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Category: List of Bases 2003 2003 ICTP activities in Trieste ICTP activities in Trieste
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lecture

Start Time:

5 May 2003 at 08:30

Ends On:

16 May 2003

Location:

Trieste - Italy

Venue:

AGH-Kastler Lecture Hall

Organizer(s):

A. Maritan, J. Banavar

Description:

The purpose of this Workshop is to provide state-of-the-art perspectives on experimental, theoretical and computational approaches to this vital problem, and to foster discussions on the challenges and new strategies for understanding biopolymers.

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The following lecture notes are available on line in .pdf format: to download, check the Programme and go to the talk you are interested in.
- "Remarks on homo- and hetero-polymeric aspects of protein folding", presented by T. Garel (talk delivered on 7 May)
- "Muscles, a complex network essential for life”, presented by A. Pastore (talk delivered on 6 May)
- "Misfolding diseases and aggregation", presented by A. Pastore (talk delivered on 9 May)
- "Topology of transmembrane proteins”, presented by I. Simon (talk delivered on 15 May)
- "Solvent effects on simple protein models”, presented by P. De Los Rios (talk delivered on 7 May)
- "Hydrophobic models of protein folding and the thermodynamics of chain-boundary interactions”, presented by A. Erzan (talk delivered on 13 May)
- "Characterization of protein interfaces: a graph theoretic approach”, presented by S. Vishveshwara (talk delivered on 13 May)
- "Towards a noncontingent biology: the proteins folds as natural forms", presented by M. Denton (talk delivered on 13 May)
- "Recognition in biomolecular energy landscapes: protein association vs protein folding", presented by G. Papoian (talk delivered on 15 May)
- "Multicanonical method and generalized-ensemble simulations of short peptides", presented by T. Celik (talk delivered on 7 May)

Material:

MONDAY, 5 MAY

Chairperson: Maritan, A.

Room: Adriatico Guest House Kastler Lecture Hall

5 May 2003
08:30
10:00
REGISTRATION
01h30'
Room: Adriatico Guest House (Lower Level 1)
Registration and administrative formalities
10:00
10:30
Coffee
30'
Room: Adriatico Guest House (Lower Level 1)
10:30
11:00
OPENING
30'
Sreenivasan, K.R.
Director, the Abdus Salam ICTP
11:00
11:45
Intracellular traffic and defense against M. Tuberculosis: protein structures in a crystallographer's view
45'
Bolognesi, M.
Università degli Studi di Genova, Italy
11:45
12:30
Basic concepts of polyelectrolyte movement in solutions
45'
Muthukumar, M.
University of Massachusetts, Amherst, MA, USA
12:30
15:30
Lunch break
03h00'
14:45
15:30
Non-linear Picosecond Dynamics of Proteins
45'
Austin, R.
Princeton University, NJ, USA
15:30
16:15
The energy landscape of protein
45'
Frauenfelder, H.
Los Alamos National Laboratory, NM, USA
TUESDAY, 6 MAY - Morning session

Chairperson: Bahar, I.

Room: Adriatico Guest House Kastler Lecture Hall

6 May 2003
09:00
09:45
How DNA worms through protein channels
45'
Muthukumar, M.
University of Massachusetts, Amherst, MA, USA
09:45
10:30
Slaving - the interaction proteins with the environment
45'
Frauenfelder, H.
Los Alamos National Laboratory, NM, USA
10:30
11:00
Coffee break
30'
Room: Adriatico Guest House (Terrace)
11:00
11:45
Efficient computation of proteins conformational dynamics
45'
Bahar, I.
University of Pittsburgh, PA, USA
11:45
12:30
Muscles, a complex protein network essential for life: structure and function
45'
Pastore, A.
National Institute for Medical Research, London, UK
12:30
14:15
Lunch break
01h45'
TUESDAY, 6 MAY - Afternoon session

Chairperson: Cieplak, M.

Room: Adriatico Guest House Kastler Lecture Hall

6 May 2003
14:15
15:00
Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding
45'
Verkhivker, G.
Pfizer Global R & D, San Diego, CA, USA
15:00
15:45
Folding times of proteins
45'
Cieplak, M.
Polish Academy of Sciences, Warsaw, Poland
15:45
16:15
Coffee break
30'
Room: Adriatico Guest House (Terrace)
WEDNESDAY, 7 MAY - Morning session

Chairperson: Chang, I.

Room: Adriatico Guest House Kastler Lecture Hall

7 May 2003
09:00
09:45
Viscoelasticity of biopolymer networks and statistical mechanics of semiflexible polymers
45'
Frey, E.
Hahn-Meitner-Institut Berlin, Germany
You may want to look at:
http://www.hmi.de/bereiche/SF/SF5
09:45
10:30
Cooperativity principles in protein folding -- Generic statisticalmechanical properties as powerful experimental constraints in modeling
45'
Chan, H.S.
University of Toronto, Canada
10:30
11:00
Coffee break
30'
Room: Adriatico Guest House (Terrace)
11:00
11:45
Hetero- and homo- polymeric view of the folding transistion
45'
Garel, Th.
Service de Physique Théorique, CEA Saclay, France
11:45
12:30
Protein Interaction Networks
45'
Vespignani, A.
Université de Paris-Sud, Orsay, France
12:30
14:15
Lunch break
01h45'
WEDNESDAY, 7 MAY - Afternoon session

Chairperson: De Los Rios, P.

Room: Adriatico Guest House Kastler Lecture Hall

7 May 2003
14:15
15:00
Experimental energy landscapes for protein folding
45'
Vendruscolo, M.
Cambridge University, UK
15:00
15:45
Multicanonical Method and Generalized-Ensemble Simulations of Short Peptides
45'
Celik, T.
Hacettepe University, Ankara, Turkey
15:45
16:15
Coffee break
30'
Room: Adriatico Guest House (Terrace)
16:15
16:45
Solvent effects on simple protein models
30'
De Los Rios, P.
University of Lausanne, Switzerland
16:45
18:30
POSTER SESSION
01h45'
Room: Adriatico Guest House (Lower Level 1)
THURSDAY, 8 MAY - Morning session

Chairperson: Lattanzi, G.

Room: Adriatico Guest House Kastler Lecture Hall

8 May 2003
09:00
09:45
Protein motions and proteins in networks
45'
Frauenfelder, H.
Los Alamos National Laboratory, NM, USA
09:45
10:30
Topological models for the elasticiy of proteins
45'
Micheletti, C.
International School for Advanced Studies, Trieste, Italy
10:30
11:00
Coffee break
30'
Room: Adriatico Guest House (Terrace)
11:00
11:45
Motor proteins: kinetics and structural properties of kinesin
45'
Lattanzi, G.
Hahn-Meitner-Institut Berlin, Germany
11:45
12:30
Studying protein aggregation using a protein engineering approach. Insight into the mechanisms of protein aggregation and the genetics of human diseases
45'
Chiti, F.
Università degli Studi di Firenze, Italy
12:30
14:15
Lunch break
01h45'
THURSDAY, 8 MAY - Afternoon session

Chairperson: Stefani, M.

Room: Adriatico Guest House Kastler Lecture Hall

8 May 2003
14:15
15:00
Cytotoxicity of aggregates of non pathological proteins: new views on amyloidosis pathogenesis and protein evolution
45'
Stefani, M.
Università degli Studi di Firenze, Italy
15:00
15:30
Mean-Field Approaches to the Finkelstein model for Protein Folding
30'
Bruscolini, P.
Politecnico di Torino, Italy
15:30
16:00
Coffee break
30'
Room: Adriatico Guest House (Terrace)
FRIDAY, 9 MAY - Morning session

Chairperson: Tiana, G.

Room: Adriatico Guest House Kastler Lecture Hall

9 May 2003
09:00
09:45
Simple two-state protein folding kinetics requires near-Levinthal thermodynamic cooperativity
45'
Chan, H.S.
University of Toronto, Canada
09:45
10:30
Model study of resistance proof, folding-inhibitor drugs
45'
Tiana, G.
Università degli Studi di Milano, Italy
10:30
11:00
Coffee break
30'
Room: Adriatico Guest House (Terrace)
11:00
11:45
Molecular mechanisms of protein function
45'
Röthlisberger, U.
Ecole Polytechnique Fédéral de Lausanne, Switzerland
11:45
12:30
Structure, energetics, dynamics, and design of convergent solutions to ligand-protein and protein-protein interfaces: the energy landscape perspective
45'
Verkhivker, G.
Pfizer Global R & D, San Diego, CA, USA
12:30
14:15
Lunch break
01h45'
FRIDAY, 9 MAY - Afternoon session

Chairperson: Verkhivker, G.

Room: Adriatico Guest House Kastler Lecture Hall

9 May 2003
14:15
15:00
Misfolding diseases and aggregation
45'
Pastore, A.
National Institute for Medical Research, London, UK
15:00
15:30
Coffee break
30'
Room: Adriatico Guest House (Terrace)
MONDAY, 12 MAY - Morning session

Chairperson: Micheletti, C.

Room: Adriatico Guest House Kastler Lecture Hall

12 May 2003
09:00
09:45
Are proteins ever really unfolded?
45'
Rose, G.
Johns Hopkins University, Baltimore, MD, USA
09:45
10:30
Annealing action of GroEL nanomachine
45'
Thirumalai, D.
University of Maryland, College Park, MD, USA
10:30
11:00
Coffee break
30'
Room: Adriatico Guest House (Terrace)
11:00
11:45
Folding and stretching in a go-like model of titin
45'
Cieplak, M.
Polish Academy of Sciences, Warsaw, Poland
12:00
14:15
Lunch break
02h15'
MONDAY, 12 MAY - Afternoon session

Chairperson: Hoang, T.X.

Room: Adriatico Guest House Kastler Lecture Hall

12 May 2003
14:15
15:00
Forcing biological molecules to stretch
45'
Thirumalai, D.
University of Maryland, College Park, MD, USA
15:00
15:45
Charting eukaryotic proteomes
45'
Ruffner, H.
VP Biology Cellzome, Heidelberg, Germany
15:45
16:15
Coffee break
30'
Room: Adriatico Guest House (Terrace)
16:15
16:45
Assembly of protein tertiary structures from secondary structures using optimized potentials
30'
Hoang, T.X.
The Abdus Salam ICTP, Trieste, Italy
TUESDAY, 13 MAY - Morning session

Chairperson: Tang, C.

Room: Adriatico Guest House Kastler Lecture Hall

13 May 2003
09:00
09:45
Characterization of protein-protein interfaces: a theoretical approach
45'
Vishveshwara, S.
Indian Institute of Science, Bangalore, India
09:45
10:30
Towards a noncontingent biology: the protein folds as natural forms
45'
Denton, M.
University of Otago, Dunedin, New Zealand
10:30
11:00
Coffee break
30'
Room: Adriatico Guest House (Terrace)
11:00
11:45
Dynamical properties of protein networks
45'
Tang, C.
NEC Research Institute, Princeton, NJ, USA
11:45
12:30
Towards an Analytic Description for the Elusive Transition State
45'
Chang, I.
Pusan National University, Rep. of Korea
12:30
14:15
Lunch break
01h45'
TUESDAY, 13 MAY - Afternoon session

Chairperson: Erzan, A.

Room: Adriatico Guest House Kastler Lecture Hall

13 May 2003
14:15
15:00
Hydrophobic models of protein folding and the thermodynamics of chain-boundary interactions - I
45'
Erzan, A.
Istanbul Technical University, Turkey
15:00
15:30
SAG phase:a new phase
30'
Kumar, S.
Banaras Hindu University, India
15:30
16:00
Coffee break
30'
Room: Adriatico Guest House (Terrace)
WEDNESDAY, 14 MAY - Morning session

Chairperson: Trovato, A.

Room: Adriatico Guest House Kastler Lecture Hall

14 May 2003
09:00
09:45
Signaling in plants: how do plants see, hear, and smell?
45'
Fedoroff, N.
Pennsylvania State University, University Park, PA, USA
09:45
10:30
Helix-helix packing preferences in globular proteins
45'
Trovato, A.
Università degli Studi di Padova, Italy
10:30
11:00
Coffee break
30'
Room: Adriatico Guest House (Terrace)
11:00
11:45
From polymers to proteins -- novel phases of short compact tubes
45'
Banavar, J.
Pennsylvania State University, University Park, USA
11:45
12:30
Non-Markovian Dynamics and single Molecule folding
45'
Wang, J.
State University of New York at Stony Brook, NY, USA
12:30
14:15
Lunch break
01h45'
WEDNESDAY, 14 MAY - Afternoon session

Room: Adriatico Guest House Kastler Lecture Hall

14 May 2003
14:15
15:00
A long day's journey into simplicity - I
45'
Rose, G.
Johns Hopkins University, Baltimore, MD, USA
15:00
15:20
Proton relaxivities of serum proteins
20'
Yilmaz, A.
Dicle University, Diyarbakir, Turkey
15:20
15:50
Coffee break
30'
Room: Adriatico Guest House (Terrace)
15:50
17:50
POSTER SESSION
02h00'
Room: Adriatico Guest House (Lower Level 1)
THURSDAY, 15 MAY - Morning session

Chairperson: Vishveshwara, S.

Room: Adriatico Guest House Kastler Lecture Hall

15 May 2003
09:00
09:45
Molecular evolution of promoters: an experimental study
45'
Libchaber, A.
The Rockefeller University, New York, NY, USA
09:45
10:30
Comparison of the Dynamics and Hydration Patterns in Ribonuclease-A Family Proteins
45'
Vishveshwara, S.
Indian Institute of Science, Bangalore, India
10:30
11:00
Coffee break
30'
Room: Adriatico Guest House (Terrace)
11:00
11:45
A long day's journey into simplicity - II
45'
Rose, G.
Johns Hopkins University, Baltimore, MD, USA
11:45
12:30
Topology of transmembrane proteins
45'
Simon, I.
Institute of Enzymology, Budapest, Hungary
12:30
14:15
Lunch break
01h45'
THURSDAY, 15 MAY - Afternoon session

Chairperson: Clementi, C.

Room: Adriatico Guest House Kastler Lecture Hall

15 May 2003
14:15
15:00
Topology and energetics in protein systems
45'
Clementi, C.
Rice University, Houston, TX, USA
15:00
15:45
Recognition in biomolecular energy landscapes: protein association vs protein folding.
45'
Papoian, G.
University of California at San Diego, CA, USA
15:45
16:15
Coffee break
30'
Room: Adriatico Guest House (Terrace)
16:15
16:45
Languages of genetic information: Why do living organisms have 4 nucleotide bases and 20 amino acids?
30'
Patel, A.
Indian Institute of Science, Bangalore, India
FRIDAY, 16 MAY

Chairperson: Banavar, J.

Room: Adriatico Guest House Kastler Lecture Hall

16 May 2003
09:00
09:45
Structure prediction of pmembrane proteins: is it possible?
45'
Casadio, R.
Università degli Studi di Bologna, Italy
09:45
10:30
Hydrophobic models of protein folding and the thermodynamics of chain-boundary interactions - II
45'
Erzan, A.
Istanbul Technical University, Turkey
10:30
11:00
Coffee break
30'
Room: Adriatico Guest House (Terrace)
11:00
11:45
Form and matter: the protein folds as platonic forms
45'
Denton, M.
University of Otago, Dunedin, New Zealand
11:45
12:30
Data deluge, the contemporary biologist's dilemma
45'
Fedoroff, N.
Pennsylvania State University, University Park, PA, USA
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