This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The study of protein complexes is crucial not only for the purpose of understanding regulatory pathways, but also for drug design. The scope of NMR or X-ray crystallography in predicting the structure of a protein complex is still limited, hence computational procedures involving docking of two proteins have gained importance. Traditionally, the problem of docking of two proteins is either based on geometry in which the protein frame is represented in the form of a mathematical model or energetics, in which the protein acts like a rigid, semi-flexible, or a flexible body. One of the major emerging trends in the later approach is to include the experimental information in the docking calculation. To this aim, this subproject deals with rigid body refinement on a complex formed by two proteins under ESR measured distance restraints. The refinement is performed by using a software package known as Crystallography and NMR System (CNS). This package has been traditionally used for macromolecular structure determination using crystallographic or NMR data as the input. It was necessary to make modifications in the program files in order to perform rigid body refinement on the basis of ESR distances. These distances were incorporated in a way similar to the NOE distances, which are in the form of a table and each distance (d) is allocated a negative error (dminus) and a positive error (dplus), thereby accounting for the flexibility of the spin label. The energy of the whole system is then minimized using the method of conjugate gradients. The refinement apart from depending on the accuracy of ESR measured distances, relies on the allocation of errors associated with each distance. At present, the program has been tested on a complex formed between chemotaxis proteins CheW and the P5 domain of delta 289 between which several ESR distances have been measured. Rigid body refinement gives a conformation of the two proteins that is close to the crystal structure of the complex. Significant is the fact that only 12 ESR distances between the two proteins were required to get a good approximation of their complex structure without any other supporting data. However, the program needs to be tested on more such systems, and a systematic way of assigning the errors associated with each ESR distance needs to be devised.
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