Volume 10, Issue 3 (2019)
JMBS 2019, 10(3): 433-440 |
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Mirzaie M. Impact of Hydrophobic Amino Acids in Protein Fold Recognition. JMBS 2019; 10 (3) :433-440
URL: http://biot.modares.ac.ir/article-22-23676-en.html
URL: http://biot.modares.ac.ir/article-22-23676-en.html
Applied Mathematics Department, Mathematical Sciences Faculty, Tarbiat Modares University, Tehran, Iran, Tarbiat Modares University, Nasr Bridge, Jalal-Al-Ahmad Highway, Tehran, Iran. , mirzaie@modares.ac.ir
Abstract: (4902 Views)
Aims: Prediction of three-dimensional structure from a sequence of amino acids is one of the important problems in structural bioinformatics. Proteins select a special structure among many possible conformations in order of seconds. Levinthal paradox expresses that random searches could not be an effective way to form a native structure and a principal mechanism should be available. Reduced alphabet fewer than 20 have been interested in protein structure because it could sufficiently simplify the protein folding problem. It is generally assumed that the native structure form in the lowest free energy among all conformational states. Therefore, it is needed to design a trustworthy potential function that could discriminate protein fold from incorrect ones.
Materials and Methods: Knowledge-based potential functions are one type of energy functions derived from a database of known protein structures. In this study, we introduce a knowledge-based potential and assess the power of five amino acids ALA, LEU, ILE, VAL, and PHE in discrimination of native structure using the reduced model. In the reduced model only the energy between the aforementioned amino acids are calculated.
Finding: The reduced model was evaluated using four criteria. The results indicate that there is no significant difference between the 20- amino acid model and the reduced model.
Conclusion: The presented model indicates that the power of discrimination of native structure is originally from the interaction between the aforementioned amino acids. Therefore, it needed a new strategy to capture the remaining interactions to improve the power of knowledge-based potential function.
Materials and Methods: Knowledge-based potential functions are one type of energy functions derived from a database of known protein structures. In this study, we introduce a knowledge-based potential and assess the power of five amino acids ALA, LEU, ILE, VAL, and PHE in discrimination of native structure using the reduced model. In the reduced model only the energy between the aforementioned amino acids are calculated.
Finding: The reduced model was evaluated using four criteria. The results indicate that there is no significant difference between the 20- amino acid model and the reduced model.
Conclusion: The presented model indicates that the power of discrimination of native structure is originally from the interaction between the aforementioned amino acids. Therefore, it needed a new strategy to capture the remaining interactions to improve the power of knowledge-based potential function.
Keywords: Protein Structure, Tertiary, Hydrophobic and Hydrophilic Interactions, Protein Folding, Atomic Energy
Article Type: Original Research |
Subject:
Bioinformatics
Received: 2018/07/31 | Accepted: 2018/09/25 | Published: 2019/09/21
Received: 2018/07/31 | Accepted: 2018/09/25 | Published: 2019/09/21
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