Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics

PARRA, R. GONZALO; TSAI, MIN-YEH; FERREIRO, DIEGO U.; SCHAFER, NICHOLAS P.; GUZOVSKY, A. BRENDA; RADUSKY, LEANDRO G.; WOLYNES, PETER G.

NUCLEIC ACIDS RESEARCH

OXFORD UNIV PRESS

Año: 2016 vol. 44 p. 356 - 360

0305-1048

The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing proteins? biological behavior. It compares the energy distributions of the native state with respect to structural decoys. The network of minimally frustrated interactions encompasses the folding core of the molecule. Sites of high local frustration often correlate with functional regions such as binding sites and regions involved in allosteric transitions. We present here an upgraded version of a webserver that measures local frustration. The new implementation that allows the inclusion of electrostatic energy terms, important to the interactions with nucleic acids, is significantly faster than the previous version enabling the analysis of large macromolecular complexes within a user-friendly interface. The webserver is freely available at URL: http://frustratometer.qb.fcen.uba.ar.