Quantum-Chemical Description of the Propensity of Amino Acids of Formation of the Peptide Bond

    

    

    Figure 2:  Dependency of the parameter of propensity of amino acids of
peptide bond formation (KP) from the normalized frequency distribution matrix
(SIJ) [9]. 1: ala-gly; 2: ala-gln; 3: ala-leu; 4: ala-asn; 5: ala-val; 6: ala-pro; 7:
ala-arg; 8: ala-ile; 9: ala-thr; 10: ala-tyr; 11: ala-lys.
    
    

The list contains pairs of amino acids 20 series, for which K_P >1 and in earlier works Senger [19-21] and [22] are found also.

Given these conditions all amino acid pairs were distributed into three groups: low (1,1,2,2,3,3,3); middle (4,4,5,5,5,5,5) and the highest (6,6,7,7,8,8), where the numbers indicate the number of amino acid pairs in these series. From the suggested classification can draw some general conclusions. In particular the pairs of amino acids from series of tyrosine, leucine, lysine, glutamine, tryptophan and methionine should meet more often. Relatively less high frequency observed for the series of alanine, serine, aspartic acid, phenylalanine and glycine. Low frequency is characteristic for a series of isoleucine, asparagine, proline, tsisteyna, histidine, and threonine. From the individual amino acids the high frequency is characterized alanine (7), serine (9), glycine (10), lysine (11) and [23].

• seria (ala): ala-gly; ala-leu; ala-asn; ala-val. (4)
• seria (cys): cys-thr; cys-his. (2)
• seria (asp): asp-leu; asp-asp; asp-glu; asp-phe; asp-trp. (5)
• seria (glu): glu-ser; glu-cys; glu-gly; glu-val; glu-leu; gluasp; glu-trp. (7)
• seria (phe): phe-asp; phe-ser; phe-gly; phe-lys; phe-ile. (5)
• seria (gly): gly-glu; gly-leu; gly-val; gly-cys; gly-met. (5)
• seria (his): his-phe; his-his; his-asn. (3)
• seria (ile): ile-cys. (1)
• seria (lys): lys-his; lys-tyr; lys-gly; lys-ala; lys-ser; lys-leu; lys-pro. (7)
• seria (leu): leu-ile; leu-arg; leu-phe; leu-val; leu-ala; leuleu; leu-gly; leu-trp. (8)
• seria (met):met-his; met-tyr; met-pro; met-trp; met-ser; met-gln. (6)
• seria (asn): asn-lys. (1)
• seria (pro): pro-pro; pro-val. (2)
• seria (gln): gln-cys; gln-lys; gln-phe; gln-val; gln-gln. (5)
• seria (arg): arg-phe; arg-gln; arg-leu; arg-val; arg-gly. (5)
• seria (ser): ser-trp; ser-ser; ser-his; ser-ala. (4)
• seria (thr): thr-leu; thr-val; thr-pro. (3)
• seria (val): val-gln; val-trp; val-leu. (3)
• seria (trp): trp-ile; trp-met; trp-leu; trp-asn; trp-ser; trpthr. (6)
• seria (tyr): tyr-tyr; tyr-ser; tyr-pro; tyr-ile; tyr-met; tyrasn; tyr-gly; tyr-lys. (8) (Figure 1).



Figure 1: Scheme of the peptide bond formation resulting from the interaction of different amino acid.

    

    

    Figure 1:  Scheme of the peptide bond formation resulting from the interaction
of different amino acid.
    
    

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The symbatic dependence of the Kp from Sij is observed for only 11 pairs of amino acids from the series of alanine. Such selection of the amino acids pairs probably is caused by different direction of influence of inductive and steric effect of R-groups with respect to formation of peptide bonds. In other words, one R-group can promote other - prevent the formation of peptide bond. The dependence of Kp from the calculated frequency (%) [18] for the ten pairs of amino acids from different series is also a symbiotic (Figure 3). The similar situation can be expected from the remaining 19 series of amino acid pairs. From Figure 4 can be seen that the calculated frequency (%) of the nine amino acids symbatically depends on the charge of the carbon atom (q_C) of the carboxy group. This relationship is consistent with the known phenomenon that in the step of initiating a amino acids aminoacyl adenylic acid on this carbon atom is acts. The higher



Figure 3: Dependency of the parameter of propensity of amino acids of peptide bond formation (K_P) from the calculated frequency (%) [18]. 1: argarg; 2: glu-ser; 3: pro-pro; 4: gln-gln; 5: glu-pro; 6: asn-asn; 7: his-pro; 8: his-glu; 9: ile-met; 10: his-sis.

    

    

    Figure 3:  Dependency of the parameter of propensity of amino acids of
peptide bond formation (KP) from the calculated frequency (%) [18]. 1: argarg;
2: glu-ser; 3: pro-pro; 4: gln-gln; 5: glu-pro; 6: asn-asn; 7: his-pro; 8:
his-glu; 9: ile-met; 10: his-sis.
    
    

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Figure 4: The dependency of the calculated frequency of amino acids (%) [9] from the charge of carbon atom of carboxy group (q_c). 1-Met; 2-Cys; 3- Asn; 4-Phe; 5- Asp; 6-Glu; 7-Val; 8-Ser; 9-Ala.

    

    

    Figure 4:  The dependency of the calculated frequency of amino acids (%) [9]
from the charge of carbon atom of carboxy group (qc). 1-Met; 2-Cys; 3- Asn;
4-Phe; 5- Asp; 6-Glu; 7-Val; 8-Ser; 9-Ala.
    
    

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the value q_C the more the calculated frequency (%) [9].

Conclusion

The proposed quantum-chemical formula, which includes the calculated values of energetic, electronic and structural characteristics of amino acids can be applied for quantitative description of the propensity of amino acids for the peptide bond formation as these values quantitatively describe inductive and steric influence of R-groups of amino acids on the reaction center during the peptide bond formation. These factors together with the coding by means nucleotide bases can have an important role in the study of the amino acid sequences in proteins. According to Atkins the orderliness can turn into chaos, and in certain conditions, from chaos it is possible the formation of the orderliness also [23].

Acknowledgment

This work was supported by the European Commission FP7, Progect High-perfomance Computing Infrastructure for South East Europe’s Research Communities, Grant No: 261499.

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Citation: Kereselidze J and Mikuchadze G. Quantum-Chemical Description of the Propensity of Amino Acids of Formation of the Peptide Bond. Austin J Comput Biol Bioinform. 2016; 3(1): 1014. ISSN: 2379-7967

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