Structure prediction techniques polypeptides

One of the most exciting new developments in protein structure prediction has been the approach of identifying whole protein folds from the amino acid sequence. With a fold being defined as the spatial position of the secondary-.structure elements relative to each other (the architecture), and their connectivity along the polypeptide chain (the topology) This approach employs techniques for aligning. sequences on... 

In addition to X-ray diffraction and NMR, which are direct techniques, methods based on the calculation of predicted three-dimensional structures of molecules in the range of 3 to 50 amino acids based on energy considerations are under rapid development. These approaches use what are commonly called molecular dynamics and energy minimization equations to specify the most probable conformation of polypeptides and small proteins. Often, when combined with information from other sources, such as X-ray crystallography or NMR studies, they have been demonstrated to be quite useful. However, when standing alone, their power and the accuracy of their predictive capability remains to be seen. 

Clearly, additional efforts to streamline 3D protein structure determination by MAS NMR are necessary. Novel concepts may make extensive use of the rapidly increasing power of bioinformatics and computational chemistry. Already, general approaches have appeared to predict 3D structure from a limited set of solution-state NMR data. " In parallel, the ability to relate molecular structure to NMR detectable parameters by ab initio quantum chemistry calculations and DFT approaches is dramatically improving.These techniques already have empowered novel material science applications of solid-state NMR and will greatly expand the use of MAS solid-state NMR for the study of polypeptides and proteins. Complementary to crystallographic... 

In the following sections we explore the molecular interactions responsible for the different levels of structure of biological macromolecules (primary, secondary, etc., as explained in Fundamentals F.1) and assemblies (such as biological membranes see Fundamentals El). We draw from the concepts developed in Sections 11.5-11.10 and describe computational techniques that can help with the prediction of the three-dimensional structure of polypeptides and polynucleotides. 

---