International Workshop on "Proteomics: Protein Structure, Function and Interactions"

Administration

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)

International Workshop on "Proteomics: Protein Structure, Function and Interactions" | (smr 1499)

Go to day

Tuesday, 6 May 2003

09:00 - 09:45 How DNA worms through protein channels

Location: Adriatico Guest House Kastler Lecture Hall
- 09:00 How DNA worms through protein channels 45'
  
  Speaker: Muthukumar, M. (University of Massachusetts, Amherst, MA, USA)
09:45 - 10:30 Slaving - the interaction proteins with the environment

Location: Adriatico Guest House Kastler Lecture Hall
- 09:45 Slaving - the interaction proteins with the environment 45'
  
  Speaker: Frauenfelder, H. (Los Alamos National Laboratory, NM, USA)
10:30 - 11:00 Coffee break

Location: Adriatico Guest House (Terrace)
- 10:30 Coffee break 30'
11:00 - 11:45 Efficient computation of proteins conformational dynamics

Location: Adriatico Guest House Kastler Lecture Hall
- 11:00 Efficient computation of proteins conformational dynamics 45'
  
  Speaker: Bahar, I. (University of Pittsburgh, PA, USA)

11:45 - 12:30 Muscles, a complex protein network essential for life: structure and function

Location:

Adriatico Guest House Kastler Lecture Hall

11:45 Muscles, a complex protein network essential for life: structure and function 45'

Speaker:	Pastore, A. (National Institute for Medical Research, London, UK)
Material:	lecture notes

12:30 - 14:15 Lunch break

Location: Adriatico Guest House Kastler Lecture Hall
- 12:30 Lunch break 1h45'
14:15 - 15:00 Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding

Location: Adriatico Guest House Kastler Lecture Hall
- 14:15 Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding 45'
  
  Speaker: Verkhivker, G. (Pfizer Global R & D, San Diego, CA, USA)
15:00 - 15:45 Folding times of proteins

Location: Adriatico Guest House Kastler Lecture Hall
- 15:00 Folding times of proteins 45'
  
  Speaker: Cieplak, M. (Polish Academy of Sciences, Warsaw, Poland)
15:45 - 16:15 Coffee break

Location: Adriatico Guest House (Terrace)
- 15:45 Coffee break 30'

Wednesday, 7 May 2003

09:00 - 09:45 Viscoelasticity of biopolymer networks and statistical mechanics of semiflexible polymers
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Location: Adriatico Guest House Kastler Lecture Hall
- 09:00 Viscoelasticity of biopolymer networks and statistical mechanics of semiflexible polymers 45'
  
  Speaker: Frey, E. (Hahn-Meitner-Institut Berlin, Germany)
09:45 - 10:30 Cooperativity principles in protein folding -- Generic statisticalmechanical properties as powerful experimental constraints in modeling

Location: Adriatico Guest House Kastler Lecture Hall
- 09:45 Cooperativity principles in protein folding -- Generic statisticalmechanical properties as powerful experimental constraints in modeling 45'
  
  Speaker: Chan, H.S. (University of Toronto, Canada)
10:30 - 11:00 Coffee break

Location: Adriatico Guest House (Terrace)
- 10:30 Coffee break 30'

11:00 - 11:45 Hetero- and homo- polymeric view of the folding transistion

Location:

Adriatico Guest House Kastler Lecture Hall

11:00 Hetero- and homo- polymeric view of the folding transistion 45'

Speaker:	Garel, Th. (Service de Physique Théorique, CEA Saclay, France)
Material:	lecture notes

11:45 - 12:30 Protein Interaction Networks

Location: Adriatico Guest House Kastler Lecture Hall
- 11:45 Protein Interaction Networks 45'
  
  Speaker: Vespignani, A. (Université de Paris-Sud, Orsay, France)
12:30 - 14:15 Lunch break

Location: Adriatico Guest House Kastler Lecture Hall
- 12:30 Lunch break 1h45'
14:15 - 15:00 Experimental energy landscapes for protein folding

Location: Adriatico Guest House Kastler Lecture Hall
- 14:15 Experimental energy landscapes for protein folding 45'
  
  Speaker: Vendruscolo, M. (Cambridge University, UK)

15:00 - 15:45 Multicanonical Method and Generalized-Ensemble Simulations of Short Peptides

Location:

Adriatico Guest House Kastler Lecture Hall

15:00 Multicanonical Method and Generalized-Ensemble Simulations of Short Peptides 45'

Speaker:	Celik, T. (Hacettepe University, Ankara, Turkey)
Material:	lecture notes

15:45 - 16:15 Coffee break

Location: Adriatico Guest House (Terrace)
- 15:45 Coffee break 30'

16:15 - 16:45 Solvent effects on simple protein models

Location:

Adriatico Guest House Kastler Lecture Hall

16:15 Solvent effects on simple protein models 30'

Speaker:	De Los Rios, P. (University of Lausanne, Switzerland)
Material:	lecture notes

16:45 - 18:30 POSTER SESSION

Location: Adriatico Guest House (Lower Level 1)
- 16:45 POSTER SESSION 1h45'

Thursday, 8 May 2003
- 09:00 - 09:45 Protein motions and proteins in networks
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 09:00 Protein motions and proteins in networks 45'
    
    Speaker: Frauenfelder, H. (Los Alamos National Laboratory, NM, USA)
- 09:45 - 10:30 Topological models for the elasticiy of proteins
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 09:45 Topological models for the elasticiy of proteins 45'
    
    Speaker: Micheletti, C. (International School for Advanced Studies, Trieste, Italy)
- 10:30 - 11:00 Coffee break
  
  Location: Adriatico Guest House (Terrace)
  - 10:30 Coffee break 30'
- 11:00 - 11:45 Motor proteins: kinetics and structural properties of kinesin
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 11:00 Motor proteins: kinetics and structural properties of kinesin 45'
    
    Speaker: 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
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 11:45 Studying protein aggregation using a protein engineering approach. Insight into the mechanisms of protein aggregation and the genetics of human diseases 45'
    
    Speaker: Chiti, F. (Università degli Studi di Firenze, Italy)
- 12:30 - 14:15 Lunch break
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 12:30 Lunch break 1h45'
- 14:15 - 15:00 Cytotoxicity of aggregates of non pathological proteins: new views on amyloidosis pathogenesis and protein evolution
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 14:15 Cytotoxicity of aggregates of non pathological proteins: new views on amyloidosis pathogenesis and protein evolution 45'
    
    Speaker: Stefani, M. (Università degli Studi di Firenze, Italy)
- 15:00 - 15:30 Mean-Field Approaches to the Finkelstein model for Protein Folding
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 15:00 Mean-Field Approaches to the Finkelstein model for Protein Folding 30'
    
    Speaker: Bruscolini, P. (Politecnico di Torino, Italy)
- 15:30 - 16:00 Coffee break
  
  Location: Adriatico Guest House (Terrace)
  - 15:30 Coffee break 30'

Friday, 9 May 2003

09:00 - 09:45 Simple two-state protein folding kinetics requires near-Levinthal thermodynamic cooperativity

Location: Adriatico Guest House Kastler Lecture Hall
- 09:00 Simple two-state protein folding kinetics requires near-Levinthal thermodynamic cooperativity 45'
  
  Speaker: Chan, H.S. (University of Toronto, Canada)
09:45 - 10:30 Model study of resistance proof, folding-inhibitor drugs

Location: Adriatico Guest House Kastler Lecture Hall
- 09:45 Model study of resistance proof, folding-inhibitor drugs 45'
  
  Speaker: Tiana, G. (Università degli Studi di Milano, Italy)
10:30 - 11:00 Coffee break

Location: Adriatico Guest House (Terrace)
- 10:30 Coffee break 30'
11:00 - 11:45 Molecular mechanisms of protein function

Location: Adriatico Guest House Kastler Lecture Hall
- 11:00 Molecular mechanisms of protein function 45'
  
  Speaker: 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

Location: Adriatico Guest House Kastler Lecture Hall
- 11:45 Structure, energetics, dynamics, and design of convergent solutions to ligand-protein and protein-protein interfaces: the energy landscape perspective 45'
  
  Speaker: Verkhivker, G. (Pfizer Global R & D, San Diego, CA, USA)
12:30 - 14:15 Lunch break

Location: Adriatico Guest House Kastler Lecture Hall
- 12:30 Lunch break 1h45'

14:15 - 15:00 Misfolding diseases and aggregation

Location:

Adriatico Guest House Kastler Lecture Hall

14:15 Misfolding diseases and aggregation 45'

Speaker:	Pastore, A. (National Institute for Medical Research, London, UK)
Material:	lecture notes

15:00 - 15:30 Coffee break

Location: Adriatico Guest House (Terrace)
- 15:00 Coffee break 30'

Monday, 12 May 2003
- 09:00 - 09:45 Are proteins ever really unfolded?
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 09:00 Are proteins ever really unfolded? 45'
    
    Speaker: Rose, G. (Johns Hopkins University, Baltimore, MD, USA)
- 09:45 - 10:30 Annealing action of GroEL nanomachine
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 09:45 Annealing action of GroEL nanomachine 45'
    
    Speaker: Thirumalai, D. (University of Maryland, College Park, MD, USA)
- 10:30 - 11:00 Coffee break
  
  Location: Adriatico Guest House (Terrace)
  - 10:30 Coffee break 30'
- 11:00 - 11:45 Folding and stretching in a go-like model of titin
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 11:00 Folding and stretching in a go-like model of titin 45'
    
    Speaker: Cieplak, M. (Polish Academy of Sciences, Warsaw, Poland)
- 12:00 - 14:15 Lunch break
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 12:00 Lunch break 2h15'
- 14:15 - 15:00 Forcing biological molecules to stretch
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 14:15 Forcing biological molecules to stretch 45'
    
    Speaker: Thirumalai, D. (University of Maryland, College Park, MD, USA)
- 15:00 - 15:45 Charting eukaryotic proteomes
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 15:00 Charting eukaryotic proteomes 45'
    
    Speaker: Ruffner, H. (VP Biology Cellzome, Heidelberg, Germany)
- 15:45 - 16:15 Coffee break
  
  Location: Adriatico Guest House (Terrace)
  - 15:45 Coffee break 30'
- 16:15 - 16:45 Assembly of protein tertiary structures from secondary structures using optimized potentials
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 16:15 Assembly of protein tertiary structures from secondary structures using optimized potentials 30'
    
    Speaker: Hoang, T.X. (The Abdus Salam ICTP, Trieste, Italy)

Tuesday, 13 May 2003

09:00 - 09:45 Characterization of protein-protein interfaces: a theoretical approach

Location:

Adriatico Guest House Kastler Lecture Hall

09:00 Characterization of protein-protein interfaces: a theoretical approach 45'

Speaker:	Vishveshwara, S. (Indian Institute of Science, Bangalore, India)
Material:	lecture notes

09:45 - 10:30 Towards a noncontingent biology: the protein folds as natural forms

Location:

Adriatico Guest House Kastler Lecture Hall

09:45 Towards a noncontingent biology: the protein folds as natural forms 45'

Speaker:	Denton, M. (University of Otago, Dunedin, New Zealand)
Material:	lecture notes

10:30 - 11:00 Coffee break

Location: Adriatico Guest House (Terrace)
- 10:30 Coffee break 30'
11:00 - 11:45 Dynamical properties of protein networks

Location: Adriatico Guest House Kastler Lecture Hall
- 11:00 Dynamical properties of protein networks 45'
  
  Speaker: Tang, C. (NEC Research Institute, Princeton, NJ, USA)
11:45 - 12:30 Towards an Analytic Description for the Elusive Transition State

Location: Adriatico Guest House Kastler Lecture Hall
- 11:45 Towards an Analytic Description for the Elusive Transition State 45'
  
  Speaker: Chang, I. (Pusan National University, Rep. of Korea)
12:30 - 14:15 Lunch break

Location: Adriatico Guest House Kastler Lecture Hall
- 12:30 Lunch break 1h45'

14:15 - 15:00 Hydrophobic models of protein folding and the thermodynamics of chain-boundary interactions - I

Location:

Adriatico Guest House Kastler Lecture Hall

14:15 Hydrophobic models of protein folding and the thermodynamics of chain-boundary interactions - I 45'

Speaker:	Erzan, A. (Istanbul Technical University, Turkey)
Material:	lecture notes

15:00 - 15:30 SAG phase:a new phase

Location: Adriatico Guest House Kastler Lecture Hall
- 15:00 SAG phase:a new phase 30'
  
  Speaker: Kumar, S. (Banaras Hindu University, India)
15:30 - 16:00 Coffee break

Location: Adriatico Guest House (Terrace)
- 15:30 Coffee break 30'

Wednesday, 14 May 2003
- 09:00 - 09:45 Signaling in plants: how do plants see, hear, and smell?
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 09:00 Signaling in plants: how do plants see, hear, and smell? 45'
    
    Speaker: Fedoroff, N. (Pennsylvania State University, University Park, PA, USA)
- 09:45 - 10:30 Helix-helix packing preferences in globular proteins
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 09:45 Helix-helix packing preferences in globular proteins 45'
    
    Speaker: Trovato, A. (Università degli Studi di Padova, Italy)
- 10:30 - 11:00 Coffee break
  
  Location: Adriatico Guest House (Terrace)
  - 10:30 Coffee break 30'
- 11:00 - 11:45 From polymers to proteins -- novel phases of short compact tubes
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 11:00 From polymers to proteins -- novel phases of short compact tubes 45'
    
    Speaker: Banavar, J. (Pennsylvania State University, University Park, USA)
- 11:45 - 12:30 Non-Markovian Dynamics and single Molecule folding
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 11:45 Non-Markovian Dynamics and single Molecule folding 45'
    
    Speaker: Wang, J. (State University of New York at Stony Brook, NY, USA)
- 12:30 - 14:15 Lunch break
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 12:30 Lunch break 1h45'
- 14:15 - 15:00 A long day's journey into simplicity - I
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 14:15 A long day's journey into simplicity - I 45'
    
    Speaker: Rose, G. (Johns Hopkins University, Baltimore, MD, USA)
- 15:00 - 15:20 Proton relaxivities of serum proteins
  
  Location: Adriatico Guest House Kastler Lecture Hall
  - 15:00 Proton relaxivities of serum proteins 20'
    
    Speaker: Yilmaz, A. (Dicle University, Diyarbakir, Turkey)
- 15:20 - 15:50 Coffee break
  
  Location: Adriatico Guest House (Terrace)
  - 15:20 Coffee break 30'
- 15:50 - 17:50 POSTER SESSION
  
  Location: Adriatico Guest House (Lower Level 1)
  - 15:50 POSTER SESSION 2h0'

Thursday, 15 May 2003

09:00 - 09:45 Molecular evolution of promoters: an experimental study

Location: Adriatico Guest House Kastler Lecture Hall
- 09:00 Molecular evolution of promoters: an experimental study 45'
  
  Speaker: 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

Location: Adriatico Guest House Kastler Lecture Hall
- 09:45 Comparison of the Dynamics and Hydration Patterns in Ribonuclease-A Family Proteins 45'
  
  Speaker: Vishveshwara, S. (Indian Institute of Science, Bangalore, India)
10:30 - 11:00 Coffee break

Location: Adriatico Guest House (Terrace)
- 10:30 Coffee break 30'
11:00 - 11:45 A long day's journey into simplicity - II

Location: Adriatico Guest House Kastler Lecture Hall
- 11:00 A long day's journey into simplicity - II 45'
  
  Speaker: Rose, G. (Johns Hopkins University, Baltimore, MD, USA)

11:45 - 12:30 Topology of transmembrane proteins

Location:

Adriatico Guest House Kastler Lecture Hall

11:45 Topology of transmembrane proteins 45'

Speaker:	Simon, I. (Institute of Enzymology, Budapest, Hungary)
Material:	lecture notes

12:30 - 14:15 Lunch break

Location: Adriatico Guest House Kastler Lecture Hall
- 12:30 Lunch break 1h45'
14:15 - 15:00 Topology and energetics in protein systems

Location: Adriatico Guest House Kastler Lecture Hall
- 14:15 Topology and energetics in protein systems 45'
  
  Speaker: Clementi, C. (Rice University, Houston, TX, USA)

15:00 - 15:45 Recognition in biomolecular energy landscapes: protein association vs protein folding.

Location:

Adriatico Guest House Kastler Lecture Hall

15:00 Recognition in biomolecular energy landscapes: protein association vs protein folding. 45'

Speaker:	Papoian, G. (University of California at San Diego, CA, USA)
Material:	lecture notes

15:45 - 16:15 Coffee break

Location: Adriatico Guest House (Terrace)
- 15:45 Coffee break 30'
16:15 - 16:45 Languages of genetic information: Why do living organisms have 4 nucleotide bases and 20 amino acids?

Location: Adriatico Guest House Kastler Lecture Hall
- 16:15 Languages of genetic information: Why do living organisms have 4 nucleotide bases and 20 amino acids? 30'
  
  Speaker: Patel, A. (Indian Institute of Science, Bangalore, India)

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