Study of peptide interactions in solution through the use of local correlation methods

by Joao Carlos Agostinho de Oliveira
Doctoral thesis
Date of Examination:2014-08-14
Date of issue:2014-12-03
Advisor:Prof. Dr. Ricardo Mata
Referee:Prof. Dr. Ricardo Jun.-Mata
Referee:Prof. Dr. Peter Botschwina
Persistent Address: http://dx.doi.org/10.53846/goediss-4805

 

 

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Abstract

English

The forces that control peptides conformations in solution have intrigued scientists over the decades. Understanding the former is of high interest, since they present a direct impact in the function and stability of enzymes and proteins. The emphasis of this work is on the study of peptide-ion interactions, as well as the effect of the solvent in the overall peptide conformation. The latter was explored for the specific case of beta-peptides. These are known to present an intrinsic propensity to fold into a variety of secondary structures. These features were verified in a variety of solvent environments and peptidic chains. In the present thesis, one proposes to study such effects by quantum mechanics. From the several methods available, one gives focus to local correlation methods, namely LMP2. Solvent effects were introduced by using an implicit solvation model. For the latter, COSMO was the model of choice. The COSMO-LMP2 model was shown to be quite promising in the treatment of amino acid-anions specific interactions, as well as in the study of the stability of beta-peptides conformers. The final work is dedicated to the development of a Perturbative Monte Carlo QM/MM scheme. Under this approach, the MM steps are treated perturbatively in their interaction with the QM system. The results revealed the potential of such approach in the treatment of properties of complex systems.
Keywords: Hofmeister Effect; Implicit Solvation Models; Local Correlation Methods; Peptide Conformations; Monte Carlo Simulations
 
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