1
|
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.
Collapse
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
- ,
| |
Collapse
|
2
|
Kepp KP. Heme isomers substantially affect heme's electronic structure and function. Phys Chem Chem Phys 2018; 19:22355-22362. [PMID: 28805222 DOI: 10.1039/c7cp03285d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Inspection of heme protein structures in the protein data bank reveals four isomers of heme characterized by different relative orientations of the vinyl side chains; remarkably, all these have been reported in multiple protein structures. Density functional theory computations explain this as due to similar energy of the isomers but with a sizable (25 kJ mol-1) barrier to interconversion arising from restricted rotation around the conjugated bonds. The four isomers, EE, EZ, ZE, and ZZ, were then investigated as 4-coordinate hemes, as 5-coordinate deoxyhemes, in 6-coordinate O2-adducts of globins and as compound I intermediates typical of heme peroxidases. Substantial differences were observed in electronic properties relevant to heme function: notably, the spin state energy gap of O2-heme adducts, important for fast reversible binding of O2, depends on the isomer state, and O2-binding enthalpies change by up to 16 kJ mol-1; redox potentials change by up to 0.2 V depending on the isomer, and the doublet-quartet energy splitting of compound I, central to "two-state" reactivity, is affected by up to ∼15 kJ mol-1. These effects are consistently seen with three distinct density functionals, i.e. the effects are not method-dependent. Thus, the nature of the isomer state is an important but overlooked feature of heme chemistry and function, and previous and future studies of hemes may be reconsidered in this new context.
Collapse
Affiliation(s)
- Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, DK, Denmark.
| |
Collapse
|
3
|
Taniguchi I. . ELECTROCHEMISTRY 2017; 85:606-609. [DOI: 10.5796/electrochemistry.85.606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
4
|
Neya S, Nagai M, Nagatomo S, Hoshino T, Yoneda T, Kawaguchi AT. Utility of heme analogues to intentionally modify heme-globin interactions in myoglobin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:582-588. [PMID: 26435388 DOI: 10.1016/j.bbabio.2015.09.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 09/12/2015] [Accepted: 09/25/2015] [Indexed: 01/01/2023]
Abstract
Myoglobin reconstitution with various synthetic heme analogues was reviewed to follow the consequences of modified heme-globin interactions. Utility of dimethyl sulfoxide as the solvent for water-insoluble hemes was emphasized. Proton NMR spectroscopy revealed that loose heme-globin contacts in the heme pocket eventually caused the dynamic heme rotation around the iron-histidine bond. The full rotational rate was estimated to be about 1400 s(-1) at room temperature for 1,4,5,8-tetramethylhemin. The X-ray analysis of the myoglobin containing iron porphine, the smallest heme without any side chains, showed that the original globin fold was well conserved despite the serious disruption of native heme-globin contacts. Comparison between the two myoglobins with static and rotatory prosthetic groups indicated that the oxygen and carbon monoxide binding profiles were almost unaffected by the heme motion. On the other hand, altered tetrapyrrole array of porphyrin dramatically changed the dissociation constant of oxygen from 0.0005 mm Hg of porphycene-myoglobin to ∞ in oxypyriporphyrin-myoglobin. Heme-globin interactions in myoglobin were also monitored with circular dichroism spectroscopy. The observation on several reconstituted protein revealed an unrecognized role of the propionate groups in protoheme. Shortening of heme 6,7-propionates to carboxylates resulted in almost complete disappearance of the positive circular dichroism band in the Soret region. The theoretical analysis suggested that the disappeared circular dichroism band reflected the cancellation effects between different conformers of the carboxyl groups directly attached to heme periphery. The above techniques were proposed to be applicable to other hemoproteins to create new biocatalysts. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
Collapse
Affiliation(s)
- Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba City, Chiba 260-8675, Japan.
| | - Masako Nagai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-0003, Japan
| | - Shigenori Nagatomo
- Department of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Tyuji Hoshino
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba City, Chiba 260-8675, Japan
| | - Tomoki Yoneda
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba City, Chiba 260-8675, Japan
| | - Akira T Kawaguchi
- School of Medicine, Tokai University, Isehara, Kanagawa 259-1193, Japan
| |
Collapse
|
5
|
Juillard S, Chevance S, Bondon A, Simonneaux G. Dynamics of heme in hemoproteins: proton NMR study of myoglobin reconstituted with iron 3-ethyl-2-methylporphyrin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1188-94. [PMID: 21600316 DOI: 10.1016/j.bbapap.2011.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/23/2011] [Accepted: 04/27/2011] [Indexed: 11/19/2022]
Abstract
The asymmetric 3-ethyl-2-methylporphyrin iron complex was synthetized and inserted into apomyoglobin. UV-visible spectroscopic studies demonstrated the capacity of iron to coordinate different exogenous axial ligands in ferrous and ferric forms. The position of synthetic heme into the hydrophobic pocket of the reconstituted myoglobin was investigated by ((1))H NMR spectroscopy. In absence of exogenous ligand, signals of the synthetic prosthetic group were not detected, suggesting a rotational disorder of the synthetic porphyrin into the heme pocket. This direct interconversion behavior is favored since site-specific interactions between the poorly substituted heme and protein in the chiral hydrophobic cavity were weak. Complexion of cyanide to the iron allowed to quench partially the heme reorientation and two interconvertible forms, around the meso-Cα-Cγ axis, were detected in solution.
Collapse
Affiliation(s)
- Sandrine Juillard
- UMR 6226 Sciences Chimiques de Rennes, Campus de Beaulieu, Université de Rennes 1, Rennes, France
| | | | | | | |
Collapse
|
6
|
Droghetti E, Nicoletti FP, Bonamore A, Boechi L, Arroyo Mañez P, Estrin DA, Boffi A, Smulevich G, Feis A. Heme pocket structural properties of a bacterial truncated hemoglobin from Thermobifida fusca. Biochemistry 2010; 49:10394-402. [PMID: 21049911 DOI: 10.1021/bi101452k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An acidic surface variant (ASV) of the "truncated" hemoglobin from Thermobifida fusca was designed with the aim of creating a versatile globin scaffold endowed with thermostability and a high level of recombinant expression in its soluble form while keeping the active site unmodified. This engineered protein was obtained by mutating the surface-exposed residues Phe107 and Arg91 to Glu. Molecular dynamics simulations showed that the mutated residues remain solvent-exposed, not affecting the overall protein structure. Thus, the ASV was used in a combinatorial mutagenesis of the distal heme pocket residues in which one, two, or three of the conserved polar residues [TyrB10(54), TyrCD1(67), and TrpG8(119)] were substituted with Phe. Mutants were characterized by infrared and resonance Raman spectroscopy and compared with the wild-type protein. Similar Fe-proximal His stretching frequencies suggest that none of the mutations alters the proximal side of the heme cavity. Two conformers were observed in the spectra of the CO complexes of both wild-type and ASV protein: form 1 with ν(FeC) and ν(CO) at 509 and 1938 cm(-1) and form 2 with ν(FeC) and ν(CO) at 518 and 1920 cm(-1), respectively. Molecular dynamics simulations were performed for the wild-type and ASV forms, as well as for the TyrB10 mutant. The spectroscopic and computational results demonstrate that CO interacts with TrpG8 in form 1 and interacts with both TrpG8 and TyrCD1 in form 2. TyrB10 does not directly interact with the bound CO.
Collapse
Affiliation(s)
- Enrica Droghetti
- Dipartimento di Chimica Ugo Schiff, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Comparing the electronic properties and docking calculations of heme derivatives on CYP2B4. J Mol Model 2008; 14:537-45. [DOI: 10.1007/s00894-008-0294-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Accepted: 02/21/2008] [Indexed: 11/25/2022]
|
8
|
Rwere F, Mak PJ, Kincaid JR. The impact of altered protein-heme interactions on the resonance Raman spectra of heme proteins. Studies of heme rotational disorder. Biopolymers 2008; 89:179-86. [PMID: 18008322 DOI: 10.1002/bip.20887] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Heme proteins that have been reconstituted with certain hemins may contain substantial fractions of a minor component in which the orientation of the heme in the folded pocket differs from the major ("native") conformation by a 180 degrees rotation about the alpha-gamma meso axis. In fact, this minor component has also been shown to exist in some native proteins, including several mammalian globins. While resonance Raman spectroscopy has emerged as a powerful probe of active site structure of heme proteins, no systematic study has yet been undertaken to elucidate the specific spectral changes associated with this disorder. In the present work, combined analyses of the temporal behavior of both NMR and RR data sets have been completed to permit the extraction of a unique RR spectrum for the disoriented form, documenting rather dramatic changes associated with this rotational disorder. In addition, the use of protohemes bearing selectively deuterated peripheral methyl groups has permitted the association of the observed modes with specific fragments of the heme residing in the reversed orientation. The studies conducted here clearly illustrate the exquisite sensitivity of low frequency heme deformation modes to altered protein-heme interactions.
Collapse
Affiliation(s)
- Freeborn Rwere
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | | | | |
Collapse
|