Mathematical and Computational Modelling of Ribosomal Movement and Protein Synthesis: An Overview

Haar, Tobias von der

doi:10.5936/csbj.201204002

Cited by 80 publications

(64 citation statements)

References 90 publications

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“…It is important to mention that while there are some thorough previous reviews related to the field or to pertinent topics (see, for example, (71,72)), here we focus on various aspects that haven't been comprehensively covered/examined before:…”

Section: Introductionmentioning

confidence: 99%

“…Translation or protein synthesis consists of a complex system of chemical reactions, which ultimately results in the decoding of the mRNA and the production of a protein. The complexity of this reaction system makes it difficult to quantitatively connect its input parameters (such as translation factors, ribosome concentrations, tRNA concentrations, mRNA codon composition or energy availability) to output parameters (such as protein synthesis rates or ribosome densities) (71). …”

Section: Introductionmentioning

confidence: 99%

“…( F ) The three different phases of the TASEP as a function of the initiation and elongation rate. ( G ) Rate limiting steps: for instance, efficient/non-efficient ribosome binding sites and weak/strong mRNA structure at the end of the 5′ UTR can promote either up/down regulation of translation (7,46,54,60–62,66,71,209,168,173). ( H ) The effect of the tRNA levels on codon decoding rates: codons that are recognized by low-abundance tRNA isoacceptors are decoded more slowly than those recognized by high-abundance tRNAs (19,42,46,48,51,54,66,68,140,149).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

2016

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mRNA translation is the fundamental process of decoding the information encoded in mRNA molecules by the ribosome for the synthesis of proteins. The centrality of this process in various biomedical disciplines such as cell biology, evolution and biotechnology, encouraged the development of dozens of mathematical and computational models of translation in recent years. These models aimed at capturing various biophysical aspects of the process. The objective of this review is to survey these models, focusing on those based and/or validated on real large-scale genomic data. We consider aspects such as the complexity of the models, the biophysical aspects they regard and the predictions they may provide. Furthermore, we survey the central systems biology discoveries reported on their basis. This review demonstrates the fundamental advantages of employing computational biophysical translation models in general, and discusses the relative advantages of the different approaches and the challenges in the field.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

2016

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“…Mathematical and computational modelling of ribosomal movement along with a discussion of the impact of modeling studies on experimentalists is summarized in [35].…”

Section: (Ijacsa) International Journal Of Advanced Computer Science Andmentioning

confidence: 99%

Computational Modeling of Proteins based on Cellular Automata

Madain¹,

Dalhoum²,

Sleit³

2016

ijacsa

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Abstract-The literature of building computational and mathematical models of proteins is rich and diverse, since its practical applications are of a vital importance in the development of many fields. Modeling proteins is not a straightforward process and in some modeling strategies, it requires to combine concepts from different fields including physics, chemistry, thermodynamics, and computer science. The focus here will be on models that are based on the concept of cellular automata and equivalent systems. Cellular automata are discrete computational models that are capable of universal computation, in other words, they are capable of doing any computation that a normal computer can do. What is special about cellular automata is its ability to produce complex and chaotic global behavior from local interactions. The paper discusses the effort done so far by the researchers community in this direction and proposes a computational model of protein folding that is based on 3D cellular automata. Unlike common models, the proposed model maintains the basic properties of cellular automata and keeps a realistic view of proteins operations. As in any cellular automata model, the dimension, neighborhood, boundary, and rules were specified. In addition, a discussion is given to clarify why these parameters are in place and what possible alternatives can be used in the protein folding context.

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“…Various mathematical model of protein synthesis process has been simulated in [12]. The mathematical model of protein chain elongation is described in [6].…”

Section: Related Workmentioning

confidence: 99%

Power Analysis of an mRNA-Ribosome System

Chatterjee

Ghosal

2018

EasyChair Preprints

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Energy is the heart to drive any device, such as any machine. As researchers have been trying to perform low energy operations more and more, energy requirements are turning out to be one of the key features in measuring the performance of a device. On the other hand, as conventional silicon-based computing is approaching a barrier, needs of non-conventional computing is increasing. Though several such computing platforms have arisen to prove itself as a suitable alternative to silicon-based computing, less energy requirement is certainly one of the most sought features in the competition among the new platforms. Moreover, there are certain scenarios where performing calculations in pure bio-molecular ways are highly desired. Although DNA computing has already agged the success of bio-molecular computing in terms of energy/power requirements, its manual nature keeps it behind from other computing techniques. Another new bio-molecular computing technique Ribosomal Computing, though still in infancy, has shown real promises due to its inherent automation. This work performs an analysis of the energy/power requirements of this computing technique. With the promising result obtained, ribosomal computing can claim itself as a promising computing technique, if combined with its inherent automation. CCS CONCEPTS• Computing methodologies → Modeling methodologies; Model veri cation and validation; • Hardware → Biology-related information processing;

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Mathematical and Computational Modelling of Ribosomal Movement and Protein Synthesis: An Overview

Cited by 80 publications

References 90 publications

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

Computational Modeling of Proteins based on Cellular Automata

Power Analysis of an mRNA-Ribosome System

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