Home Page


Recent Focus Currently, our research is focused on three aspects of ATP synthase (1) Characterization/modulation of the phosphate binding subdomain in the catalytic sites. (2) Inhibitory effects of natural and modified polyphenol compounds on E. coli ATP synthase. (3) Identification molecular probes for Pi binding/release. (4) Characterization of the folding/unfolding profiles of E. coli ATP synthase subunits. So far, using biochemical, biophysical, molecular biology and genetic techniques, we have identified the following five Pi binding residues: bLys-155, bArg-182, bArg-246, aArg-376, and aSer-347. It was shown in our recent work that the Pi binding residues appear as a triangle with ßLys-155 being at the apex and αArg-376, ßArg-182, ßArg-246, and aSer-347 being at the base (see figure above).
Significance Significant aspects are: (1). ATP synthase is the smallest known molecular motor; this has brought it to the forefront of nanotechnology and nanomedicine. Nanomedicine, an offshoot of nanotechnology, refers to highly specific medical interventions on the molecular scale for curing disease or repairing damaged tissues. Questions that scientists and researchers are grappling with are “how many?”, “how big?”, and “how fast?” do nanomotors need to be? These questions must be addressed in order to build “nano machines” that are compatible with living tissues and can safely operate inside the body. We feel that one approach to learn more about these three basic “hows” is to generate a catalytically controllable ATP Synthase. (2). ATP synthase is critical to human health. Malfunction of this complex has been implicated in a wide variety of diseases including Alzheimer’s, Parkinson’s, and the class of severely debilitating diseases known collectively as mitochondrial myopathies. In addition to the above-mentioned conditions, ATP synthase also plays a vital role in antimicrobial activity. Streptococcus mutans is a primary microbial agent in the pathogenesis of dental caries through biofilm formation and acid production. Inhibition of S. mutans ATP synthase inhibits biofilm formation and acid production. In Mycobacterium, mutations in the c-subunit confer resistance to the new tuberculosis drug diarylquinoline. Another study showing ATP synthase binding to angiostatin on the surface of human endothelial cells is of great value. This makes ATP synthase a potential model in anti-microbial and anti-tumor research. A better understanding of this enzyme will greatly aid patients with these diseases and will have a broad impact on biology and medicine.
Future Research Plan (A) Our long-term goal is to develop a catalytically controllable, superior ATP synthase nanomotor, which could be used as a base model in defining the size, number and speed for biological nanomotors in nanomedicine usage. Employing the knowledge of biochemical, biophysical, genetic and molecular biology techniques, along with available x-ray crystal structures, should allow us to accomplish this goal. (B) A wide range of health related beneficial effects such as protection against cardiovascular disease, cancer, aging, etc have been credited to the ingestion of polyphenols. The beneficial effects of polyphenols may be derived in part by preventing mitochondrial ATP synthesis in tumor cells, thereby inducing apoptosis. Polyphenols have been shown to prevent both the synthetic and hydrolytic activities of bovine ATP synthase by blocking both clockwise and anti-clockwise rotation of the γ-subunit. Thus we are interested in understanding the inhibitory effects of natural and modified polyphenols on E. coli ATP synthase.
Relevance of Work The ATP Synthase is critical to human health. Malfunction of this complex has been implicated in a wide variety of diseases including Alzheimer’s, Parkinson’s, and the class of severely debilitating diseases known collectively as mitochondrial myopathies. In addition to the above-mentioned conditions recently it was shown that in Mycobacterium, mutations in the c subunit confer resistance to the new tuberculosis drug diarylquinoline. Another study showing binding of ATP Synthase to angiostatin on the surface of human endothelial cell is of great importance in making it a potential ant-tumor target. A better understanding of this enzyme has the potential to greatly aid patients with these diseases. A catalytically controllable ATP Synthase nanomotor will be suitable for harnessing ATP Synthase as a molecular nanomotor for a multitude of medical and engineering purposes. The long-term goal of this study is to lead to new therapies for diseases that afflict millions of people worldwide. Once we have this, we will be able to design better diagnostic tools and engineering structures for more specific treatment of disease and repair of tissues.
This research will provide extensive opportunities for students. As discussed below, undergraduates and graduates (MS) will have ample opportunities to learn a wide variety of molecular biology, genetic, biochemical, and biophysical techniques. Some of which are mutagenesis, cloning, protein purification, spectroscopy, etc. This will also bring fervor among our colleagues and in our institute as ETSU is not a major recipient of NIH funding. A total of eleven students, four graduates and seven undergraduates, are currently being trained in my lab; four of them have already published or submitted research papers as coauthors in peer-reviewed journals with me.

Publications Ahmad, Z. and Laughlin, T. F. (2010) Medicinal Chemistry of ATP synthase: a potential drug target of dietary polyphenols and amphibian antimicrobial peptides, Current Medicinal Chemistry (In Press). Chinnam, N., Dadi, P.K., Sabri, S.A., Ahmad, M., and Ahmad, Z. (2010) Dietary bioflavonoids inhibit Escherichia coli ATP synthase in a differential manner Int. J. Biol. Macromol. 46, 478-486. Laughlin, F. and Ahmad, Z. (2010) Inhibition of Escherichia coli ATP synthase by amphibian antimicrobial peptides. Int. J. Biol. Macromol 46, 367-374. Dadi, P. K., Ahmad, M., and Ahmad, Z. (2009) Inhibition of ATPase activity of Escherichia coli ATP synthase by polyphenols Int. J. Biol. Macromol. 45, 72-79. Li, W., Brudecki, L.E., Senior, A.E., and Ahmad, Z. (2009) Role of a-subunit VISIT-DG sequence residues Ser-347 and Gly-351 in the catalytic sites of Escherichia coli ATP synthase. J. Biol. Chem. 284, 10747-10754. Ahmad, S. and Ahmad, Z. (2008) “ ATP-binding site as a further application of neural network to residue level prediction” In Proceedings of International Joint Conference on Neural Networks (IJCNN), World Conference on Computational Intelligence (WCCI), June 1-8, Hong Kong, IEEE. pp. 2431-2435. Brudecki LE, Grindstaff JJ & Ahmad Z. (2008) Role of aPhe-291 residue in the phosphate-binding subdomain of catalytic sites of Escherichia coli ATP Synthase Arch. Biochem. Biophys. 471, 168-175. *Ahmad Z. & Senior AE (2006) Inhibition of the ATPase activity of Escherichia coli* ATP synthase by magnesium fluoride. FEBS Lett. 580, 517-520. Ahmad Z. & Senior AE (2005) Identification of phosphate binding residues of Escherichia coli ATP synthase. J. Bioenerg. Biomembr. 37, 437-440. Ahmad Z. & Senior AE (2005) Modulation of charge in the phosphate binding site of Escherichia coli ATP synthase. J. Biol. Chem. 280, 27981-27989. Ahmad Z. & Senior AE (2005) Involvement of ATP synthase residues αArg-376, ßArg-182, and ßLys-155 in Pi binding. FEBS Lett. 579, 523-528. Ahmad Z. & Senior AE (2004) Role of residue ß-Asn-243 in the phosphate-binding subdomain of catalytic sites of Escherichia coli F₁-ATPase. J. Biol. Chem. 279, 46057-46064. Ahmad Z & Senior AE (2004) Mutagenesis of residue ß-Arg-246 in the phosphate-binding subdomain of catalytic sites of Escherichia coli F₁-ATPase. J. Biol. Chem. 279, 31505-31513. Ahmad A, Ahmad Z** and MA Baig (2003) Hepatic Sulfite oxidase: effect of anions on its activity. Trends Clinical. Biochem. Lab Medicine. 1, 751-755. Ahmad Z, Salim M & Maines MD (2002) Human biliverdin reductase is a leucine zipper like DNA-binding protein and functions in transcriptional activation of heme oxygenase-1 by oxidative stress J. Biol. Chem. 277, 9226-9232. *Ahmad Z & Sherman F (2001) Role of Arg-166 in yeast cytochrome C₁ J. Biol. Chem.* 276, 18450-18456. Ahmad Z, Yadav S, Ahmad F & Khan NZ (1996) Effects of salts of alkali earth metals and calcium chloride on the stability of cytochrome c and myoglobin. Biochem. Biophys. Acta 1294, 63-71. Ahmad Z** & Ahmad F (1994) Physicochemical characterization of products of unfolding of cytochrome c by calcium chloride. Biochem. Biophys. Acta. 1207, 223-230. *Ahmad Z & Ahmad F (1992) Mechanism of denaturation of cytochrome c by lithium salts. Ind. J. Chem.* 31b, 874-879. Research opportunities** Research opportunities for graduates, and undergraduates are available to work on recently funded NIH research grant. Those of you who would like to be a part of my research group or would like to learn more about the the role of ATP synthase in human health and diseases please visit our lab, or email us at: ahmadz@etsu.edu Current Lab Members: Mubeen Ahmad, Mubeen is lab Technician. She helps in maintaining day-to-day activities of the lab including, ordering supplies, helping in dish washing, maintaining E. coli stock cultures, and preparing media plates. Mubeen also performs and helps in routine experiments such as biochemical assays, site directed mutagenesis, cloning, and protein/membrane purification. Graduate students: Laura E. Brudecki, Laura became a graduate student in the spring of 2009. She initially joined my lab as an undergraduate in the fall 2006. She has been working on the characterization of Pi binging site residues of E. coli ATP synthase. Her current work involves the characterization of the a-subunit VISIT-DG sequence residues in the Pi binding subdomain of the catalytic sites. Nagababu Chinnam, NBC joined our lab in January 2009 as a graduate student. His is joining the project with PKD on the inhibitory effects of polyphenols/bioflavonoids. Sneha Reddy, Sneha joined our lab in January 2009 as a graduate student. She has joined the project on characterization of the a-subunit VISITDG sequence residues in the Pi binding subdomain of the catalytic sites and will specifically focus on the DG residues. Chao Zhao , Chao joined us in August 2008. He will be working on characterization of the a-subunit VISITDG sequence residues in the Pi binding subdomain of the catalytic sites and will focus on the aI346 and aI348 residues. Junior Tayou, Junior also joined us in August 2008. He is working on the inhibitory effects of peptides and their binding site on ATP synthse. Undergraduate students: Steven Sherman, Nitin Sachan, Saurabh Sachan, Mai Xiong, Shabaaz Sabri, and Mohammad Bowers Each of these students is undertaking their own specific project or has been coupled with a graduate student. Teaching Biochemistry of macromolecules Lecture and lab; Biochemistry of Metabolism lab; Honors Discussion group; Non-major Biology I, Graduate topics course