More is less: Use of Chemical Shifts for Protein Structure Determination

MARTIN, OSVALDO A.; ARNAUTOVA, YELENA A.; SCHERAGA, HAROLD A.; VILA, JORGE A.

San Javier, Tucumán

Congreso; XLI SAB 2012; 2012

It is well known that knowledge-based chemical shift (CS) servers, suchas SHIFTX [1], are able to predict the chemical shifts of all C and N nuclei in proteins, namely 13Calpha, 13Cbeta, 13C, and 15N. Moreover, it is also known that many CS-based protein structure determination methods [2, 3] make use of such information without questioning whether all of them are necessary. In other words, how many and which heavy-nuclei CS are needed for protein structure determination? Even more important, what is the advantage and dis-advantage to include information from all nuclei? These are very important questions for physics-based predictive methods, such as those derived by using quantum-mechanics calculations [4], because these methods, although very sensitive and accurate[5, 6], are very CPU time-demanding and, hence, it is necessary to precisely determine which nuclei are necessary, and sufficient, in order to accurately determine, validate and refine protein structures. Here, we will present some results indicating that the use of all C and N nuclei CS, rather than some of them, may not necessarily be more helpful for protein structure determination, validation and refinement.