Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data

and Computer Simulations

Poster Abstracts

107

72-POS

Board 32

Local Descriptors of RNA Structures

Tymoteusz Oleniecki

2,1

, Agnieszka Mykowiecka

, Pawel Daniluk

1,4

Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland,

University of Warsaw, Warsaw, Poland,

University

of Warsaw, Warsaw, Poland.

Local Descriptors of Structure (LDS) have been proven useful in comparison and classification

of protein structures [1]. In this approach a protein is divided into overlapping fragments

representing neighbourhoods of each residue according to the chosen definition of inter-residue

contact. This allows to treat structures as non-rigid objects leaving out residue order, but putting

emphasis on architectural similarities [2]. Aim of this study was to generalize descriptor

approach to other biopolymers i.e. nucleic acids.

We have prepared two sets of RNA structures: a non-redundant set of 96 pure RNA structures to

develop and validate contact criteria on (CCV), and a set of nearly one thousand RNA chains,

which differ either in sequence or in structure, used for proper study (NR-RNA). We have also

designed a set of geometrical contact criteria of different accuracy and computational efficiency,

and assessed their feasibility by measuring contact preservation and genericity of descriptors

extracted from CCV. We have selected the simplest and most general criterion, which was

physico-chemically accurate. We used that criterion to compute a set of LDSs based on

structures in NR-RNA. Finally we assessed similarity of these LDSs and clustered them.

We have obtained a database of representative recurrent RNA structural patterns present in

PDB/NDB which, like their protein counterparts, could be useful in classification and statistical

analysis of RNA structures as well as prediction of tertiary structure.

These studies were supported by National Science Centre (DEC-2011/03/D/NZ2/02004), and by

the BST-176600/BF (task 22) funds of Faculty of Physics, University of Warsaw. Computations

were carried out using infrastructures financed by the POIG.02.03.00-00-003/09 (Biocentrum-

Ochota) and POIG.02.01.00-14-122/09 (Physics at the basis of new technologies) projects.