Conformational Space Modelling


Responsible for the project: Ajasja Ljubetič

Membrane proteins (MP) play a pivotal role in such diverse processes as cell signalling, cell differentiation and viral infections. The structure of MP is vital for understanding such processes, but determining it is not a trivial task. This can easily be seen in the Protein Data Base. In 2011 the database held only ~1% MPs, while the human genome is estimated to contain about 30 % MPs.
Conformational space modelling (CSM) is a promising method for MP structure determination. It is based on the concept of side-chain conformational spaces (SCCS), which are formed by the allowed side chain conformations of a given residue. Each SCCS can be calculated from a 3D structure or measured via EPR-SDSL experiments. For structure determination a set of singly spin-labelled mutants is needed. The final structure is obtained by altering an initial (possibly random) 3D structure until the best fit between the calculated and measured SCCS for the whole set is found. The result is a set of best-fit structures, similar to NMR structure determination.

We have applied this this method to study:

  1. the protein complex of Measles virus (interaction of C-terminal end of the nucleoprotein with X-domain of phosphoprotein) in collaboration with Prof. Sonia Longhi (CNRS - Marseille - France)
  2. the major coat protein of the M13 bacteriophage in membrane in collaboration with Dr. Marcus A. Hemminga (Wageningen University - The Netherlands)
  3. the light harvesting complex CP29 in collaboration with Dr. Marcus A. Hemminga (Wageningen University - The Netherlands)

While calculating the SCCS the effect of neibhouring side-chains and of lipid tails has to be taken into account. We are in the process of improving the description of this lipid effect using enhanced sampling molecular dynamics. We are also improving the optimization method used for the fitting of structures.


People involved:

Project leader: Janez Štrancar

Responsible: Ajasja Ljubetič

Previous members: Aleh Kavalenka


Publications:

ŠTRANCAR, Janez, KAVALENKA, Aleh A., URBANČIČ, Iztok, LJUBETIČ, Ajasja, HEMMINGA, Marcus A.
SDSL-ESR-based protein structure characterization.
Eur. biophys. j., 2010, vol. 39, no. 4, p. 499-511,doi: 10.1007/s00249-009-0510-5 (pdf).

KAVALENKA, Aleh A., URBANČIČ, Iztok, BELLE, Valérie, SOUGER, Sabrina, CONSTANZO, Stéphanie, KURE, Sandra, FOURNEL, André, LONGHI, Sonia, GUIGLIARELLI, Bruno, ŠTRANCAR, Janez.
Conformational analysis of the partially disordered measles virus NTAIL-XD complex by SDSL EPR spectroscopy.
Biophys. j., 2010, vol. 98, no. 6, p. 1055-1064. doi: 10.1016/j.bpj.2009.11.036 (pdf).

KAVALENKA, Aleh A., SPRUIJT, Ruud B., WOLFS, Cor J.A.M., ŠTRANCAR, Janez, CROCE, Roberta, HEMMINGA, Marcus A., VAN AMERONGEN, Herbert.
Site-directed spin-labeling study of the light-harvesting comlex CP29.
Biophys. j., 2009, vol. 96, no. 9, p. 3620-3628. doi: 10.1016/j.bpj.2009.01.038.

ŠTRANCAR, Janez, KAVALENKA, Aleh A., ZIHERL, Primož, STOPAR, David, HEMMINGA, Marcus A.
Analysis of side chain rotational restrictions of membrane-embedded proteins by spin-label ESR spectroscopy.
J. magn. reson. (San Diego, Calif., 1997), 2009, vol. 197, no. 2, p. 245-248.

BELLE, Valerie, ROUGER, Sabrina, CONSTANZO, Stéphanie, LIQUIERE, Elodie, ŠTRANCAR, Janez, GUIGLIARELLI, Bruno, FOURNEL, André, LONGHI, Sonia.
Mapping [alpha]-helical induced folding within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by site-directed spin-labeling EPR spectroscopy.
Proteins, 2008, issue 4, vol. 73, p. 973-988, doi: 10.1002/prot.22125.

STOPAR, David, ŠTRANCAR, Janez, SPRUIJT, Ruud B., HEMMINGA, Marcus A.
Motional restrictions of membrane proteins: a site-directed spin labeling study.
Biophys. j., 2006, vol. 91, no. 9, p. 3341-3348. doi: 10.1529/biophysj.106.090308.

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