Search for: molecular-evolution
Article Chemistry and Biodiversity ; Volume 4, Issue 12 , 2007 , Pages 2766-2771 ; 16121872 (ISSN) ; Kargar, M ; Katanforoush, A ; Abolhassani, H ; Sadeghi, M ; Sharif University of Technology
Lattice models have been previously used to model ligand diffusion on protein surfaces. Using such models, it has been shown that the presence of pathways (or 'chreodes') of consecutive residues with certain properties can decrease the number of steps required for the arrival of a ligand at the active site. In this work, we show that, based on a genetic algorithm, ligand-diffusion pathways can evolve on a protein surface, when this surface is selected for shortening the travel length toward the active site. Biological implications of these results are discussed. © 2007 Verlag Helvetica Chimica Acta AG, Zürich
Article Bulletin of Mathematical Biology ; Volume 67, Issue 6 , 2005 , Pages 1355-1368 ; 00928240 (ISSN) ; Shateri Najafabadi, H ; Ahmadi Nejad, H ; Torabi, N ; Sharif University of Technology
Statistical and biochemical studies have revealed nonrandom patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslational errors and point mutations, since it is known that, when an amino acid is converted to another due to error, the biochemical properties of the resulted amino acid are usually very similar to those of the original one. In this study, we have taken into consideration both relative frequencies of amino acids and relative gene copy frequencies of tRNAs in genomic sequences in order to introduce a fitness function which models the mistranslational probabilities more accurately in modern organisms. The...
A quantum mechanical approach towards the calculation of transition probabilities between DNA codons, Article BioSystems ; Volume 184 , 2019 ; 03032647 (ISSN) ; Shafiee, A ; Sharif University of Technology
Elsevier Ireland Ltd 2019
The role of quantum tunneling in altering the structure of nucleotides to each other and causing a mutational event in DNA has been a topic of debate for years. Here, we introduce a new quantum mechanical approach for analyzing a typical point-mutation in DNA strands. Assuming each codon as a base state, a superposition of codon states could provide a physical description for a set of codons encoding the same amino acid and there are transition amplitudes between them. We choose the amino acids Phe and Ile as our understudy bio-systems which are encoded by two and three codons, respectively. We treat them as large quantum systems and use double- and triple-well potential models to study the...
On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices, Article Journal of Theoretical Biology ; Volume 235, Issue 3 , 2005 , Pages 318-325 ; 00225193 (ISSN) ; Shateri Najafabadi, H ; Hassani, K ; Ahmadi Nejad, H ; Torabi, N ; Sharif University of Technology
Statistical and biochemical studies have revealed non-random patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslation errors and point mutations, since it is known that when an amino acid is converted to another due to error, the biochemical properties of the resulted amino acid are usually very similar to those of the original one. In this study, using altered forms of the fitness functions used in the prior studies, we have optimized the parameters involved in the calculation of the error minimizing property of the genetic code so that the genetic code outscores the random codes as much as possible. This work also...
Article Journal of Theoretical Biology ; Volume 461 , 2019 , Pages 76-83 ; 00225193 (ISSN) ; Calvo, B ; Zohoor, H ; Firoozbakhsh, K ; Grasa, J ; Sharif University of Technology
Academic Press 2019
The Calcium ion Ca2+ plays a critical role as an initiator and preserving agent of the cross-bridge cycle in the force generation of skeletal muscle. A new multi-scale chemo-mechanical model is presented in order to analyze the role of Ca2+ in muscle fatigue and to predict fatigue behavior. To this end, a cross-bridge kinematic model was incorporated in a continuum based mechanical model, considering a thermodynamic compatible framework. The contractile velocity and the generated active force were directly related to the force-bearing states that were considered for the cross-bridge cycle. In order to determine the values of the model parameters, the output results of an isometric simulation...
A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins, Article BMC Bioinformatics ; Volume 9 , 2008 ; 14712105 (ISSN) ; Kargar, M ; Katanforoush, A ; Arab, S ; Sadeghi, M ; Pezeshk, H ; Eslahchi, C ; Marashi, S. A ; Sharif University of Technology
Background: It has been previously shown that palindromic sequences are frequently observed in proteins. However, our knowledge about their evolutionary origin and their possible importance is incomplete. Results: In this work, we tried to revisit this relatively neglected phenomenon. Several questions are addressed in this work. (1) It is known that there is a large chance of finding a palindrome in low complexity sequences (i.e. sequences with extreme amino acid usage bias). What is the role of sequence complexity in the evolution of palindromic sequences in proteins? (2) Do palindromes coincide with conserved protein sequences? If yes, what are the functions of these conserved segments?...