Potential Charge Transfer Probe Induced Conformational Changes of Model Plasma Protein Human Serum Albumin: Spectroscopic, Molecular Docking, and Molecular Dynamics Simulation Study Sankar Jana, Sasanka Dalapati, Shalini Ghosh, Nikhil Guchhait Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata-700009, India Received 28 November 2011; revised 13 February 2012; accepted 1 March 2012 Published online 19 March 2012 in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/bip.22057 This article was originally published online as an accepted preprint. The ‘‘Published Online’’ date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley. com INTRODUCTION F or many years, fluorescent probes containing donor and acceptor groups producing polarity sensitive intramolecular charge transfer (ICT) emission are finding novel applications in the development of fluo- rescent pH and ion detectors, optoelectronic devices, solar cells, and thin film transistors. 1–4 They find extensive application as probes for the study of bio-mimetic environ- ments, 5,6 providing information about the immediate polar- ity around the binding sites of the biological microheteroge- neous environments like proteins. 7 Therefore, fluorescent probe spectroscopy is rapidly developing as a nondestructive but very efficient sensitive technique for studying these sys- tems as well as their response to chemical and thermal per- turbations. Structural and dynamical aspects of biological systems like proteins, DNA, enzymes, and so forth, are being studied using new synthetic extrinsic polarity sensitive fluo- rescent probes and these studies are further authenticated when the experimental results find support from theoretical studies like molecular docking 8,9 and molecular dynamics (MD) simulations. 9,10 Serum albumins are the most abundant proteins (0.6 mmol dm 21 ) in the blood plasma and act primarily as trans- port proteins, 11 capable of binding to large range of endoge- nous and exogenous compounds like hormones, enzymes, surfactants, fatty acids, nutrients, steroids, and a variety of therapeutic drugs 12,13 and delivering them to their target organs. 14 The crystal structure of human serum albumin (HSA) is well-established. 15 HSA is a helical monomer of 66.5 kD containing 585 amino acid residues with 67% alpha helix and 17 disulphide linkages 8,16 in its six turns. The terti- ary structure contains three homologous domains I ? III, each of which is divided into two subdomains A and B. 15,17 There is only one tryptophan residue Trp-214 in the IIA sub domains 8,10 which is responsible for its intrinsic fluorescence and energy transfer phenomena. HSA also contains two Potential Charge Transfer Probe Induced Conformational Changes of Model Plasma Protein Human Serum Albumin: Spectroscopic, Molecular Docking, and Molecular Dynamics Simulation Study Additional Supporting Information may be found in the online version of this article. Correspondence to: N. Guchhait; e-mail: nguchhait@yahoo.com ABSTRACT: The nature of binding of specially designed charge transfer (CT) fluorophore at the hydrophobic protein interior of human serum albumin (HSA) has been explored by massive blue-shift (82 nm) of the polarity sensitive probe emission accompanying increase in emission intensity, fluorescence anisotropy, red edge excitation shift, and average fluorescence lifetimes. Thermal unfolding of the intramolecular CT probe bound HSA produces almost opposite spectral changes. The spectral responses of the molecule reveal that it can be used as an extrinsic fluorescent reporter for similar biological systems. Circular dichrosim spectra, molecular docking, and molecular dynamics simulation studies scrutinize this binding process and stability of the protein probe complex more closely. # 2012 Wiley Periodicals, Inc. Biopolymers 97: 766–777, 2012. Keywords: human serum albumin; molecular docking; fluorescent probe; molecular dynamics simulation; 5-(4- dimethylamino-phenyl)-penta-2,4-dienenitrile Contract grant sponsor: Department of Science and Technology, India (N.G.) Contract grant number: SR/S1/PC-26/2008 V V C 2012 Wiley Periodicals, Inc. 766 Biopolymers Volume 97 / Number 10