecular Dynamics and Monte Carlo Simulations: Application to a Biomolecule

    I proposed the partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations [1].  The partial multicanonical simulation samples a wide range of a part of the potential energy terms which is necessary to sample the conformational space widely, whereas a wide range of total potential energy is sampled in the multicanonical algorithm.  Thus, one can concentrate the effort to determine the weight factor only on the important energy terms in the partial multicanonical simulation.  I applied the partial multicanonical, multicanonical, and canonical molecular dynamics algorithms to an alanine dipeptide in explicit water solvent.  I found that the partial multicanonical algorithm has higher sampling efficiency than the multicanonical and canonical algorithms.
　

References
[1] H. Okumura: J. Chem. Phys. 129, 124116 (2008).

Dr. Sheau-Yann Shieh

Institute of Biomedical Sciences, Academia Sinica, TAIWAN

E-mail: sy88@ibms.sinica.edu.tw

The Role of the Candidate Tumor Suppressor BTG3 at the Crossroad of Cellular Senescence and Neoplastic Transition

    BTG3 (B-cell translocation gene 3) is a member of the antiproliferative BTG gene family which also includes BTG1, BTG2/TIS21, Tob, Tob2, and PC3b. We have recently demonstrated that BTG3 is a downstream target of p53 involved in proper maintenance of the G2/M block after DNA damage. BTG3 binds and inhibits E2F1, a transcription factor required for cell proliferation. BTG3 depletion leads to increased E2F1 activity, and bypass of the inhibitory effect of RB on E2F1. Here we demonstrate that BTG3 ablation in normal human cells mimics oncogenic activation in inducing cellular senescence. Senescence-associated b-galactosidase (SA-b-Gal) staining was increased in BTG3-knockdown IMR-90 cells, concomitant with other senescence markers such as MMP-1, PAI-1, and p16. Moreover, senescence-associated heterochromatic foci (SAHFs) were observed in these knockdown cells, along with a marked increase in HP-1g and H3K9 tri-methylation-positive foci. These results suggest that BTG3 depletion recapitulates the effect of oncogenic activation in driving unscheduled cell proliferation, leading to senescence in normal cells.

    In contrast to the senescence phenotype observed in normal fibroblasts, depletion of BTG3 in cancer cell lines not only enhanced cell proliferation but also led to a 50% increase in cell migration as well as upregulation of vimentin and downregulation of E-cadherin, two markers for epithelial-mesenchymal transition (EMT). As loss of function of antiproliferative genes represents a major route to tumor progression, a cancer profiling study was conducted to examine the expression of BTG3 and to explore the possible role of BTG3 in tumorigenesis. While BTG3 expression was not significantly altered in several types of cancers, it was found to be reduced in several others including prostate cancer. This was further confirmed at the protein level by IHC staining of tissue specimen from at least five prostate cancer patients, and at the RNA level by RT-PCR analysis on tissues captured by LCM. 

    Collectively, our data highlight the importance of BTG3 at the crossroad of carcinogenesis and further implicate its role as a tumor suppressor.

Prof. Takashi Shimada

Department of Applied Physics, The University of Tokyo, JAPAN

E-mail: shimada@ap.t.u-tokyo.ac.jp

1. Universalities in Real and Model Ecosystems

    The mechanism of producing and sustaining diversity in ecosystems and the universal characteristics in structure and temporal behavior of ecosystems have attracted broad interest.
    We proposed a simple population-dynamics-based model in which interaction terms among species have nonlinear and scale-invariant form against the population size. This interaction let the system spontaneously grow to rich and realistic structure under successive invasion of new species.  Furthermore, the model reproduces the characteristic statistics evaluated from fossil data such as the q-exponential distribution of the life span of species.
    To examine the relevance and the origin of such universal features, We also adopt a different class of individual-based model.  The q-exponential distribution in species lifetime is obtained when we have invasions, while the distribution shows broader profile for a model with mutations: new species have correlation with resident species.
    These findings, in total, suggest that the characteristic statistics found in empirical data and model systems are universal in the sense that that appears independently from the details of the underlying community dynamics.

2. Characteristic Behavior in a Japanese Movie-Uploading Site

    How the contents or word becomes popular, and be forgotten, is an interesting and currently hot topic.  However, there is little study which is based on exhaustive data of the system.  We studied the entire record of a movie uploading site (http://www.nicovideo.jp), Japanese largest movie sharing site which has about 10,000,000 free users and over 200,000 dues-paying members.
    We found that the rank-size distribution of total views for top-ranked (most popular) movies obeys to a power-law.  The distribution in lower-ranked region also obeys to a power-law, but with steeper exponent.  It is also found that the daily number of views of movies show power-law decay.  The exponent is slightly dependent on the popularity of the movies: unpopular movies decays faster.

Dr. An-Jan Ten

Ten An-Jan Chinese Medicine Clinic, TAIWAN

E-mail: loveonelu@yahoo.com.tw

Exploration of the Combination of Traditional Chinese and Western Medicine (In Chinese)

中西醫結合義理探要

Dr. Pang-Hsien Tu

Institute of Biomedical sciences, Academia Sinica, TAIWAN

E-mail: btu@ibms.sinica.edu.tw

The Role of TDP Inclusions in Neurodegeneration