| Post: | Senior Lecturer in Chemical Biology |
| Location: | Chichester 3 |
| Email: | P.Varnai@sussex.ac.uk |
| Telephone numbers | |
| Internal: | 3881 |
| UK: | (01273) 873881 |
| International: | +44 1273 873881 |
Biography
1990-1993 BSc Technical University, Budapest (Hungary)
1993-1995 MSc in Chemical Engineering, Technical University, Budapest (Hungary)
1995-1996 research associate, Technical University, Budapest (Hungary)
1996-2000 DPhil in Physical Chemistry, University of Oxford
2000-2003 Wellcome International Prize Travelling Research fellow, Institut de Biologie Physico-Chimique, Paris (France)
2003-2007 Post-doctoral research associate, University of Cambridge
2007- Senior lecturer in Chemical Biology
Role
Degree programme convenor: MSc in Chemical Biology
Member of exam board (Chemistry)
Research
Our research is focused on understanding the physical principles how biomolecules attain their function. We develop and apply theoretical methods to study the interaction and conformational behaviour of nucleic acids and proteins at the atomic level in close collaboration with experiments. Our long-term goal is to use these ideas in the rational design of molecules for application in medicine and biotechnology.
Teaching
Courses organised and taught:
States of Matter (2nd year), Chemical Kinetics (2nd year), Chemical Biology (Master)
Courses taught (in part):
Advanced Physical Chemistry (4th year), Chemistry Project (3rd year), Chemical Principles (3rd year), Conceptual models (2nd year)
Publications
2010
Gáspári Z, Várnai P, Szappanos B, Perczel A
Reconciling the lock-and-key and dynamic views of canonical serine protease inhibitor action
FEBS LETTERS 584 (1): 203-206, 2010
2009
Allison JR, Varnai P, Dobson CM, Vendruscolo M
Determination of the free energy landscape of a-Synuclein using spin label nuclear magnetic resonance measurements
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 131 (51): 18314-18326, 2009
de Marco G, Varnai P
Molecular simulation of conformational transitions in biomolecules using a combination of structure-based potential and empirical valence bond theory
Physical Chemistry Chemical Physics 11: 10694-10700, 2009
Hsu ST, Varnai P, Bugaut A, Reszka AP, Neidle S, Balasubramanian S
A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 131 (37): 13399-13409, 2009
2008
Varnai P, Dobson CM, Vendruscolo M
Determination of the folding transition state of ubiquitin using experimental Phi- and Psi-values
JOURNAL OF MOLECULAR BIOLOGY 377 (2): 575-588, 2008
2007
Richter B, Gsponer J, Varnai P, Salvatella X, Vendruscolo M
The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins
JOURNAL OF BIOMOLECULAR NMR 37 (2): 117-135, 2007
2006
Varnai P, Lavery R
Book chapter: Modelling DNA deformations, Chapter 7 in Computational Studies of RNA and DNA, eds J. Sponer and F. Lankas, Springer Verlag 2006
2000-2005
Dixit SB, Beveridge DL, Case DA, Cheatham TE, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Sklenar H, Thayer KM, Varnai P
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
BIOPHYSICAL JOURNAL 89 (6): 3721-3740, 2005
Beveridge DL, Barreiro G, Byun KS, Case DA, Cheatham TE, Dixit SB, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Seibert E, Sklenar H, Stoll G, Thayer KM, Varnai P, Young MA
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(C(p)G) steps
BIOPHYSICAL JOURNAL 87 (6): 3799-3813, 2004
Varnai P, Canalia M, Leroy JL
Opening mechanism of G.T/U pairs in DNA and RNA duplexes: A combined study of imino proton exchange and molecular dynamics simulation
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 126 (44): 14659-14667, 2004
Varnai P, Zakrzewska K
DNA and its counterions: A molecular dynamics study
NUCLEIC ACIDS RESEARCH 32 (14): 4269-4280, 2004
Giudice E, Varnai P, Lavery R
Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations
NUCLEIC ACIDS RESEARCH 31 (5): 1434-1443, 2003
Varnai P, Djuranovic D, Lavery R, Hartmann B
alpha/gamma Transitions in the B-DNA backbone
NUCLEIC ACIDS RESEARCH 30 (24): 5398-5406, 2002
Topf M, Varnai P, Richards WG
Ab initio QM/MM dynamics simulation of the tetrahedral intermediate of serine proteases: Insights into the active site hydrogen-bonding network
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 124 (49): 14780-14788, 2002
Varnai P, Lavery R
Base flipping in DNA: Pathways and energetics studied with molecular dynamic simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 124 (25): 7272-7273, 2002
Topf M, Varnai P, Schofield CJ, Richards WG
Molecular dynamics simulations of the acyl-enzyme and the tetrahedral intermediate in the deacylation step of serine proteases
PROTEINS-STRUCTURE FUNCTION AND GENETICS 47 (3): 357-369, 2002
Giudice E, Varnai P, Lavery R
Energetic and conformational aspects of A : T base-pair opening within the DNA double helix
CHEMPHYSCHEM 2 (11): 673-677, 2001
Varnai P, Richards WG
A density functional study of the interconversion of carbonyls and alcohols in solution: Comparison of reaction mechanisms involving NADPH, histidine, and tyrosine
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 84 (2): 276-281, 2001
Topf M, Varnai P, Richards WG
Quantum mechanical/molecular mechanical study of three stationary points along the deacylation step of the catalytic mechanism of elastase
THEORETICAL CHEMISTRY ACCOUNTS 106 (1-2): 146-151, 2001
Varnai P, Warshel A
Computer simulation studies of the catalytic mechanism of human aldose reductase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 122 (16): 3849-3860, 2000