Abstract
Thermal oscillations observed in proteins are acknowledged as essential to managing the biological capabilities of this complex molecule. However, their behavior and characteristics are yet to be clarified. In this research, affinities of tetrapeptides in active areas of ficin, where domain oscillations were observed, were analyzed using dual artificial intelligence methods and computer simulations. The results show that the oscillations were able to handle temporal alteration of their affinities in its active areas. Moreover, it was inferred that the improvement in the flexibility of the β strand between the domains would enhance the oscillations and reduce the optimal temperature. Finally, the decision tree presented important attributes that would play key roles in molecular design.
Highlights
Thermal oscillations occurring within the structure of proteins are widely recognized as key factors in controlling its biological potentials.1–4 In many cases, the protein structure is composed of several domains in which thermal oscillations are observed
The behavior of the candidates was analyzed by molecular dynamics (MD) and docking simulations, and the analytical results were stored in the training data
The temperature of the system was retained at 300 K by means of MD simulation, and the peculiar structural changes were checked at several time intervals
Summary
Thermal oscillations occurring within the structure of proteins are widely recognized as key factors in controlling its biological potentials. In many cases, the protein structure is composed of several domains in which thermal oscillations are observed. Thermal oscillations occurring within the structure of proteins are widely recognized as key factors in controlling its biological potentials.. The protein structure is composed of several domains in which thermal oscillations are observed. The behavior and capabilities of proteins and their relationship with these oscillatory phenomena would receive considerable attention once explored. The protein ficin is used for the fabrication of novel antimicrobial therapeutics and in the enhancement of transfusion safety and tenderization of meat among others.. Ficin is composed of two domains, in which some of the decomposed peptides were fitted neatly in between these domains. Oscillations occurring between the ficin’s domains would substantially influence the activities of the protein. The detailed activities of the said protein are not elucidated with regard to its oscillating structure Ficin is a type of protease, and studies on protease inhibitors have supported the discussion on peptides interposed between the two domains of ficin. the detailed activities of the said protein are not elucidated with regard to its oscillating structure
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