Amino acid classes and the protein folding problem

Amino acid classes and the protein folding problem

Marek Cieplak, Neal S. Holter, Amos Maritan and Jayanth R. Banavar 1 Department of Physics and Center for Materials Physics, 104 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802 Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland 3 International School for Advanced Studies (SISSA), Via Beirut 2-4, 34014 Trieste, INF...

An amino acid code for protein folding.

Direct structural information obtained for many proteins supports the following conclusions. The amino acid sequences of proteins can stabilize not only the final native state but also a small set of discrete partially folded native-like intermediates. Intermediates are formed in steps that use as units the cooperative secondary structural elements of the native protein. Earlier intermediates g...

The Protein Non-Folding Problem: Amino Acid Determinants of Intrinsic Order and Disorder

To investigate the determinants of protein order and disorder, three primary and one derivative database of intrinsically disordered proteins were compiled. The segments in each primary database were characterized by one of the following: X-ray crystallography, nuclear magnetic resonance (NMR), or circular dichroism (CD). The derivative database was based on homology. The three primary disorder...

The protein folding problem.

The "protein folding problem" consists of three closely related puzzles: (a) What is the folding code? (b) What is the folding mechanism? (c) Can we predict the native structure of a protein from its amino acid sequence? Once regarded as a grand challenge, protein folding has seen great progress in recent years. Now, foldable proteins and nonbiological polymers are being designed routinely and ...

Protein Folding Recognition Based on Amino Acid Physicochemical Property Profiles