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Oda M. Analysis of the Structural Dynamics of Proteins in the Ligand-Unbound and -Bound States by Diffracted X-ray Tracking. Int J Mol Sci 2023; 24:13717. [PMID: 37762021 PMCID: PMC10531450 DOI: 10.3390/ijms241813717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Although many protein structures have been determined at atomic resolution, the majority of them are static and represent only the most stable or averaged structures in solution. When a protein binds to its ligand, it usually undergoes fluctuation and changes its conformation. One attractive method for obtaining an accurate view of proteins in solution, which is required for applications such as the rational design of proteins and structure-based drug design, is diffracted X-ray tracking (DXT). DXT can detect the protein structural dynamics on a timeline via gold nanocrystals attached to the protein. Here, the structure dynamics of single-chain Fv antibodies, helix bundle-forming de novo designed proteins, and DNA-binding proteins in both ligand-unbound and ligand-bound states were analyzed using the DXT method. The resultant mean square angular displacements (MSD) curves in both the tilting and twisting directions clearly demonstrated that structural fluctuations were suppressed upon ligand binding, and the binding energies determined using the angular diffusion coefficients from the MSD agreed well with the binding thermodynamics determined using isothermal titration calorimetry. In addition, the size of gold nanocrystals is discussed, which is one of the technical concerns of DXT.
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Affiliation(s)
- Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
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2
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D’Arrigo G, Autiero I, Gianquinto E, Siragusa L, Baroni M, Cruciani G, Spyrakis F. Exploring Ligand Binding Domain Dynamics in the NRs Superfamily. Int J Mol Sci 2022; 23:ijms23158732. [PMID: 35955864 PMCID: PMC9369052 DOI: 10.3390/ijms23158732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Nuclear receptors (NRs) are transcription factors that play an important role in multiple diseases, such as cancer, inflammation, and metabolic disorders. They share a common structural organization composed of five domains, of which the ligand-binding domain (LBD) can adopt different conformations in response to substrate, agonist, and antagonist binding, leading to distinct transcription effects. A key feature of NRs is, indeed, their intrinsic dynamics that make them a challenging target in drug discovery. This work aims to provide a meaningful investigation of NR structural variability to outline a dynamic profile for each of them. To do that, we propose a methodology based on the computation and comparison of protein cavities among the crystallographic structures of NR LBDs. First, pockets were detected with the FLAPsite algorithm and then an "all against all" approach was applied by comparing each pair of pockets within the same sub-family on the basis of their similarity score. The analysis concerned all the detectable cavities in NRs, with particular attention paid to the active site pockets. This approach can guide the investigation of NR intrinsic dynamics, the selection of reference structures to be used in drug design and the easy identification of alternative binding sites.
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Affiliation(s)
- Giulia D’Arrigo
- Department of Drug Science and Technology, University of Turin, Via Giuria 9, 10125 Turin, Italy
| | - Ida Autiero
- Molecular Horizon Srl, Via Montelino 30, 06084 Bettona, Italy
- National Research Council, Institute of Biostructures and Bioimaging, 80138 Naples, Italy
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Via Giuria 9, 10125 Turin, Italy
| | - Lydia Siragusa
- Molecular Horizon Srl, Via Montelino 30, 06084 Bettona, Italy
- Molecular Discovery Ltd., Theobald Street, Elstree Borehamwood, Hertfordshire WD6 4PJ, UK
| | - Massimo Baroni
- Molecular Discovery Ltd., Theobald Street, Elstree Borehamwood, Hertfordshire WD6 4PJ, UK
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS), Via Elce di Sotto 8, 06123 Perugia, Italy
- Correspondence: (G.C.); (F.S.); Tel.: +39-075-5855629 (G.C.); +39-011-6707185 (F.S.)
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Giuria 9, 10125 Turin, Italy
- Correspondence: (G.C.); (F.S.); Tel.: +39-075-5855629 (G.C.); +39-011-6707185 (F.S.)
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Mavani A, Ovung A, Luikham S, Suresh Kumar G, Das A, Ray D, Aswal VK, Bhattacharyya J. Biophysical and molecular modeling evidences for the binding of sulfa molecules with hemoglobin. J Biomol Struct Dyn 2022; 41:3779-3790. [PMID: 35380096 DOI: 10.1080/07391102.2022.2057358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The molecular mechanism of the heme protein, hemoglobin (Hb) interaction with sulfa molecule, sulfadiazine (SDZ) has been investigated through spectroscopic, neutron scattering and molecular modeling techniques. Absorption and emission spectroscopic studies showed that SDZ molecules were bound to Hb protein, non-cooperatively. The binding affinityof SDZ-Hb complex at standard experimental condition was evaluated to be around (4.2 ± 0.07) ×104, M-1with 1:1 stoichiometry. Drug induced structural perturbation of the 3 D protein moiety was confirmed through circular dichroism (CD), synchronous fluorescence and small angle neutron scattering methods. From the temperature dependent spectrofluorometric studies, the negative standard molar Gibbs energy change suggested the spontaneity of the reaction. The negative enthalpy and positive entropy change(s) indicated towards the involvement of both electrostatic and hydrophobic forces during the association process. Salt dependent fluorescence study revealed major contributions from non-poly-electrolytic forces. Molecular modeling studies determined the probable binding sites, types of interaction involved and the conformational alteration of the compactness of the Hb structure upon interaction with SDZ molecule. Overall, the study provides detailed insights into the binding mechanism of SDZ antibiotics to Hb protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- A. Mavani
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Aben Ovung
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Soching Luikham
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Abhi Das
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Debes Ray
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Vinod K. Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
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4
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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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Maity A, Majumdar S, Ghosh Dastidar S. Flexibility enables to discriminate between ligands: Lessons from structural ensembles of Bcl-xl and Mcl-1. Comput Biol Chem 2018; 77:17-27. [PMID: 30195235 DOI: 10.1016/j.compbiolchem.2018.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/24/2018] [Accepted: 08/17/2018] [Indexed: 12/19/2022]
Abstract
The proteins of Bcl-2 family, which are promising anti-cancer-drug targets, have substantial similarity in primary sequence and share homologous domains as well as similar structural folds. In spite of similarities in sequence and structures, the members of its pro- and anti- apoptotic subgroups form complexes with different type of partners with discriminating binding affinities. Understanding the origin of this discrimination is very important for designing ligands that can either selectively target a protein or could be made broad ranged as necessary. Using principal component analysis (PCA) of the available structures and from the analysis of the evolution of the binding pocket residues, the correlation has been investigated considering two important anti-apoptotic protein Bcl-xl and Mcl-1, which serve as two ideal representatives of this family. The flexibility of the receptor enables them to discriminate between the ligands or the binding partners. It has been observed that although Bcl-xl and Mcl-1 are classified as homologous proteins, through the course of evolution the binding pocket residues are highly conserved for Bcl-xl; whereas they have been substituted frequently in Mcl-1. The investigation has revealed that the Bcl-xl can adjust the backbone conformation of the binding pocket residues to a larger extent to complement with the shape of different binding partners whereas the Mcl-1 shows more variation in the side chain conformation of binding pocket residues for the same purpose.
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Affiliation(s)
- Atanu Maity
- Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700054, India
| | - Sarmistha Majumdar
- Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700054, India
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Macalino SJY, Basith S, Clavio NAB, Chang H, Kang S, Choi S. Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. Molecules 2018; 23:E1963. [PMID: 30082644 PMCID: PMC6222862 DOI: 10.3390/molecules23081963] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/14/2022] Open
Abstract
The advent of advanced molecular modeling software, big data analytics, and high-speed processing units has led to the exponential evolution of modern drug discovery and better insights into complex biological processes and disease networks. This has progressively steered current research interests to understanding protein-protein interaction (PPI) systems that are related to a number of relevant diseases, such as cancer, neurological illnesses, metabolic disorders, etc. However, targeting PPIs are challenging due to their "undruggable" binding interfaces. In this review, we focus on the current obstacles that impede PPI drug discovery, and how recent discoveries and advances in in silico approaches can alleviate these barriers to expedite the search for potential leads, as shown in several exemplary studies. We will also discuss about currently available information on PPI compounds and systems, along with their usefulness in molecular modeling. Finally, we conclude by presenting the limits of in silico application in drug discovery and offer a perspective in the field of computer-aided PPI drug discovery.
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Affiliation(s)
- Stephani Joy Y Macalino
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Shaherin Basith
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Nina Abigail B Clavio
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Hyerim Chang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Soosung Kang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Sun Choi
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
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Fonin AV, Golikova AD, Zvereva IA, D'Auria S, Staiano M, Uversky VN, Kuznetsova IM, Turoverov KK. Osmolyte-Like Stabilizing Effects of Low GdnHCl Concentrations on d-Glucose/d-Galactose-Binding Protein. Int J Mol Sci 2017; 18:E2008. [PMID: 28925982 PMCID: PMC5618657 DOI: 10.3390/ijms18092008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/14/2017] [Accepted: 09/16/2017] [Indexed: 11/16/2022] Open
Abstract
The ability of d-glucose/d-galactose-binding protein (GGBP) to reversibly interact with its ligands, glucose and galactose, makes this protein an attractive candidate for sensing elements of glucose biosensors. This potential is largely responsible for attracting researchers to study the conformational properties of this protein. Previously, we showed that an increase in the fluorescence intensity of the fluorescent dye 6-bromoacetyl-2-dimetylaminonaphtalene (BADAN) is linked to the holo-form of the GGBP/H152C mutant in solutions containing sub-denaturing concentrations of guanidine hydrochloride (GdnHCl). It was hypothesized that low GdnHCl concentrations might lead to compaction of the protein, thereby facilitating ligand binding. In this work, we utilize BADAN fluorescence spectroscopy, intrinsic protein UV fluorescence spectroscopy, and isothermal titration calorimetry (ITC) to show that the sub-denaturing GdnHCl concentrations possess osmolyte-like stabilizing effects on the structural dynamics, conformational stability, and functional activity of GGBP/H152C and the wild type of this protein (wtGGBP). Our data are consistent with the model where low GdnHCl concentrations promote a shift in the dynamic distribution of the protein molecules toward a conformational ensemble enriched in molecules with a tighter structure and a more closed conformation. This promotes the increase in the configurational complementarity between the protein and glucose molecules that leads to the increase in glucose affinity in both GGBP/H152C and wtGGBP.
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Affiliation(s)
- Alexander V Fonin
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, 194064 St. Petersburg, Russia.
| | - Alexandra D Golikova
- Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia.
| | - Irina A Zvereva
- Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia.
| | - Sabato D'Auria
- CNR, Institute of Food Science, via Roma 64, 83100 Avellino, Italy.
| | - Maria Staiano
- CNR, Institute of Food Science, via Roma 64, 83100 Avellino, Italy.
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., Tampa, FL 33612, USA.
| | - Irina M Kuznetsova
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, 194064 St. Petersburg, Russia.
| | - Konstantin K Turoverov
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, 194064 St. Petersburg, Russia.
- Department of Biophysics, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya av. 29, 195251 St. Petersburg, Russia.
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Interactions between Bcl-xl and its inhibitors: Insights into ligand design from molecular dynamics simulation. J Mol Graph Model 2015; 59:1-13. [DOI: 10.1016/j.jmgm.2015.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 11/21/2022]
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