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Functional Residues in Proteins Journal of Amino Acids Functional Residues in Proteins Guest Editors: Shandar Ahmad, Jung-Ying Wang, Zulfiqar Ahmad, and Faizan Ahmad Functional Residues in Proteins Journal of Amino Acids Functional Residues in Proteins Guest Editors: Shandar Ahmad, Jung-Ying Wang, Zulfiqar Ahmad, and Faizan Ahmad Copyright © 2011 SAGE-Hindawi Access to Research. All rights reserved. This is a special issue published in volume 2011 of “Journal of Amino Acids.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Editorial Board Fernando Albericio, Spain Mario Herrera-Marschitz, Chile Vadim A. Soloshonok, USA Jordi Bella, UK Riccardo Ientile, Italy Imre Sovago, Hungary Simone Beninati, Italy Hieronim Jakubowski, USA Heather M. Wallace, UK Carlo Chiarla, Italy Madeleine M. Joullie, USA Peter W. Watt, UK Kuo-Chen Chou, USA Sambasivarao Kotha, India Robert Wolfe, USA Arthur Conigrave, Australia Rentala Madhubala, India Guoyao Wu, USA Arthur J. L. Cooper, USA Andrei Malkov, UK Andreas Wyttenbach, UK Zbigniew Czarnocki, Poland Yasufumi Ohfune, Japan Nigel Yarlett, USA Dorothy Gietzen, USA Norbert Sewald, Germany Axel G. Griesbeck, Germany H. S. Sharma, Sweden Contents Functional Residues in Proteins, Shandar Ahmad, Jung-Ying Wang, Zulfiqar Ahmad, and Faizan Ahmad Volume 2011, Article ID 606354, 1 page Small Changes Huge Impact: The Role of Protein Posttranslational Modifications in Cellular Homeostasis and Disease, Tejaswita M. Karve and Amrita K. Cheema Volume 2011, Article ID 207691, 13 pages Role of Charged Residues in the Catalytic Sites of Escherichia coli ATP Synthase,ZulfiqarAhmad, Florence Okafor, and Thomas F. Laughlin Volume 2011, Article ID 785741, 12 pages Functionally Relevant Residues of Cdr1p: A Multidrug ABC Transporter of Human Pathogenic Candida albicans, Rajendra Prasad, Monika Sharma, and Manpreet Kaur Rawal Volume 2011, Article ID 531412, 12 pages The Dynamic Structure of the Estrogen Receptor, Raj Kumar, Mikhail N. Zakharov, Shagufta H. Khan, Rika Miki, Hyeran Jang, Gianluca Toraldo, Rajan Singh, Shalender Bhasin, and Ravi Jasuja Volume 2011, Article ID 812540, 7 pages Catalytic Site Cysteines of Thiol Enzyme: Sulfurtransferases, Noriyuki Nagahara Volume 2011, Article ID 709404, 7 pages The Catalytic Machinery of a Key Enzyme in Amino Acid Biosynthesis,RonaldE.Viola, Christopher R. Faehnle, Julio Blanco, Roger A. Moore, Xuying Liu, Buenafe T. Arachea, and Alexander G. Pavlovsky Volume 2011, Article ID 352538, 11 pages Metal Preferences of Zinc-Binding Motif on Metalloproteases, Kayoko M. Fukasawa, Toshiyuki Hata, Yukio Ono, and Junzo Hirose Volume 2011, Article ID 574816, 7 pages Serpin Inhibition Mechanism: A Delicate Balance between Native Metastable State and Polymerization, Mohammad Sazzad Khan, Poonam Singh, Asim Azhar, Asma Naseem, Qudsia Rashid, Mohammad Anaul Kabir, and Mohamad Aman Jairajpuri Volume 2011, Article ID 606797, 10 pages Functional Subunits of Eukaryotic Chaperonin CCT/TRiC in Protein Folding,M.AnaulKabir, Wasim Uddin, Aswathy Narayanan, Praveen Kumar Reddy, M. Aman Jairajpuri, Fred Sherman, and Zulfiqar Ahmad Volume 2011, Article ID 843206, 16 pages SAGE-Hindawi Access to Research Journal of Amino Acids Volume 2011, Article ID 606354, 1 page doi:10.4061/2011/606354 Editorial Functional Residues in Proteins Shandar Ahmad,1 Jung-Ying Wang,2 Zulfiqar Ahmad,3 and Faizan Ahmad4 1 National Institute of Biomedical Innovation, Osaka, Japan 2 Lunghwa University of Science and Technology, Taiwan 3 Department of Biology, Alabama A&M University, Normal, AL 35762, USA 4 Centre for Interdisciplinary Research in Basic Sciences, India Correspondence should be addressed to Shandar Ahmad, [email protected] Received 15 September 2011; Accepted 15 September 2011 Copyright © 2011 Shandar Ahmad et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. We are delighted to present a special issue on the subject M. A. Kabir et al. present an investigation of a eukaryotic of functional residues of proteins. Finding focused articles chaperon, involved in protein-folding. within the time frame of a special issue is always challenging, Thus, the special issue covers a wide range of systems and which is further compounded by authors’ reluctance in describes an overview of some of the most significant studies making their contributions to new journals. We have been on the subject of finding functional residues in proteins. fortunate enough that some leading researchers in the field We would like to express our most sincere gratitude to the agreed to support this special issue and contributed their authors who agreed to contribute and referees who provided work at our request. We present here nine articles on various useful feedback, allowing the papers to meet the high stand- aspects of the subject. We received some more submis- ards of publication. sions, which could not be accommodated because of a strict We hope that the readers of Journal of Amino Acids will quality control, we tried to maintain. Finally compiled spe- find these articles of great interest and look forward to any cial issue starts with a very interesting commentary on post- comments to improve our future efforts. translated modifications leading to normal and disease- associated biological functions, contributed by T. M. Karve Shandar Ahmad and A. K. Cheema. This is followed by the analysis of a Jung-Ying Wang specific biological system of ATP synthetase, contributed by Zulfiqar Ahmad Z. Ahmad et al., exploring its catalytic sites and focusing Faizan Ahmad on charged residues. R. Prasad et al. then describe a related system of ABC transporters and review the state of the knowledge on its functional residues. Functional residues in a protein do not always follow a universal pattern, and this is demonstrated by R. Kumar et al. in describing the dynamic structure of estrogen receptors. This paper is then followed by a special group of functional residues, that is, cysteins in sulfurtransferases by N. Nagahara. Viola et al. present an excellent study of catalytic machinery in the biosynthesis of amino acids. Subsequntly, K. M. Fukasawa et al. then present their analysis of functionally relevant zinc-binding sites in metalloproteases. Subsequently, M. S. Khan et al. provide an elaborate discussion on the mechanism of serpin inhibition, specially focusing on the role of polymerization. Finally, SAGE-Hindawi Access to Research Journal of Amino Acids Volume 2011, Article ID 207691, 13 pages doi:10.4061/2011/207691 Review Article Small Changes Huge Impact: The Role of Protein Posttranslational Modifications in Cellular Homeostasis and Disease Tejaswita M. Karve 1 and Amrita K. Cheema2 1 Department of Biochemistry, Cellular & Molecular Biology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, 3900 Reservoir Road, NW, Washington DC 20057, USA 2 Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057, USA Correspondence should be addressed to Amrita K. Cheema, [email protected] Received 23 February 2011; Accepted 18 April 2011 Academic Editor: Zulfiqar Ahmad Copyright © 2011 T. M. Karve and A. K. Cheema. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Posttranslational modifications (PTMs) modulate protein function in most eukaryotes and have a ubiquitous role in diverse range of cellular functions. Identification, characterization, and mapping of these modifications to specific amino acid residues on proteins are critical towards understanding their functional significance in a biological context. The interpretation of proteome data obtained from the high-throughput methods cannot be deciphered unambiguously without a priori knowledge of protein modifications. An in-depth understanding of protein PTMs is important not only for gaining a perception of a wide array of cellular functions but also towards developing drug therapies for many life-threatening diseases like cancer and neurodegenerative disorders. Many of the protein modifications like ubiquitination play a decisive role in various drug response(s) and eventually in disease prognosis. Thus, many commonly observed PTMs are routinely tracked as disease markers while many others are used as molecular targets for developing target-specific therapies. In this paper, we summarize some of the major, well-studied protein alterations and highlight their importance in various chronic diseases and normal development. In addition, other promising minor modifications such as SUMOylation, observed to impact cellular dynamics as well as disease pathology, are mentioned briefly. 1. Introduction and hydroxylation. Posttranslational modifications (PTMs) of proteins influence the enzyme activity, protein turnover With current advances in the fields of systems biology and and localization, protein-protein interactions, modulation proteomics, the interest in deciphering protein modifications for various signaling cascades, DNA repair, and cell division. and their impact on the cellular microenvironment and dis- Given the pivotal role of PTMs in the regulation of ease
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