[phenixbb] modelling of disordered protein

intekhab alam faisaldbg at gmail.com
Tue Aug 16 00:24:31 PDT 2011

```Hi
I solved an RNA polymerase structure in its native as well as in complex
with chemical ligands (2.5A and C2 space group). The structure has been
solved by MR a protein having 60% identity. The ASU has a monomer and dimer.

Recently i complexed this RNA polymerase (protein A) with a highly flexible
protein B and got the crystal. These crytsal also have C2 space group
(resolution 2.3A) having similar cell parameters but has psudotranslation
(17.34%). I tried MR using rosetta. HHpred server selected one of my
deposited structure in PDB (3NAI 100% identity) as template. Rosetta MR gave
2 solutions one of which is dimer-monomer arrangement while the other one is
a trimer. The values of these solution are below.

Solution 1: trimer
REMARK Log-Likelihood Gain:  10662.548
REMARK  RFZ=16.5 TFZ=14.4 PAK=0 LLG=959 TFZ==23.2 RFZ=0.0 TFZ=48.9 PAK=0
LLG=3195 TFZ==55.6 (& TFZ==52.6) LLG+=(3191 & 7008) LLG=7024 TFZ==72.0
LLG=10663 TFZ==90.1
Solution 2: Monomer and dimer in ASU

REMARK Log-Likelihood Gain:  2120.965
REMARK  RFZ=39.7 TFZ=21.9 PAK=0 LLG=811 TFZ==37.7 LLG=2121 TFZ==43.6
REMARK ENSEMBLE ensemble_1 EULER 204.07 178.91 204.37 FRAC  0.499

Map and model fits well in both the cases with R and R free 26 and 30%
respectively.

My queries:
1. which one will be the correct solution? Is it possible that the protein B
has resulted in the trimeric arrangement?
2. i cannot find any continuous 2Fo-Fc map for proteinB, but there are some
continuous density at 0.7 which is very ambiguous. how can i improve the map
so that i can model some fragments of my  proteinB (protein B is of 73 amino
acids and is predicted to be highly flexible and disordered. ((biochemical
as well as bioinformatical analysis done ))

I already have tried autobuild but it fails to build even a partial fragment
of the proteinB.

Kindly suggest how to proceed , or how can i prove the presence of protein B
in the structure.

Regards
INTEKHAB ALAM
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL
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