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Structures Closed into Cycles in Proteins Containing 3β-Corners

E. A. Boshkova and A. V. Efimov*

Institute of Protein Research, Russian Academy of Sciences, ul. Institutskaya 4, 142290 Pushchino, Moscow Region, Russia; fax: (495) 514-0218; E-mail: efimov@protres.ru

* To whom correspondence should be addressed.

Received April 21, 2010
In the present study, pathways of growth of protein structures represented in the structural tree for β-proteins containing 3β-corners are analyzed. It is shown that the frequency of occurrence of the completed structures of known proteins within branches of the tree is quite different. This means that allowed pathways of growth of protein structures are not equal and their usage is quite different. In most cases, addition of one or two β-strands nearest along the chain to the root 3β-corner (67%) or addition of three β-strands to the 3β-corner results in the formation of structures closed into cycles or barrels. Therefore, the pathways that result in closed structures are used most often in the first steps of growth of the root 3β-corner. Amino acid sequences coding for left-handed superhelices that close into cycles the 3β-corners are also analyzed. It is demonstrated that most crossover sites where the polypeptide chain passes from one β-layer to the other have one or two residues in sterically constrained αL- or ε-conformations, which should be glycines or residues with flexible side chains in order to reduce the steric constraints.
KEY WORDS: protein structure modeling, protein folding, structural trees

DOI: 10.1134/S000629791010007X