TY - JOUR

T1 - Topological nature of the genetic code

AU - Karasev, V. A.

AU - Stefanov, V. E.

N1 - Funding Information: We are grateful to V. V. Luchinin for his support of this work and useful discussion of the paper. We also highly appreciate facilities o!ered in the laboratory of Dr Madariaga from Barcelona University during preparation of the manuscript and interesting discussions of the material. The work was "nancially supported by the research grants from Russian Foundation for Basic Research (RFFI) code 99-04-49836 and GR/CMID No. 50 from Ministry of Education of Russian Federation.

PY - 2001/4/7

Y1 - 2001/4/7

N2 - A model for topological coding of proteins is proposed. The model is based on the capacity of hydrogen bonds (property of connectivity) to fix conformations of protein molecules. The protein chain is modeled by an n-arc graph with the following elements: vertices (α-carbon atoms), structural edges (peptide bonds) and connectivity edges (virtual edges connecting non-adjacent atoms). It was shown that 64 conformations of the 4-arc graph can be described in the binary system by matrices of six variables which form a supermatrix containing four blocks. On the basis of correspondences between the pairs of variables in matrices and four letters of the genetic code matrices and supermatrix are converted, respectively, into the triplets and the table of the genetic code. An algorithm admitting computer programming is proposed for coding the n-arc graph and protein chain. Connectivity operators (polar amino acids) are assigned to blocks of triplets coding for cyclic conformations (G, A - In the second position), while anti-connectivity operators (non-polar amino acids) correspond to blocks of triplets coding for open conformations (C, U - In the second position). Amino acids coded by triplets differing by the first base have different structures. The third base for C, U and G, A is degenerated. Properties of the real genetic code are in full agreement with the model. The model provides an insight into the topological nature of the genetic code and can be used for development of algorithms for the prediction of the protein structure.

AB - A model for topological coding of proteins is proposed. The model is based on the capacity of hydrogen bonds (property of connectivity) to fix conformations of protein molecules. The protein chain is modeled by an n-arc graph with the following elements: vertices (α-carbon atoms), structural edges (peptide bonds) and connectivity edges (virtual edges connecting non-adjacent atoms). It was shown that 64 conformations of the 4-arc graph can be described in the binary system by matrices of six variables which form a supermatrix containing four blocks. On the basis of correspondences between the pairs of variables in matrices and four letters of the genetic code matrices and supermatrix are converted, respectively, into the triplets and the table of the genetic code. An algorithm admitting computer programming is proposed for coding the n-arc graph and protein chain. Connectivity operators (polar amino acids) are assigned to blocks of triplets coding for cyclic conformations (G, A - In the second position), while anti-connectivity operators (non-polar amino acids) correspond to blocks of triplets coding for open conformations (C, U - In the second position). Amino acids coded by triplets differing by the first base have different structures. The third base for C, U and G, A is degenerated. Properties of the real genetic code are in full agreement with the model. The model provides an insight into the topological nature of the genetic code and can be used for development of algorithms for the prediction of the protein structure.

UR - http://www.scopus.com/inward/record.url?scp=0035820188&partnerID=8YFLogxK

U2 - 10.1006/jtbi.2001.2265

DO - 10.1006/jtbi.2001.2265

M3 - Article

C2 - 11312591

AN - SCOPUS:0035820188

VL - 209

SP - 303

EP - 317

JO - Journal of Theoretical Biology

JF - Journal of Theoretical Biology

SN - 0022-5193

IS - 3

ER -