Download The basis of specific ligand recognition by proteins

The basis of specific ligand recognition by proteins
Goal
Characterise the role of internal molecular dynamics (entropy) for binding and specificity in protein-DNA
complexes through comparative database searches.
Background
Experimental structure determination by X-ray crystallography or NMR has provided many examples of
high-resolution structures of complexes between proteins and drugs, DNA or simply other proteins [1].
However, what really determines binding specificity is still largely unknown, as the very limited success of
drug design and protein modelling clearly shows. Many observations on proteins demonstrate the decisive
role of water, internal molecular dynamics and entropy in general. Consider the following few examples:
water molecules are essential elements in many macromolecular interfaces yet their residence times in these
interfaces are in the nano- to microsecond range [2-3]; binding sites of proteins exhibit significant
nanosecond mobility [4]; many enzymes could not work without sizeable motions of loops (opening/closing
of active sites) [5]; finally, a growing number of proteins adopt a define 3D structure only when binding to a
partner [6].
Project description
Interfaces of molecular complexes with proteins exhibit significant and relevant mobility, also referred to as
fluctuating networks of interactions; these often involve water molecules with very short residence times. The
general problem of mobility will be addressed by specifically looking at interfaces between proteins and
DNA, where the protein binds specifically to a certain DNA sequence (“reading” of DNA). Available
experimental data from the PDB database [1] will be collected and compared (sequence and structure). Next,
the conformational space for protein side chains that contact the DNA will be explored. Similarly, possible
mobility of water molecules will be characterised with computer simulations (“molecular dynamics
simulations”). The goal is to search for alternative protein-DNA interaction networks. Tthe outcome will be
statistically analysed, e.g. by comparing the number of alternative interactions, lifetimes of interaction
networks etc., and correlating these with binding strength and specificity. The final steps consist of an attempt
to derive a model for DNA sequence specificity and to suggest experimental tests on this model.
Project plan
1) Search the PDB for high-resolution protein-DNA
complexes involving critical water molecules.
2) Structurally compare the protein-DNA interfaces
both visually and in a quantitative manner.
3) Short molecular dynamics simulations on (selected)
protein-DNA complexes.
4) Analysis of the above calculations.
5) Model description and suggestions for experimental
tests; writing of thesis.
Handledare
Martin Billeter
Biophysics Group, Department of Chemistry
Email: [email protected]
Phone: +46 (0)31 773 3925
Website: www.bcbp.gu.se/~martinb
1) Protein Data Bank (PDB): www.rcsb.org/pdb.
2) Billeter M, Güntert P, Luginbühl P & Wüthrich K, Cell 85, 1057-1065 (1996).
3) Gutmanas A & Billeter M, Proteins 57, 772-782 (2004).
4) Zhuravleva A, Korzhnev DM, Kupce E, Arseniev AS, Billeter M & Orekhov VY, J.Mol.Biol. 342, 1599-1611 (2004).
5) Hammes GG, Biochemistry 41,8221-8228 (2002).
6) Love JJ, Li X, Chung J, Dyson HJ & Wright P, Biochemistry 43, 8725-8734 (2004).