Title

The Effect of Insertion of D-Amino Acid on The Conformation of Cysteine Poly-Alanine Oligopeptides

Poster Number

7

Lead Author Major

Chemistry

Lead Author Status

Senior

Format

Poster Presentation

Faculty Mentor Name

Jianhua Ren

Faculty Mentor Department

Chemistry

Graduate Student Mentor Name

Yuntao Zhang

Graduate Student Mentor Department

Chemistry

Abstract/Artist Statement

Introduction :

Amino acids have two different enantiomeric forms (L- and D- forms) which are analogous to right- and left- handed configurations. Even though there is a dramatic preference for L-amino acids in biological systems, D-amino acids play important roles, the details of which are not yet discovered. Therefore, there is a significant gap in our knowledge of D-amino acids and their roles in biological systems as they were discovered in the early 19th century.

D-amino acids are found in single celled organisms to humans, playing critical roles in the functionality of organisms. D-alanine specifically has been found in the human brain, binding to NMDA receptors, which is important in controlling the memory function, it can improve the symptoms of patients with schizophrenia. In pharmaceuticals D-amino acids are used to stabilize peptides in therapeutics. The purpose of this study is to look at the effect of the position of D-amino acids on the structure and stability of peptides.

Method:

The conformation and energetics for seven cystine poly-alanine peptides are determined through molecular modeling, which includes low-level conformational searches and high-accuracy quantum calculations. The Conformer-Rotamer Ensemble Sampling Tool (CREST) is a utility program for the xtb program, working together to run an exhaustive conformation search. Further geometry optimization and energy calculations are conducted at HF/3-21G* and B3LYP/6-31+G**. The final lowest energy conformation of these peptides are compared and investigated in detail.

Result:

Looking at the anionic species, the CA5 peptide contains all L-amino acids, giving an alpha-helical conformation. Among D-amino acid containing peptides dCA5 and CAdAAAA maintain the alpha-helical conformation. CdAAAAA and CAAdAAA change to give a 3.10-helix conformation. CAAAdAA and CAAAAdA adopt a random coiled structure . For the neutral species, there is a loose coiled structure containing hydrogen bonds between the oxygen in peptide bonds and the hydrogen on the N-H.

Location

University of the Pacific, 3601 Pacific Ave., Stockton, CA 95211

Start Date

24-4-2021 1:00 PM

End Date

24-4-2021 2:15 PM

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Apr 24th, 1:00 PM Apr 24th, 2:15 PM

The Effect of Insertion of D-Amino Acid on The Conformation of Cysteine Poly-Alanine Oligopeptides

University of the Pacific, 3601 Pacific Ave., Stockton, CA 95211

Introduction :

Amino acids have two different enantiomeric forms (L- and D- forms) which are analogous to right- and left- handed configurations. Even though there is a dramatic preference for L-amino acids in biological systems, D-amino acids play important roles, the details of which are not yet discovered. Therefore, there is a significant gap in our knowledge of D-amino acids and their roles in biological systems as they were discovered in the early 19th century.

D-amino acids are found in single celled organisms to humans, playing critical roles in the functionality of organisms. D-alanine specifically has been found in the human brain, binding to NMDA receptors, which is important in controlling the memory function, it can improve the symptoms of patients with schizophrenia. In pharmaceuticals D-amino acids are used to stabilize peptides in therapeutics. The purpose of this study is to look at the effect of the position of D-amino acids on the structure and stability of peptides.

Method:

The conformation and energetics for seven cystine poly-alanine peptides are determined through molecular modeling, which includes low-level conformational searches and high-accuracy quantum calculations. The Conformer-Rotamer Ensemble Sampling Tool (CREST) is a utility program for the xtb program, working together to run an exhaustive conformation search. Further geometry optimization and energy calculations are conducted at HF/3-21G* and B3LYP/6-31+G**. The final lowest energy conformation of these peptides are compared and investigated in detail.

Result:

Looking at the anionic species, the CA5 peptide contains all L-amino acids, giving an alpha-helical conformation. Among D-amino acid containing peptides dCA5 and CAdAAAA maintain the alpha-helical conformation. CdAAAAA and CAAdAAA change to give a 3.10-helix conformation. CAAAdAA and CAAAAdA adopt a random coiled structure . For the neutral species, there is a loose coiled structure containing hydrogen bonds between the oxygen in peptide bonds and the hydrogen on the N-H.