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Ovung A, Mavani A, Ghosh A, Chatterjee S, Das A, Suresh Kumar G, Ray D, Aswal VK, Bhattacharyya J. Heme Protein Binding of Sulfonamide Compounds: A Correlation Study by Spectroscopic, Calorimetric, and Computational Methods. ACS OMEGA 2022; 7:4932-4944. [PMID: 35187312 PMCID: PMC8851458 DOI: 10.1021/acsomega.1c05554] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/24/2022] [Indexed: 05/16/2023]
Abstract
Protein-ligand interaction studies are useful to determine the molecular mechanism of the binding phenomenon, leading to the establishment of the structure-function relationship. Here, we report the binding of well-known antibiotic sulfonamide drugs (sulfamethazine, SMZ; and sulfadiazine, SDZ) with heme protein myoglobin (Mb) using spectroscopic, calorimetric, ζ potential, and computational methods. Formation of a 1:1 complex between the ligand and Mb through well-defined equilibrium was observed. The binding constants obtained between Mb and SMZ/SDZ drugs were on the order of 104 M-1. SMZ with two additional methyl (-CH3) substitutions has higher affinity than SDZ. Upon drug binding, a notable loss in the helicity (via circular dichroism) and perturbation of the three-dimensional (3D) protein structure (via infrared and synchronous fluorescence experiments) were observed. The binding also indicated the dominance of non-polyelectrolytic forces between the amino acid residues of the protein and the drugs. The ligand-protein binding distance signified high probability of energy transfer between them. Destabilization of the protein structure upon binding was evident from differential scanning calorimetry results and ζ potential analyses. Molecular docking presented the best probable binding sites of the drugs inside protein pockets. Thus, the present study explores the potential binding characteristics of two sulfonamide drugs (with different substitutions) with myoglobin, correlating the structural and energetic aspects.
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Affiliation(s)
- Aben Ovung
- Department
of Chemistry, National Institute of Technology
Nagaland, Chumukedima, Dimapur 797103, India
| | - A. Mavani
- Department
of Chemistry, National Institute of Technology
Nagaland, Chumukedima, Dimapur 797103, India
| | - Ambarnil Ghosh
- UCD
Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sabyasachi Chatterjee
- Biophysical
Chemistry Laboratory, CSIR—Indian
Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Abhi Das
- Biophysical
Chemistry Laboratory, CSIR—Indian
Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Gopinatha Suresh Kumar
- Biophysical
Chemistry Laboratory, CSIR—Indian
Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Debes Ray
- Solid
State Physics Division, Bhabha Atomic Research
Centre, Mumbai 400085, India
| | - Vinod K. Aswal
- Solid
State Physics Division, Bhabha Atomic Research
Centre, Mumbai 400085, India
| | - Jhimli Bhattacharyya
- Department
of Chemistry, National Institute of Technology
Nagaland, Chumukedima, Dimapur 797103, India
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Zahler CT, Shaw BF. What Are We Missing by Not Measuring the Net Charge of Proteins? Chemistry 2019; 25:7581-7590. [PMID: 30779227 DOI: 10.1002/chem.201900178] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Indexed: 12/21/2022]
Abstract
The net electrostatic charge (Z) of a folded protein in solution represents a bird's eye view of its surface potentials-including contributions from tightly bound metal, solvent, buffer, and cosolvent ions-and remains one of its most enigmatic properties. Few tools are available to the average biochemist to rapidly and accurately measure Z at pH≠pI. Tools that have been developed more recently seem to go unnoticed. Most scientists are content with this void and estimate the net charge of a protein from its amino acid sequence, using textbook values of pKa . Thus, Z remains unmeasured for nearly all folded proteins at pH≠pI. When marveling at all that has been learned from accurately measuring the other fundamental property of a protein-its mass-one wonders: what are we missing by not measuring the net charge of folded, solvated proteins? A few big questions immediately emerge in bioinorganic chemistry. When a single electron is transferred to a metalloprotein, does the net charge of the protein change by approximately one elementary unit of charge or does charge regulation dominate, that is, do the pKa values of most ionizable residues (or just a few residues) adjust in response to (or in concert with) electron transfer? Would the free energy of charge regulation (ΔΔGz ) account for most of the outer sphere reorganization energy associated with electron transfer? Or would ΔΔGz contribute more to the redox potential? And what about metal binding itself? When an apo-metalloprotein, bearing minimal net negative charge (e.g., Z=-2.0) binds one or more metal cations, is the net charge abolished or inverted to positive? Or do metalloproteins regulate net charge when coordinating metal ions? The author's group has recently dusted off a relatively obscure tool-the "protein charge ladder"-and used it to begin to answer these basic questions.
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Affiliation(s)
- Collin T Zahler
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
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Design of artificial metalloproteins/metalloenzymes by tuning noncovalent interactions. J Biol Inorg Chem 2017; 23:7-25. [DOI: 10.1007/s00775-017-1506-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 09/20/2017] [Indexed: 12/12/2022]
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Zhang M, Nakanishi T, Yamanaka M, Nagao S, Yanagisawa S, Shomura Y, Shibata N, Ogura T, Higuchi Y, Hirota S. Rational Design of Domain-Swapping-Based c
-Type Cytochrome Heterodimers by Using Chimeric Proteins. Chembiochem 2017; 18:1712-1715. [DOI: 10.1002/cbic.201700219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Mohan Zhang
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama Ikoma Nara 630-0192 Japan
| | - Tsukasa Nakanishi
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama Ikoma Nara 630-0192 Japan
| | - Masaru Yamanaka
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama Ikoma Nara 630-0192 Japan
| | - Satoshi Nagao
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama Ikoma Nara 630-0192 Japan
| | - Sachiko Yanagisawa
- Graduate School of Life Science; University of Hyogo; RSC-UH Leading Program Center; 1-1-1 Koto Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Yasuhito Shomura
- Graduate School of Science and Engineering; Ibaraki University; 4-12-1 Nakanarusawa Hitachi Ibaraki 316-8511 Japan
| | - Naoki Shibata
- Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho Ako-gun Hyogo 678-1297 Japan
- RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Takashi Ogura
- Graduate School of Life Science; University of Hyogo; RSC-UH Leading Program Center; 1-1-1 Koto Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Yoshiki Higuchi
- Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho Ako-gun Hyogo 678-1297 Japan
- RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Shun Hirota
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama Ikoma Nara 630-0192 Japan
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