INVESTIGATION ON THE STRUCTURE DIPEPTIDES INCLUDING HISTIDINE

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BAGHERI N.; MOMENI Z.

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Seminar Paper

Paper Information

Seminar: IRANIAN CHEMISTRY CONGRESS
Year:2014 | Issue:17

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Title

INVESTIGATION ON THE STRUCTURE DIPEPTIDES INCLUDING HISTIDINE

Author(s)

BAGHERI N. | MOMENI Z. | Issue Writer Certificate

Keywords

DIPEPTIDE

DIHEDRAL ANGLES

DFT CALCULATION

HISTIDINE

Abstract

BACKGROUND: AB INITIO CALCULATION ON PEPTIDE STRUCTURES HAS BEEN DONE [1]. BY OBSERVING RELEVANT DIHEDRAL ANGLES IN THE OPTIMIZED STRUCTURES OF SMALL AMINO ACID SEQUENCES, IT CAN BE DETERMINED IF SUCH PLANARITY IS ACTUALLY EXPECTED. THE USE OF Y 'S AND F 'S AS THE ONLY RELEVANT PARAMETERS TO CONSIDER IN PROTEIN STRUCTURE PREDICTIONS IS ALSO CONTINGENT ON THE GEOMETRY OF EACH A -CARBON. WHILE IT IS NOT EXPECTED THAT THE A -CARBON WILL HAVE PERFECT TETRAHEDRAL GEOMETRY DUE TO THE FACT THAT IT IS STEREOGENIC, IT IS ASSUMED THAT ITS BOND ANGLES THROUGHOUT EACH AMINO ACID IN A SEQUENCE SHOULD BE SIMILAR.METHODS: THE EIGHT DIPEPTIDE STRUCTURES STUDIED IN THIS PAPER WERE OPTIMIZED BOTH AT HF AND DFT LEVEL INDIVIDUALLY. OPTIMIZED ENERGY VALUES ARE OBTAINED WITH 6-311++G** BASIS SET IN EACH CASE. ALL THE COMPUTATIONS HAVE BEEN DONE USING GAUSSIAN 09 PROGROM.RESULTS: BOND ANGLE AROUND CARBON ATOM IS 109.5. BUT DUE TO THE STREOGENIC NATURE OF A-C ATOM THE IDEAL NATURE IS NOT EXPECTED. THE COMPARISON BETWEEN A-CARBON BOND ANGLES WHEN TWO HITIDINES ARE PRESENT SHOWS INTERESTING FACTS. THIS REVEALS THAT A-CARBON BOND ANGLES ARE DIFFERENT THOUGH IN BOTH SIDE HISTIDINE RESIDUES ARE PRESENT. THIS DIFFERENCE CAN BE EXPLAINED BY THE FACT THAT THE AMINE AND THE CARBOXYL ENVIRONMENT OF BOTH THE FIRST AMINO ACID AND THE X-AMINO ACID ARE DIFFERENT. DIHEDRAL ANGLE OF THE DIPEPTIDE BOND CAN GIVE SOME INFORMATION IN THIS REGARD. THE DIHEDRAL ANGLE D (DIHEDRAL ANGLE) SHOULD BE 180 IF THE AMIDE PLANE IS PLANAR.CONCLUSION: DIHEDRAL ANGLE OF THE DIPEPTIDE BOND CAN GIVE SOME INFORMATION IN THIS REGARD. AFTER A THOROUGH STUDY WITH DIFFERENT HIS-X COMBINATION WE CONCLUDE THAT HYDROGEN BONDING 19H AND OXYGEN 27O OF CARBOXYLIC ACID TERMINUS OF DIPEPTIDE PLAYS THE MAJER ROLE FOR DETERMINING THE VALUES OF D. THE INTERATOMIC DISTANCES (BETWEEN O AND H) ARE COMPATIDLE TO WEAK HYDROGEN BONDING IN PEPTIDE SYSTEMS.

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APA: Copy

BAGHERI, N., & MOMENI, Z.. (2014). INVESTIGATION ON THE STRUCTURE DIPEPTIDES INCLUDING HISTIDINE. IRANIAN CHEMISTRY CONGRESS. SID. https://sid.ir/paper/912876/en

Vancouver: Copy

BAGHERI N., MOMENI Z.. INVESTIGATION ON THE STRUCTURE DIPEPTIDES INCLUDING HISTIDINE. 2014. Available from: https://sid.ir/paper/912876/en

IEEE: Copy

N. BAGHERI, and Z. MOMENI, “INVESTIGATION ON THE STRUCTURE DIPEPTIDES INCLUDING HISTIDINE,” presented at the IRANIAN CHEMISTRY CONGRESS. 2014, [Online]. Available: https://sid.ir/paper/912876/en

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