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An approach towards the prediction of protein tertiary structures: molecular modeling perspectives

Impressive advances in genomic sequencing technologies are flooding us with the complete genetic blueprints of human, rat, mouse, chimpanzee and various microorganisms at an extremely rapid pace. As these DNA sequences continue to accumulate, the challenge to determine the function of each gene i...

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Main Authors: Ahmad Khairudin, Nurul Bahiyah, A. Wahab, Habibah, Samian, Mohd. Razip, Najimudin, Nazalan
Format: Book Section
Published: Penerbit UTM 2008
Subjects:
QD Chemistry
Online Access:http://eprints.utm.my/id/eprint/16773/
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spelling my.utm.167732017-10-08T07:03:45Z http://eprints.utm.my/id/eprint/16773/ An approach towards the prediction of protein tertiary structures: molecular modeling perspectives Ahmad Khairudin, Nurul Bahiyah A. Wahab, Habibah Samian, Mohd. Razip Najimudin, Nazalan QD Chemistry Impressive advances in genomic sequencing technologies are flooding us with the complete genetic blueprints of human, rat, mouse, chimpanzee and various microorganisms at an extremely rapid pace. As these DNA sequences continue to accumulate, the challenge to determine the function of each gene is paramount. These functions are determined by their unique three-dimensional (3D) structures as a result of protein folding. Protein folding can be defined as the process in which proteins spontaneously arrange their linear sequence of amino acids into native 3D structures that will allow them to function properly. Thus, elucidation of the 3D structure of a protein is vital in understanding its function. However, it is not known how the newly synthesized polypeptide chains fold into a protein with specific function. It was not until 1973 that Anfinsen [1] postulated that all the information needed for a protein to correctly fold into its native structure is encoded solely in its amino acid sequence and that the native state of the protein is the conformation with the lowest energy. Consequently, this important principle has brought immense interests among the scientists to investigate how proteins fold into their native structures and eventually determine the correct functional fold for the proteins. The two most mature and conventional experimental techniques to solve the structure of a protein are the X-ray crystallography and Nuclear Magnetic Resonance (NMR). John Kendrew and Max Perutz shared the Nobel Prize in 1962 for their pioneering achievement in solving the atomic level structure of the protein myoglobin and hemoglobin, respectively, using X-ray diffraction. Since then, many protein structures were solved and various roles of proteins in living cells were known. Despite the accuracy and the advances of these experimental techniques, such methods are very costly and it may take months to years for solving one structure. The current number of 3D protein structures is very small compared to the number of protein sequences, creating a huge gap between them. It has become more pressing with the growth of genome sequencing projects providing protein sequences for which structural information is not available. As this gap is expected to keep on growing with the ongoing genome projects, the experimental techniques certainly cannot be expected to keep pace with the rapid flow of the sequences. This has caused an urgent need to accurately predict the 3D structure of proteins from the linear chain of amino acid sequence using other methods especially computational work that relies heavily on theoretical studies. However, despite decades of active research and the impressive advances [2,3,4,5], computational protein structure prediction and protein folding remain one of the most important unsolved problems in structural biology today [6,7,8]. Penerbit UTM 2008 Book Section PeerReviewed Ahmad Khairudin, Nurul Bahiyah and A. Wahab, Habibah and Samian, Mohd. Razip and Najimudin, Nazalan (2008) An approach towards the prediction of protein tertiary structures: molecular modeling perspectives. In: Special Topics In Bioprocess Engineering Volume III. Penerbit UTM , Johor, 1 - 34. ISBN 978-983-52-0602-3
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
topic QD Chemistry
spellingShingle QD Chemistry
Ahmad Khairudin, Nurul Bahiyah
A. Wahab, Habibah
Samian, Mohd. Razip
Najimudin, Nazalan
An approach towards the prediction of protein tertiary structures: molecular modeling perspectives
description Impressive advances in genomic sequencing technologies are flooding us with the complete genetic blueprints of human, rat, mouse, chimpanzee and various microorganisms at an extremely rapid pace. As these DNA sequences continue to accumulate, the challenge to determine the function of each gene is paramount. These functions are determined by their unique three-dimensional (3D) structures as a result of protein folding. Protein folding can be defined as the process in which proteins spontaneously arrange their linear sequence of amino acids into native 3D structures that will allow them to function properly. Thus, elucidation of the 3D structure of a protein is vital in understanding its function. However, it is not known how the newly synthesized polypeptide chains fold into a protein with specific function. It was not until 1973 that Anfinsen [1] postulated that all the information needed for a protein to correctly fold into its native structure is encoded solely in its amino acid sequence and that the native state of the protein is the conformation with the lowest energy. Consequently, this important principle has brought immense interests among the scientists to investigate how proteins fold into their native structures and eventually determine the correct functional fold for the proteins. The two most mature and conventional experimental techniques to solve the structure of a protein are the X-ray crystallography and Nuclear Magnetic Resonance (NMR). John Kendrew and Max Perutz shared the Nobel Prize in 1962 for their pioneering achievement in solving the atomic level structure of the protein myoglobin and hemoglobin, respectively, using X-ray diffraction. Since then, many protein structures were solved and various roles of proteins in living cells were known. Despite the accuracy and the advances of these experimental techniques, such methods are very costly and it may take months to years for solving one structure. The current number of 3D protein structures is very small compared to the number of protein sequences, creating a huge gap between them. It has become more pressing with the growth of genome sequencing projects providing protein sequences for which structural information is not available. As this gap is expected to keep on growing with the ongoing genome projects, the experimental techniques certainly cannot be expected to keep pace with the rapid flow of the sequences. This has caused an urgent need to accurately predict the 3D structure of proteins from the linear chain of amino acid sequence using other methods especially computational work that relies heavily on theoretical studies. However, despite decades of active research and the impressive advances [2,3,4,5], computational protein structure prediction and protein folding remain one of the most important unsolved problems in structural biology today [6,7,8].
format Book Section
author Ahmad Khairudin, Nurul Bahiyah
A. Wahab, Habibah
Samian, Mohd. Razip
Najimudin, Nazalan
author_facet Ahmad Khairudin, Nurul Bahiyah
A. Wahab, Habibah
Samian, Mohd. Razip
Najimudin, Nazalan
author_sort Ahmad Khairudin, Nurul Bahiyah
title An approach towards the prediction of protein tertiary structures: molecular modeling perspectives
title_short An approach towards the prediction of protein tertiary structures: molecular modeling perspectives
title_full An approach towards the prediction of protein tertiary structures: molecular modeling perspectives
title_fullStr An approach towards the prediction of protein tertiary structures: molecular modeling perspectives
title_full_unstemmed An approach towards the prediction of protein tertiary structures: molecular modeling perspectives
title_sort approach towards the prediction of protein tertiary structures: molecular modeling perspectives
publisher Penerbit UTM
publishDate 2008
url http://eprints.utm.my/id/eprint/16773/
_version_ 1643646656542932992
score 13.211869

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