THREADING EXAMPLE

Ana Rojas Mendoza.

ProteinDesign Group.
Centro Nacional de Biotecnologia (C.N.B.- C.S.I.C.)
Campus Universidad Autonoma.Cantoblanco. 28049 Madrid.
Tlf: +34-91-5854570. Fax: +34-91-5854506.
e-mail: arojas@gredos.cnb.uam.es

Madrid-Feb-04

3D Structure Prediction: A Threading Example.

Sequence:
>BX842656_101
MLKNTSSNLDAPVARSCDFAMKKMDLRKAFTLIEPGPVTLVTTSAGGTNNVMTISWTMAV
DFTPKLAITTGPWNFSYKALTKSRECVIAIPTVDLLDKVVGVGTCSGKDTDKFDTFRLTP
IKGKYVEAPLIKECVANIECKVVDIIKKHDIVVLEGVAAYFDTSRKEKRTLHAVGDGTFV
VDGRTLDRKKQMRSKLLGIF

Steps to follow:

0.- 1D data from the target	This is the Predict protein [ OUTPUT]
1.-Is this protein similar to another with known structure?	The results of "BLAST search against PDB. There IS NOT a known structure with sequence simmilarity to our query.
2.-What can I get from the annotation?:	SwissProtFile. In this case, swissprot indicates it is an hypothetical protein containing a Flavin reductase like domain. functions.
3.-Results from some threading steps	Some Meta PP server results: second and third predictions. FFAS03 Genesilico Metaserver
4.- How consistent is my fold assignment?	Some of the predicted folds are structuraly related: FSSP comparison results file
*5.a- Threading on 1EJE_A* structure**	Based on the secondary structure data, the protein might have 2 domains, one seems to be "all beta" and another the other one "mixed alpha-beta". The active site (FMN binding) of the query protein is located in the same spatial place as the template (`1EJE_A`) structure. Alignment structure-sequence : text format
*5.b- Mapping the query on 1EJE_A* structure** YELLOW: B-Strands. RED: Helices. GREY: No secondary structure elements. Note the loops (are missing)
*5.c- Threading on 1EJE_A* structure** A comparison between the threading predicted structure and the actual one: RED: The threading predicted model. GREEN: The template. REST: FMN (flavin) group and Ni heteratms. And, [HERE],the PDB file of the above comparison structure.