1
|
Paketurytė-Latvė V, Smirnov A, Manakova E, Baranauskiene L, Petrauskas V, Zubrienė A, Matulienė J, Dudutienė V, Čapkauskaitė E, Zakšauskas A, Leitans J, Gražulis S, Tars K, Matulis D. From X-ray crystallographic structure to intrinsic thermodynamics of protein-ligand binding using carbonic anhydrase isozymes as a model system. IUCRJ 2024; 11:556-569. [PMID: 38856178 PMCID: PMC11220870 DOI: 10.1107/s2052252524004627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/17/2024] [Indexed: 06/11/2024]
Abstract
Carbonic anhydrase (CA) was among the first proteins whose X-ray crystal structure was solved to atomic resolution. CA proteins have essentially the same fold and similar active centers that differ in only several amino acids. Primary sulfonamides are well defined, strong and specific binders of CA. However, minor variations in chemical structure can significantly alter their binding properties. Over 1000 sulfonamides have been designed, synthesized and evaluated to understand the correlations between the structure and thermodynamics of their binding to the human CA isozyme family. Compound binding was determined by several binding assays: fluorescence-based thermal shift assay, stopped-flow enzyme activity inhibition assay, isothermal titration calorimetry and competition assay for enzyme expressed on cancer cell surfaces. All assays have advantages and limitations but are necessary for deeper characterization of these protein-ligand interactions. Here, the concept and importance of intrinsic binding thermodynamics is emphasized and the role of structure-thermodynamics correlations for the novel inhibitors of CA IX is discussed - an isozyme that is overexpressed in solid hypoxic tumors, and thus these inhibitors may serve as anticancer drugs. The abundant structural and thermodynamic data are assembled into the Protein-Ligand Binding Database to understand general protein-ligand recognition principles that could be used in drug discovery.
Collapse
Affiliation(s)
- Vaida Paketurytė-Latvė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Elena Manakova
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Jurgita Matulienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Virginija Dudutienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Audrius Zakšauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Janis Leitans
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, 1067 Riga, Latvia
| | - Saulius Gražulis
- Sector of Crystallography and Chemical Informatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, 1067 Riga, Latvia
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| |
Collapse
|
2
|
Prout-Holm RA, van Walstijn CC, Hitsman A, Rowley MJ, Olsen JE, Page BDG, Frankel A. Investigating Protein Binding with the Isothermal Ligand-induced Resolubilization Assay. Chembiochem 2024; 25:e202300773. [PMID: 38266114 DOI: 10.1002/cbic.202300773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 01/26/2024]
Abstract
Target engagement assays typically detect and quantify the direct physical interaction of a protein of interest and its ligand through stability changes upon ligand binding. Commonly used target engagement methods detect ligand-induced stability by subjecting samples to thermal or proteolytic stress. Here we describe a new variation to these approaches called Isothermal Ligand-induced Resolubilization Assay (ILIRA), which utilizes lyotropic solubility stress to measure ligand binding through changes in target protein solubility. We identified distinct buffer systems and salt concentrations that compromised protein solubility for four diverse proteins: dihydrofolate reductase (DHFR), nucleoside diphosphate-linked moiety X motif 5 (NUDT5), poly [ADP-ribose] polymerase 1 (PARP1), and protein arginine N-methyltransferase 1 (PRMT1). Ligand-induced solubility rescue was demonstrated for these proteins, suggesting that ILIRA can be used as an additional target engagement technique. Differences in ligand-induced protein solubility were assessed by Coomassie blue staining for SDS-PAGE and dot blot, as well as by NanoOrange, Thioflavin T, and Proteostat fluorescence, thus offering flexibility for readout and assay throughput.
Collapse
Affiliation(s)
- Riley A Prout-Holm
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Cerissa C van Walstijn
- Faculty of Science, Utrecht University, Heidelberglaan 8, 3584 CS, Utrecht, The Netherlands
| | - Alana Hitsman
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Michael J Rowley
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jonas E Olsen
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Brent D G Page
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Adam Frankel
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| |
Collapse
|
3
|
Galano-Frutos JJ, Nerín-Fonz F, Sancho J. Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:7791-7806. [PMID: 37955428 PMCID: PMC10751793 DOI: 10.1021/acs.jcim.3c01107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023]
Abstract
Despite advances in artificial intelligence methods, protein folding remains in many ways an enigma to be solved. Accurate computation of protein folding energetics could help drive fields such as protein and drug design and genetic interpretation. However, the challenge of calculating the state functions governing protein folding from first-principles remains unaddressed. We present here a simple approach that allows us to accurately calculate the energetics of protein folding. It is based on computing the energy of the folded and unfolded states at different temperatures using molecular dynamics simulations. From this, two essential quantities (ΔH and ΔCp) are obtained and used to calculate the conformational stability of the protein (ΔG). With this approach, we have successfully calculated the energetics of two- and three-state proteins, representatives of the major structural classes, as well as small stability differences (ΔΔG) due to changes in solution conditions or variations in an amino acid residue.
Collapse
Affiliation(s)
- Juan J. Galano-Frutos
- Department
of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Biocomputation
and Complex Systems Physics Institute (BIFI), Joint Unit GBs-CSIC, University of Zaragoza, 50018 Zaragoza, Spain
| | - Francho Nerín-Fonz
- Department
of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
| | - Javier Sancho
- Department
of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Biocomputation
and Complex Systems Physics Institute (BIFI), Joint Unit GBs-CSIC, University of Zaragoza, 50018 Zaragoza, Spain
- Aragon
Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
| |
Collapse
|
4
|
Mahran R, Vello N, Komulainen A, Malakoutikhah M, Härmä H, Kopra K. Isothermal chemical denaturation assay for monitoring protein stability and inhibitor interactions. Sci Rep 2023; 13:20066. [PMID: 37973851 PMCID: PMC10654576 DOI: 10.1038/s41598-023-46720-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Thermal shift assay (TSA) with altered temperature has been the most widely used method for monitoring protein stability for drug research. However, there is a pressing need for isothermal techniques as alternatives. This urgent demand arises from the limitations of TSA, which can sometimes provide misleading ranking of protein stability and fail to accurately reflect protein stability under physiological conditions. Although differential scanning fluorimetry has significantly improved throughput in comparison to differential scanning calorimetry and differential static light scattering throughput, all these methods exhibit moderate sensitivity. In contrast, current isothermal chemical denaturation (ICD) techniques may not offer the same throughput capabilities as TSA, but it provides more precise information about protein stability and interactions. Unfortunately, ICD also suffers from limited sensitivity, typically in micromolar range. We have developed a novel method to overcome these challenges, namely throughput and sensitivity. The novel Förster Resonance Energy Transfer (FRET)-Probe as an external probe is highly applicable to isothermal protein stability monitoring but also to conventional TSA. We have investigated ICD for multiple proteins with focus on KRASG12C with covalent inhibitors and three chemical denaturants performed at nanomolar protein concentration. Data showed corresponding inhibitor-induced stabilization of KRASG12C to those reported by nucleotide exchange assay.
Collapse
Affiliation(s)
- Randa Mahran
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland.
| | - Niklas Vello
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Anita Komulainen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | | | - Harri Härmä
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| |
Collapse
|
5
|
Michel F, Romero‐Romero S, Höcker B. Retracing the evolution of a modern periplasmic binding protein. Protein Sci 2023; 32:e4793. [PMID: 37788980 PMCID: PMC10601554 DOI: 10.1002/pro.4793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023]
Abstract
Investigating the evolution of structural features in modern multidomain proteins helps to understand their immense diversity and functional versatility. The class of periplasmic binding proteins (PBPs) offers an opportunity to interrogate one of the main processes driving diversification: the duplication and fusion of protein sequences to generate new architectures. The symmetry of their two-lobed topology, their mechanism of binding, and the organization of their operon structure led to the hypothesis that PBPs arose through a duplication and fusion event of a single common ancestor. To investigate this claim, we set out to reverse the evolutionary process and recreate the structural equivalent of a single-lobed progenitor using ribose-binding protein (RBP) as our model. We found that this modern PBP can be deconstructed into its lobes, producing two proteins that represent possible progenitor halves. The isolated halves of RBP are well folded and monomeric proteins, albeit with a lower thermostability, and do not retain the original binding function. However, the two entities readily form a heterodimer in vitro and in-cell. The x-ray structure of the heterodimer closely resembles the parental protein. Moreover, the binding function is fully regained upon formation of the heterodimer with a ligand affinity similar to that observed in the modern RBP. This highlights how a duplication event could have given rise to a stable and functional PBP-like fold and provides insights into how more complex functional structures can evolve from simpler molecular components.
Collapse
Affiliation(s)
- Florian Michel
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
| | | | - Birte Höcker
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
| |
Collapse
|
6
|
Vergara R, Berrocal T, Juárez Mejía EI, Romero-Romero S, Velázquez-López I, Pulido NO, López Sanchez HA, Silva DA, Costas M, Rodríguez-Romero A, Rodríguez-Sotres R, Sosa-Peinado A, Fernández-Velasco DA. Thermodynamic and kinetic analysis of the LAO binding protein and its isolated domains reveal non-additivity in stability, folding and function. FEBS J 2023; 290:4496-4512. [PMID: 37178351 DOI: 10.1111/febs.16819] [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: 03/29/2023] [Accepted: 05/12/2023] [Indexed: 05/15/2023]
Abstract
Substrate-binding proteins (SBPs) are used by organisms from the three domains of life for transport and signalling. SBPs are composed of two domains that collectively trap ligands with high affinity and selectivity. To explore the role of the domains and the integrity of the hinge region between them in the function and conformation of SBPs, here, we describe the ligand binding, conformational stability and folding kinetics of the Lysine Arginine Ornithine (LAO) binding protein from Salmonella thiphimurium and constructs corresponding to its two independent domains. LAO is a class II SBP formed by a continuous and a discontinuous domain. Contrary to the expected behaviour based on their connectivity, the discontinuous domain shows a stable native-like structure that binds l-arginine with moderate affinity, whereas the continuous domain is barely stable and shows no detectable ligand binding. Regarding folding kinetics, studies of the entire protein revealed the presence of at least two intermediates. While the unfolding and refolding of the continuous domain exhibited only a single intermediate and simpler and faster kinetics than LAO, the folding mechanism of the discontinuous domain was complex and involved multiple intermediates. These findings suggest that in the complete protein the continuous domain nucleates folding and that its presence funnels the folding of the discontinuous domain avoiding nonproductive interactions. The strong dependence of the function, stability and folding pathway of the lobes on their covalent association is most likely the result of the coevolution of both domains as a single unit.
Collapse
Affiliation(s)
- Renan Vergara
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Tania Berrocal
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Eva Isela Juárez Mejía
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Department of Biochemistry, University of Bayreuth, Germany
| | - Isabel Velázquez-López
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Nancy O Pulido
- Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Haven A López Sanchez
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Daniel-Adriano Silva
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Rogelio Rodríguez-Sotres
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alejandro Sosa-Peinado
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - D Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| |
Collapse
|
7
|
Christofi E, Barran P. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chem Rev 2023; 123:2902-2949. [PMID: 36827511 PMCID: PMC10037255 DOI: 10.1021/acs.chemrev.2c00600] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.
Collapse
Affiliation(s)
- Emilia Christofi
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
8
|
Lyndem S, Gazi R, Belwal VK, Bhatta A, Jana M, Roy AS. Binding of bioactive esculin and esculetin with hen egg white lysozyme: Spectroscopic and computational methods to comprehensively elucidate the binding affinities, interacting forces, and conformational alterations at molecular level. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
9
|
Milicaj J, Hassan BA, Cote JM, Ramirez-Mondragon CA, Jaunbocus N, Rafalowski A, Patel KR, Castro CD, Muthyala R, Sham YY, Taylor EA. Discovery of first-in-class nanomolar inhibitors of heptosyltransferase I reveals a new aminoglycoside target and potential alternative mechanism of action. Sci Rep 2022; 12:7302. [PMID: 35508636 PMCID: PMC9068772 DOI: 10.1038/s41598-022-10776-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 04/04/2022] [Indexed: 11/08/2022] Open
Abstract
A clinically relevant inhibitor for Heptosyltransferase I (HepI) has been sought after for many years because of its critical role in the biosynthesis of lipopolysaccharides on bacterial cell surfaces. While many labs have discovered or designed novel small molecule inhibitors, these compounds lacked the bioavailability and potency necessary for therapeutic use. Extensive characterization of the HepI protein has provided valuable insight into the dynamic motions necessary for catalysis that could be targeted for inhibition. Structural inspection of Kdo2-lipid A suggested aminoglycoside antibiotics as potential inhibitors for HepI. Multiple aminoglycosides have been experimentally validated to be first-in-class nanomolar inhibitors of HepI, with the best inhibitor demonstrating a Ki of 600 ± 90 nM. Detailed kinetic analyses were performed to determine the mechanism of inhibition while circular dichroism spectroscopy, intrinsic tryptophan fluorescence, docking, and molecular dynamics simulations were used to corroborate kinetic experimental findings. While aminoglycosides have long been described as potent antibiotics targeting bacterial ribosomes' protein synthesis leading to disruption of the stability of bacterial cell membranes, more recently researchers have shown that they only modestly impact protein production. Our research suggests an alternative and novel mechanism of action of aminoglycosides in the inhibition of HepI, which directly leads to modification of LPS production in vivo. This finding could change our understanding of how aminoglycoside antibiotics function, with interruption of LPS biosynthesis being an additional and important mechanism of aminoglycoside action. Further research to discern the microbiological impact of aminoglycosides on cells is warranted, as inhibition of the ribosome may not be the sole and primary mechanism of action. The inhibition of HepI by aminoglycosides may dramatically alter strategies to modify the structure of aminoglycosides to improve the efficacy in fighting bacterial infections.
Collapse
Affiliation(s)
- Jozafina Milicaj
- Department of Chemistry, Wesleyan University, Middletown, CT, 06459, USA
| | - Bakar A Hassan
- Department of Chemistry, Wesleyan University, Middletown, CT, 06459, USA
| | - Joy M Cote
- Department of Chemistry, Wesleyan University, Middletown, CT, 06459, USA
| | | | - Nadiya Jaunbocus
- Department of Chemistry, Wesleyan University, Middletown, CT, 06459, USA
| | | | - Kaelan R Patel
- Department of Integrative Biology and Physiology, Medical School, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Colleen D Castro
- Department of Chemistry, Wesleyan University, Middletown, CT, 06459, USA
| | - Ramaiah Muthyala
- Department of Experimental and Clinical Pharmacology, College Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Yuk Y Sham
- Department of Integrative Biology and Physiology, Medical School, University of Minnesota, Minneapolis, MN, 55455, USA.
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Erika A Taylor
- Department of Chemistry, Wesleyan University, Middletown, CT, 06459, USA.
| |
Collapse
|
10
|
Gedgaudas M, Baronas D, Kazlauskas E, Petrauskas V, Matulis D. Thermott: a comprehensive online tool for protein–ligand binding constant determination. Drug Discov Today 2022; 27:2076-2079. [DOI: 10.1016/j.drudis.2022.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/17/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022]
|
11
|
A Trade-off Between Thermostability and Binding Affinity of Anti-(4-hydroxy-3-nitrophenyl)Acetyl Antibodies During the Course of Affinity Maturation. Protein J 2022; 41:293-303. [DOI: 10.1007/s10930-022-10053-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2022] [Indexed: 10/18/2022]
|
12
|
Kumar A, Jernigan RL. Ligand Binding Introduces Significant Allosteric Shifts in the Locations of Protein Fluctuations. Front Mol Biosci 2021; 8:733148. [PMID: 34540902 PMCID: PMC8440829 DOI: 10.3389/fmolb.2021.733148] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022] Open
Abstract
Allostery is usually considered to be a mechanism for transmission of signals associated with physical or dynamic changes in some part of a protein. Here, we investigate the changes in fluctuations across the protein upon ligand binding based on the fluctuations computed with elastic network models. These results suggest that binding reduces the fluctuations at the binding site but increases fluctuations at remote sites, but not to fully compensating extents. If there were complete conservation of entropy, then only the enthalpies of binding would matter and not the entropies; however this does not appear to be the case. Experimental evidence also suggests that energies and entropies of binding can compensate but that the extent of compensation varies widely from case to case. Our results do however always show transmission of an allosteric signal to distant locations where the fluctuations are increased. These fluctuations could be used to compute entropies to improve evaluations of the thermodynamics of binding. We also show the allosteric relationship between peptide binding in the GroEL trans-ring that leads directly to the release of GroES from the GroEL-GroES cis-ring. This finding provides an example of how calculating these changes to protein dynamics induced by the binding of an allosteric ligand can regulate protein function and mechanism.
Collapse
Affiliation(s)
- Ambuj Kumar
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Robert L Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| |
Collapse
|
13
|
Abdel-Hady GN, Ikeda T, Ishida T, Funabashi H, Kuroda A, Hirota R. Engineering Cofactor Specificity of a Thermostable Phosphite Dehydrogenase for a Highly Efficient and Robust NADPH Regeneration System. Front Bioeng Biotechnol 2021; 9:647176. [PMID: 33869158 PMCID: PMC8047080 DOI: 10.3389/fbioe.2021.647176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Nicotinamide adenine dinucleotide phosphate (NADP)-dependent dehydrogenases catalyze a range of chemical reactions useful for practical applications. However, their dependence on the costly cofactor, NAD(P)H remains a challenge which must be addressed. Here, we engineered a thermotolerant phosphite dehydrogenase from Ralstonia sp. 4506 (RsPtxD) by relaxing the cofactor specificity for a highly efficient and robust NADPH regeneration system. The five amino acid residues, Cys174-Pro178, located at the C-terminus of β7-strand region in the Rossmann-fold domain of RsPtxD, were changed by site-directed mutagenesis, resulting in four mutants with a significantly increased preference for NADP. The catalytic efficiency of mutant RsPtxDHARRA for NADP (K cat/K M)NADP was 44.1 μM-1 min-1, which was the highest among the previously reported phosphite dehydrogenases. Moreover, the RsPtxDHARRA mutant exhibited high thermostability at 45°C for up to 6 h and high tolerance to organic solvents, when bound with NADP. We also demonstrated the applicability of RsPtxDHARRA as an NADPH regeneration system in the coupled reaction of chiral conversion of 3-dehydroshikimate to shikimic acid by the thermophilic shikimate dehydrogenase of Thermus thermophilus HB8 at 45°C, which could not be supported by the parent RsPtxD enzyme. Therefore, the RsPtxDHARRA mutant might be a promising alternative NADPH regeneration system for practical applications.
Collapse
Affiliation(s)
- Gamal Nasser Abdel-Hady
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Department of Genetics, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Takeshi Ikeda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takenori Ishida
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Hisakage Funabashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Ryuichi Hirota
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
14
|
Favinha AG, Barreiro DS, Martins JN, O'Toole P, Pauleta SR. Acrylamide-hemoglobin adduct: A spectroscopic study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 241:118644. [PMID: 32622051 DOI: 10.1016/j.saa.2020.118644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/18/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
Acrylamide is a neurotoxic and carcinogenic organic compound that is able to bind to several biomolecules and form adducts, through nucleophilic addition and in vivo by the Maillard Reaction, interfering with the biological functions of these molecules. Hemoglobin is one of the most abundant intracellular blood proteins, and thus it is of high interest to understand whether the binding of acrylamide can alter its properties. The interaction of acrylamide with hemoglobin was assessed in a 20:1 ratio, and after a 72 h-incubation period, a decrease of ca. 50% in the absorbance of the hemoglobin's Soret band was observed at 37 °C. This together with the analysis of circular dichroism spectra indicate that acrylamide binds in close proximity to the heme group. These perturbations were confirmed to not correspond to the loss of the heme group and were mostly reverted after passing the protein through a size-exclusion chromatographic matrix, suggesting a dominant non-covalent interaction for the observed effect. The thermodynamic parameters of unfolding in the absence and presence of acrylamide, suggest an interaction based on H-bonds and van der Waals forces that slightly stabilizes hemoglobin. The oxygen binding capacity of hemoglobin does not seem to be hindered, as no differences in the Q bands were observed in the adduct.
Collapse
Affiliation(s)
- André G Favinha
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Daniela S Barreiro
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Joana N Martins
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Philip O'Toole
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal.
| |
Collapse
|
15
|
Musa KA, Ning T, Mohamad SB, Tayyab S. Intermolecular recognition between pyrimethamine, an antimalarial drug and human serum albumin: Spectroscopic and docking study. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113270] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
16
|
Roig-Molina E, Sánchez-Angulo M, Seele J, García-Asencio F, Nau R, Sanz JM, Maestro B. Searching for Antipneumococcal Targets: Choline-Binding Modules as Phagocytosis Enhancers. ACS Infect Dis 2020; 6:954-974. [PMID: 32135064 DOI: 10.1021/acsinfecdis.9b00344] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Choline-binding proteins (CBPs) from Streptococcus pneumoniae comprise a family of modular polypeptides involved in essential events of this pathogen. They recognize the choline residues present in the teichoic and lipoteichoic acids of the cell wall using the so-called choline-binding modules (CBMs). The importance of CBPs in pneumococcal physiology points to them as novel targets to combat antimicrobial resistances shown by this organism. In this work we have tested the ability of exogenously added CBMs to act as CBP inhibitors by competing with the latter for the binding to the choline molecules in the bacterial surface. First, we carried out a thorough physicochemical characterization of three native CBMs, namely C-LytA, C-Cpl1, and C-CbpD, and assessed their affinity for choline and macromolecular, pneumococcal cell-wall mimics. The interaction with these substrates was evaluated by molecular modeling, analytical ultracentrifugation, surface plasmon resonance, and fluorescence and circular dichroism spectroscopies. Van't Hoff thermal analyses unveiled the existence of one noncanonical choline binding site in each of the C-Cpl1 and C-CbpD proteins, leading in total to 5 ligand-binding sites per dimer and 4 sites per monomer, respectively. Remarkably, the binding affinities of the CBMs do not directly correlate with their native oligomeric state or with the number of choline-binding sites, suggesting that choline recognition by these modules is a complex phenomenon. On the other hand, the exogenous addition of CBMs to pneumococcal planktonic cultures caused extensive cell-chaining probably as a consequence of the inhibition of CBP attachment to the cell wall. This was accompanied by bacterial aggregation and sedimentation, causing an enhancement of bacterial phagocytosis by peritoneal macrophages. In addition, the rational design of an oligomeric variant of a native CBM led to a substantial increase in its antibacterial activity by multivalency effects. These results suggest that CBMs might constitute promising nonlytic antimicrobial candidates based on the natural induction of the host defense system.
Collapse
Affiliation(s)
- Emma Roig-Molina
- Institute of Research, Development, and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University, Avda Universidad s/n, Elche-03202, Spain
| | - Manuel Sánchez-Angulo
- Department of Vegetal Production and Microbiology, Miguel Hernández University, Avda Universidad s/n, Elche-03202, Spain
| | - Jana Seele
- Department of Geriatrics, Evangelisches Krankenhaus Göttingen-Weende, An der Lutter 24, 37075 Göttingen, Germany
- Department of Neuropathology, University Medical Center Göttingen, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Francisco García-Asencio
- Institute of Research, Development, and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University, Avda Universidad s/n, Elche-03202, Spain
| | - Roland Nau
- Department of Geriatrics, Evangelisches Krankenhaus Göttingen-Weende, An der Lutter 24, 37075 Göttingen, Germany
- Department of Neuropathology, University Medical Center Göttingen, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Jesús M. Sanz
- Institute of Research, Development, and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University, Avda Universidad s/n, Elche-03202, Spain
- Biological Research Centre, Spanish National Research Council (CSIC), c/Ramiro de Maeztu, 9, Madrid-28040, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid-28040, Spain
| | - Beatriz Maestro
- Institute of Research, Development, and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University, Avda Universidad s/n, Elche-03202, Spain
- Biological Research Centre, Spanish National Research Council (CSIC), c/Ramiro de Maeztu, 9, Madrid-28040, Spain
| |
Collapse
|
17
|
Miyake M, Terada T, Shimokawa M, Sugimoto N, Arakawa T, Shimizu K, Igarashi K, Fujita K, Fushinobu S. Structural analysis of β-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum. FEBS J 2020; 287:5114-5129. [PMID: 32246585 DOI: 10.1111/febs.15315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/09/2020] [Accepted: 03/26/2020] [Indexed: 12/29/2022]
Abstract
Bifidobacterium longum is a symbiotic human gut bacterium that has a degradation system for β-arabinooligosaccharides, which are present in the hydroxyproline-rich glycoproteins of edible plants. Whereas microbial degradation systems for α-linked arabinofuranosyl carbohydrates have been extensively studied, little is understood about the degradation systems targeting β-linked arabinofuranosyl carbohydrates. We functionally and structurally analyzed a substrate-binding protein (SBP) of a putative ABC transporter (BLLJ_0208) in the β-arabinooligosaccharide degradation system. Thermal shift assays and isothermal titration calorimetry revealed that the SBP specifically bound Araf-β1,2-Araf (β-Ara2 ) with a Kd of 0.150 μm, but did not bind L-arabinose or methyl-β-Ara2 . Therefore, the SBP was termed β-arabinobiose-binding protein (BABP). Crystal structures of BABP complexed with β-Ara2 were determined at resolutions of up to 1.78 Å. The findings showed that β-Ara2 was bound to BABP within a short tunnel between two lobes as an α-anomeric form at its reducing end. BABP forms extensive interactions with β-Ara2 , and its binding mode was unique among SBPs. A molecular dynamics simulation revealed that the closed conformation of substrate-bound BABP is stable, whereas substrate-free form can adopt a fully open and two distinct semi-open states. The importer system specific for β-Ara2 may contribute to microbial survival in biological niches with limited amounts of digestible carbohydrates. DATABASE: Atomic coordinates and structure factors (codes 6LCE and 6LCF) have been deposited in the Protein Data Bank (http://wwpdb.org/).
Collapse
Affiliation(s)
| | - Tohru Terada
- The Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | | | - Naohisa Sugimoto
- Department of Biomaterial Sciences, The University of Tokyo, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | | | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, The University of Tokyo, Japan.,VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| |
Collapse
|
18
|
Musa KA, Ridzwan NFW, Mohamad SB, Tayyab S. Exploring the combination characteristics of lumefantrine, an antimalarial drug and human serum albumin through spectroscopic and molecular docking studies. J Biomol Struct Dyn 2020; 39:691-702. [PMID: 31913089 DOI: 10.1080/07391102.2020.1713215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Binding of lumefantrine (LUM), an antimalarial drug to human serum albumin (HSA), the main carrier protein in human blood circulation was investigated using fluorescence quenching titration, UV-vis absorption and circular dichroism (CD) spectroscopy as well as molecular docking. LUM-induced quenching of the protein (HSA) fluorescence was characterized as static quenching, as revealed by the decrease in the value of the Stern-Volmer quenching constant, Ksv with increasing temperature, thus suggesting LUM-HSA complex formation. This was also confirmed from the UV-vis absorption spectral results. Values of the association constant, Ka for LUM-HSA interaction were found to be within the range, 7.27-5.01 × 104 M-1 at three different temperatures, i.e. 288 K, 298 K and 308 K, which indicated moderate binding affinity between LUM and HSA. The LUM-HSA complex was stabilized by hydrophobic interactions, H-bonds, as well as van der Waals forces, as predicted from the thermodynamic data (ΔS = +50.34 J mol-1 K-1 and ΔH = -12.3 kJ mol-1) of the binding reaction. Far-UV and near-UV CD spectral results demonstrated smaller changes in both secondary and tertiary structures of HSA upon LUM binding, while three-dimensional fluorescence spectra suggested alterations in the microenvironment around protein fluorophores (Trp and Tyr). LUM binding to HSA offered stability to the protein against thermal stress. Competitive drug displacement results designated Sudlow's Site I, located in subdomain IIA of HSA as the preferred binding site of LUM on HSA, which was well supported by molecular docking analysis.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Kabiru Abubakar Musa
- Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Nor Farrah Wahidah Ridzwan
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Saharuddin B Mohamad
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture and Healthcare, University of Malaya, Kuala Lumpur, Malaysia
| | - Saad Tayyab
- Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture and Healthcare, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
19
|
Sugimoto H, Nakajima Y, Motoyama A, Katagiri E, Watanabe T, Suzuki K. Unfolding of CBP21, a lytic polysaccharide monooxygenase, without dissociation of its copper ion cofactor. Biopolymers 2019; 111:e23339. [PMID: 31688961 DOI: 10.1002/bip.23339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/10/2019] [Accepted: 10/17/2019] [Indexed: 01/22/2023]
Abstract
Chitin-binding protein 21 (CBP21) from Serratia marcescens is a lytic polysaccharide monooxygenase that contains a copper ion as a cofactor. We aimed to elucidate the unfolding mechanism of CBP21 and the effects of Cu2+ on its structural stability at pH 5.0. Thermal unfolding of both apo- and holoCBP21 was reversible. ApoCBP21 unfolded in a simple two-state transition manner. The peak temperature of the DSC curve, tp , for holoCBP21 (74.4°C) was about nine degrees higher than that for apoCBP21 (65.6°C). The value of tp in the presence of excess Cu2+ was around 75°C, indicating that Cu2+ does not dissociate from the protein molecule during unfolding. The unfolding mechanism of holoCBP21 was considered to be as follows: N∙Cu2+ ⇌ U∙Cu2+ , where N and U represent the native and unfolded states, respectively. Urea-induced equilibrium unfolding analysis showed that holoCBP21 was stabilized by 35 kJ mol-1 in terms of the Gibbs energy change for unfolding (pH 5.0, 25°C), compared with apoCBP21. The increased stability of holoCBP21 was considered to result from the structural stabilization of the protein-Cu2+ complex itself.
Collapse
Affiliation(s)
- Hayuki Sugimoto
- Graduate School of Science and Technology, Niigata University, Niigata, Japan.,Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Yuichi Nakajima
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Ayaka Motoyama
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Erina Katagiri
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Takeshi Watanabe
- Graduate School of Science and Technology, Niigata University, Niigata, Japan.,Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Kazushi Suzuki
- Graduate School of Science and Technology, Niigata University, Niigata, Japan.,Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| |
Collapse
|
20
|
Hirano A, Nagatoishi S, Wada M, Tsumoto K, Maluf KN, Arakawa T. Technical Capabilities and Limitations of Optical Spectroscopy and Calorimetry Using Water-Miscible Solvents: The Case of Dimethyl Sulfoxide, Acetonitrile, and 1,4-Dioxane. J Pharm Sci 2019; 109:524-531. [PMID: 31682831 DOI: 10.1016/j.xphs.2019.10.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/22/2019] [Accepted: 10/29/2019] [Indexed: 01/09/2023]
Abstract
In drug development, water-miscible solvents are commonly used to dissolve drug substances. Typical routine procedures in drug development include dilution of the stock drug solution into an aqueous solution containing target macromolecules for drug binding assays. However, water-miscible solvents impose some technical limitations on the assays on account of their light absorption and heat capacity. Here, we examined the effects of the dilution of 3 water-miscible solvents, that is, dimethyl sulfoxide, acetonitrile, and 1,4-dioxane, on the baseline stability and signal/noise ratio in circular dichroism spectroscopy, isothermal titration calorimetry, and differential scanning calorimetry. Dimethyl sulfoxide and 1,4-dioxane affect the signal/noise ratio of circular dichroism spectra at typically used concentrations due to their light absorbance. The water-miscible solvents generate interfering signals in the isothermal titration calorimetry due to their mixing heat. They show negative or positive slope in the differential scanning calorimetry. Such interfering effects of the solvents are reduced by appropriate dilution according to the analytical techniques. Because the water-miscible solvents have solubilization capacity for alkyl chain moieties and aromatic moieties of chemicals, drug substances containing these moieties can be dissolved into the solvents and then subjected to the analyses to examine their interactions with target proteins after appropriate dilution of the drug solutions.
Collapse
Affiliation(s)
- Atsushi Hirano
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan.
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Momoyo Wada
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Kouhei Tsumoto
- The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Karl N Maluf
- Alliance Protein Laboratories, Division of KBI Biopharma, San Diego, California 92121
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, Division of KBI Biopharma, San Diego, California 92121
| |
Collapse
|
21
|
Vergara R, Romero‐Romero S, Velázquez‐López I, Espinoza‐Pérez G, Rodríguez‐Hernández A, Pulido NO, Sosa‐Peinado A, Rodríguez‐Romero A, Fernández‐Velasco DA. The interplay of protein–ligand and water‐mediated interactions shape affinity and selectivity in the LAO binding protein. FEBS J 2019; 287:763-782. [DOI: 10.1111/febs.15019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/25/2019] [Accepted: 07/24/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Renan Vergara
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Sergio Romero‐Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Isabel Velázquez‐López
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Georgina Espinoza‐Pérez
- Laboratorio de Química de Biomacromoléculas 3, Departamento de Química de Biomacromoléculas, Instituto de Química Universidad Nacional Autónoma de México Ciudad de México México
| | - Annia Rodríguez‐Hernández
- Laboratorio de Química de Biomacromoléculas 3, Departamento de Química de Biomacromoléculas, Instituto de Química Universidad Nacional Autónoma de México Ciudad de México México
| | - Nancy O. Pulido
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Alejandro Sosa‐Peinado
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Adela Rodríguez‐Romero
- Laboratorio de Química de Biomacromoléculas 3, Departamento de Química de Biomacromoléculas, Instituto de Química Universidad Nacional Autónoma de México Ciudad de México México
| | - Daniel Alejandro Fernández‐Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| |
Collapse
|
22
|
Fontaine F, Overman J, Moustaqil M, Mamidyala S, Salim A, Narasimhan K, Prokoph N, Robertson AAB, Lua L, Alexandrov K, Koopman P, Capon RJ, Sierecki E, Gambin Y, Jauch R, Cooper MA, Zuegg J, Francois M. Small-Molecule Inhibitors of the SOX18 Transcription Factor. Cell Chem Biol 2017; 24:346-359. [PMID: 28163017 DOI: 10.1016/j.chembiol.2017.01.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/14/2016] [Accepted: 01/10/2017] [Indexed: 12/13/2022]
Abstract
Pharmacological modulation of transcription factors (TFs) has only met little success over the past four decades. This is mostly due to standard drug discovery approaches centered on blocking protein/DNA binding or interfering with post-translational modifications. Recent advances in the field of TF biology have revealed a central role of protein-protein interaction in their mode of action. In an attempt to modulate the activity of SOX18 TF, a known regulator of vascular growth in development and disease, we screened a marine extract library for potential small-molecule inhibitors. We identified two compounds, which inspired a series of synthetic SOX18 inhibitors, able to interfere with the SOX18 HMG DNA-binding domain, and to disrupt HMG-dependent protein-protein interaction with RBPJ. These compounds also perturbed SOX18 transcriptional activity in a cell-based reporter gene system. This approach may prove useful in developing a new class of anti-angiogenic compounds based on the inhibition of TF activity.
Collapse
Affiliation(s)
- Frank Fontaine
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeroen Overman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mehdi Moustaqil
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Sreeman Mamidyala
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Angela Salim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kamesh Narasimhan
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Nina Prokoph
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Avril A B Robertson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Linda Lua
- Protein Expression Facility, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Emma Sierecki
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Yann Gambin
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Ralf Jauch
- Genome Regulation Laboratory, Drug Discovery Pipeline, Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; Guangzhou Medical University, Guangzhou 511436, China
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Johannes Zuegg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Mathias Francois
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
| |
Collapse
|
23
|
Paul S, Banerjee S, Vogel HJ. Ligand binding specificity of the Escherichia coli periplasmic histidine binding protein, HisJ. Protein Sci 2016; 26:268-279. [PMID: 27865021 DOI: 10.1002/pro.3079] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 12/13/2022]
Abstract
The HisJ protein from Escherichia coli and related Gram negative bacteria is the periplasmic component of a bacterial ATP-cassette (ABC) transporter system. Together these proteins form a transmembrane complex that can take up L-histidine from the environment and translocate it into the cytosol. We have studied the specificity of HisJ for binding L-His and many related naturally occurring compounds. Our data confirm that L-His is the preferred ligand, but that 1-methyl-L-His and 3-methyl-L-His can also bind, while the dipeptide carnosine binds weakly and D-histidine and the histidine degradation products, histamine, urocanic acid and imidazole do not bind. L-Arg, homo-L-Arg, and post-translationally modified methylated Arg-analogs also bind with reasonable avidity, with the exception of symmetric dimethylated-L-Arg. In contrast, L-Lys and L-Orn have considerably weaker interactions with HisJ and methylated and acetylated Lys variants show relatively poor binding. It was also observed that the carboxylate group of these amino acids and their variants was very important for proper recognition of the ligand. Taken together our results are a key step towards designing HisJ as a specific protein-based reagentless biosensor.
Collapse
Affiliation(s)
- Subrata Paul
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta, T2N 1N4, Canada
| | - Sambuddha Banerjee
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta, T2N 1N4, Canada
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta, T2N 1N4, Canada
| |
Collapse
|
24
|
Siddiqui AA, Khaki PSS, Bano B. Interaction of almond cystatin with pesticides: Structural and functional analysis. J Mol Recognit 2016; 30. [DOI: 10.1002/jmr.2586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/06/2016] [Accepted: 09/27/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Azad Alam Siddiqui
- Department of Biochemistry, Faculty of life Sciences; Aligarh Muslim University; Aligarh India
| | | | - Bilqees Bano
- Department of Biochemistry, Faculty of life Sciences; Aligarh Muslim University; Aligarh India
| |
Collapse
|
25
|
Tripathi A, Gupta K, Khare S, Jain PC, Patel S, Kumar P, Pulianmackal AJ, Aghera N, Varadarajan R. Molecular Determinants of Mutant Phenotypes, Inferred from Saturation Mutagenesis Data. Mol Biol Evol 2016; 33:2960-2975. [PMID: 27563054 PMCID: PMC5062330 DOI: 10.1093/molbev/msw182] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Understanding how mutations affect protein activity and organismal fitness is a major challenge. We used saturation mutagenesis combined with deep sequencing to determine mutational sensitivity scores for 1,664 single-site mutants of the 101 residue Escherichia coli cytotoxin, CcdB at seven different expression levels. Active-site residues could be distinguished from buried ones, based on their differential tolerance to aliphatic and charged amino acid substitutions. At nonactive-site positions, the average mutational tolerance correlated better with depth from the protein surface than with accessibility. Remarkably, similar results were observed for two other small proteins, PDZ domain (PSD95pdz3) and IgG-binding domain of protein G (GB1). Mutational sensitivity data obtained with CcdB were used to derive a procedure for predicting functional effects of mutations. Results compared favorably with those of two widely used computational predictors. In vitro characterization of 80 single, nonactive-site mutants of CcdB showed that activity in vivo correlates moderately with thermal stability and solubility. The inability to refold reversibly, as well as a decreased folding rate in vitro, is associated with decreased activity in vivo. Upon probing the effect of modulating expression of various proteases and chaperones on mutant phenotypes, most deleterious mutants showed an increased in vivo activity and solubility only upon over-expression of either Trigger factor or SecB ATP-independent chaperones. Collectively, these data suggest that folding kinetics rather than protein stability is the primary determinant of activity in vivo. This study enhances our understanding of how mutations affect phenotype, as well as the ability to predict fitness effects of point mutations.
Collapse
Affiliation(s)
- Arti Tripathi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kritika Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Pankaj C Jain
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Siddharth Patel
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Prasanth Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Nilesh Aghera
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
| |
Collapse
|
26
|
Krumova S, Todinova S, Tileva M, Bouzhir-Sima L, Vos MH, Liebl U, Taneva SG. Thermal stability and binding energetics of thymidylate synthase ThyX. Int J Biol Macromol 2016; 91:560-7. [PMID: 27268384 DOI: 10.1016/j.ijbiomac.2016.05.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/20/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
The bacterial thymidylate synthase ThyX is a multisubstrate flavoenzyme that takes part in the de novo synthesis of thymidylate in a variety of microorganisms. Herein we study the effect of FAD and dUMP binding on the thermal stability of wild type (WT) ThyX from the mesophilic Paramecium bursaria chlorella virus-1 (PBCV-1) and from the thermophilic bacterium Thermotoga maritima (TmThyX), and from two variants of TmThyX, Y91F and S88W, using differential scanning calorimetry. The energetics underlying these processes was characterized by isothermal titration calorimetry. The PBCV-1 protein is significantly less stable against the thermal challenge than the TmThyX WT. FAD exerted stabilizing effect greater for PBCV-1 than for TmThyX and for both mutants, whereas binding of dUMP to FAD-loaded proteins stabilized further only TmThyX. Different thermodynamic signatures describe the FAD binding to the WT ThyX proteins. While TmThyX binds FAD with a low μM binding affinity in a process characterized by a favorable entropy change, the assembly of PBCV-1 with FAD is governed by a large enthalpy change opposed by an unfavorable entropy change resulting in a relatively strong nM binding. An enthalpy-driven formation of a high affinity ternary ThyX/FAD/dUMP complex was observed only for TmThyX.
Collapse
Affiliation(s)
- Sashka Krumova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 21, 1113 Sofia, Bulgaria
| | - Svetla Todinova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 21, 1113 Sofia, Bulgaria
| | - Milena Tileva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 21, 1113 Sofia, Bulgaria
| | | | - Marten H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM, 91128 Palaiseau Cedex, France
| | - Ursula Liebl
- LOB, Ecole Polytechnique, CNRS, INSERM, 91128 Palaiseau Cedex, France
| | - Stefka G Taneva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 21, 1113 Sofia, Bulgaria.
| |
Collapse
|
27
|
Faroongsarng D. Assessment of the Dissociation Energetics of Some Selected Ligand Drugs Bound on Human Serum Albumin by Differential Scanning Calorimetry. AAPS PharmSciTech 2016; 17:474-81. [PMID: 26246411 DOI: 10.1208/s12249-015-0372-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/15/2015] [Indexed: 11/30/2022] Open
Abstract
Drug-protein binding may play a role in the thermal energetics of protein denaturation and could lead to the determination of its equilibrium dissociation parameter. The aim of this study was to assess the energetics of a drug that was bound to human serum albumin (HSA) during thermal denaturation. Drugs that were bound at a single high-affinity primary binding site on HSA, including diazepam and ibuprofen, were employed. Commercial HSA was treated with charcoal to remove stabilizers and adjusted to 20% w/v in a pH 7.4 buffered solution. Serial concentrations of individual drugs up to 0.16 mmole/g-protein were added to the cleaned HSA solutions whereas diazepam was added to a commercial HSA solution. Samples were subjected to differential scanning calorimetry (DSC) set to run from 37 to 90°C at 3.0°C/min. Binding of the drug slightly increased the denaturing temperature of the cleaned HSA due to a shift in the equilibrium toward the native protein bound with the drug. Diazepam depressed the denaturing temperature of the commercial HSA by competing with the stabilizers already bound to the primary site of the HSA. This yielded not only the HSA-stabilizer but also the HSA-diazepam type complexes that exhibited a different denaturation process. A rational approximation of the Lumry-Eyring protein denaturation model was used to treat the DSC endotherms. The approximated scheme: [Formula: see text] was successfully fitted to the data. It was used to determine the dissociation parameters for diazepam and ibuprofen bound to the HSA. These results were comparable to those obtained from other methods.
Collapse
|
28
|
de Diego Puente T, Gallego-Jara J, Castaño-Cerezo S, Bernal Sánchez V, Fernández Espín V, García de la Torre J, Manjón Rubio A, Cánovas Díaz M. The Protein Acetyltransferase PatZ from Escherichia coli Is Regulated by Autoacetylation-induced Oligomerization. J Biol Chem 2015; 290:23077-93. [PMID: 26251518 DOI: 10.1074/jbc.m115.649806] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 01/31/2023] Open
Abstract
Lysine acetylation is an important post-translational modification in the metabolic regulation of both prokaryotes and eukaryotes. In Escherichia coli, PatZ (formerly YfiQ) is the only known acetyltransferase protein and is responsible for acetyl-CoA synthetase acetylation. In this study, we demonstrated PatZ-positive cooperativity in response to acetyl-CoA and the regulation of acetyl-CoA synthetase activity by the acetylation level. Furthermore, functional analysis of an E809A mutant showed that the conserved glutamate residue is not relevant for the PatZ catalytic mechanism. Biophysical studies demonstrated that PatZ is a stable tetramer in solution and is transformed to its octameric form by autoacetylation. Moreover, this modification is reversed by the sirtuin CobB. Finally, an in silico PatZ tetramerization model based on hydrophobic and electrostatic interactions is proposed and validated by three-dimensional hydrodynamic analysis. These data reveal, for the first time, the structural regulation of an acetyltransferase by autoacetylation in a prokaryotic organism.
Collapse
Affiliation(s)
| | - Julia Gallego-Jara
- From the Departments of Biochemistry and Molecular Biology and Immunology (B) and
| | - Sara Castaño-Cerezo
- From the Departments of Biochemistry and Molecular Biology and Immunology (B) and
| | | | - Vanesa Fernández Espín
- Physical Chemistry, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum," P. O. Box 4021, Murcia E-30100, Spain
| | - José García de la Torre
- Physical Chemistry, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum," P. O. Box 4021, Murcia E-30100, Spain
| | - Arturo Manjón Rubio
- From the Departments of Biochemistry and Molecular Biology and Immunology (B) and
| | - Manuel Cánovas Díaz
- From the Departments of Biochemistry and Molecular Biology and Immunology (B) and
| |
Collapse
|
29
|
Pulido NO, Silva DA, Tellez LA, Pérez-Hernández G, García-Hernández E, Sosa-Peinado A, Fernández-Velasco DA. On the molecular basis of the high affinity binding of basic amino acids to LAOBP, a periplasmic binding protein fromSalmonella typhimurium. J Mol Recognit 2015; 28:108-16. [DOI: 10.1002/jmr.2434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 08/20/2014] [Accepted: 09/15/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Nancy O. Pulido
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina; Universidad Nacional Autónoma de México; México DF Mexico
| | - Daniel-Adriano Silva
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina; Universidad Nacional Autónoma de México; México DF Mexico
- Biochemistry Department; University of Washington; Seattle WA USA
| | - Luis A. Tellez
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina; Universidad Nacional Autónoma de México; México DF Mexico
- Department of Psychiatry; Yale University School of Medicine; New Haven CT USA
| | - Gerardo Pérez-Hernández
- Departamento de Ciencias Naturales; Universidad Autónoma Metropolitana- Cuajimalpa; México DF Mexico
| | - Enrique García-Hernández
- Instituto de Química; Universidad Nacional Autónoma de México; Circuito Exterior, Ciudad Universitaria México 04510 DF Mexico
| | - Alejandro Sosa-Peinado
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina; Universidad Nacional Autónoma de México; México DF Mexico
| | - D. Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina; Universidad Nacional Autónoma de México; México DF Mexico
| |
Collapse
|
30
|
Thermal, chemical and pH induced unfolding of turmeric root lectin: modes of denaturation. PLoS One 2014; 9:e103579. [PMID: 25140525 PMCID: PMC4139268 DOI: 10.1371/journal.pone.0103579] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/02/2014] [Indexed: 11/19/2022] Open
Abstract
Curcuma longa rhizome lectin, of non-seed origin having antifungal, antibacterial and α-glucosidase inhibitory activities, forms a homodimer with high thermal stability as well as acid tolerance. Size exclusion chromatography and dynamic light scattering show it to be a dimer at pH 7, but it converts to a monomer near pH 2. Circular dichroism spectra and fluorescence emission maxima are virtually indistinguishable from pH 7 to 2, indicating secondary and tertiary structures remain the same in dimer and monomer within experimental error. The tryptophan environment as probed by acrylamide quenching data yielded very similar data at pH 2 and pH 7, implying very similar folding for monomer and dimer. Differential scanning calorimetry shows a transition at 350.3 K for dimer and at 327.0 K for monomer. Thermal unfolding and chemical unfolding induced by guanidinium chloride for dimer are both reversible and can be described by two-state models. The temperatures and the denaturant concentrations at which one-half of the protein molecules are unfolded, are protein concentration-dependent for dimer but protein concentration-independent for monomer. The free energy of unfolding at 298 K was found to be 5.23 Kcal mol−1 and 14.90 Kcal mol−1 for the monomer and dimer respectively. The value of change in excess heat capacity upon protein denaturation (ΔCp) is 3.42 Kcal mol−1 K−1 for dimer. The small ΔCp for unfolding of CLA reflects a buried hydrophobic core in the folded dimeric protein. These unfolding experiments, temperature dependent circular dichroism and dynamic light scattering for the dimer at pH 7 indicate its higher stability than for the monomer at pH 2. This difference in stability of dimeric and monomeric forms highlights the contribution of inter-subunit interactions in the former.
Collapse
|
31
|
Hu X, Li H. Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective. FEBS Lett 2014; 588:3613-20. [PMID: 24747422 DOI: 10.1016/j.febslet.2014.04.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 01/04/2023]
Abstract
Protein-ligand interactions are ubiquitous and play important roles in almost every biological process. The direct elucidation of the thermodynamic, structural and functional consequences of protein-ligand interactions is thus of critical importance to decipher the mechanism underlying these biological processes. A toolbox containing a variety of powerful techniques has been developed to quantitatively study protein-ligand interactions in vitro as well as in living systems. The development of atomic force microscopy-based single molecule force spectroscopy techniques has expanded this toolbox and made it possible to directly probe the mechanical consequence of ligand binding on proteins. Many recent experiments have revealed how ligand binding affects the mechanical stability and mechanical unfolding dynamics of proteins, and provided mechanistic understanding on these effects. The enhancement effect of mechanical stability by ligand binding has been used to help tune the mechanical stability of proteins in a rational manner and develop novel functional binding assays for protein-ligand interactions. Single molecule force spectroscopy studies have started to shed new lights on the structural and functional consequence of ligand binding on proteins that bear force under their biological settings.
Collapse
Affiliation(s)
- Xiaotang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments, School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin 300072, PR China
| | - Hongbin Li
- State Key Laboratory of Precision Measurements Technology and Instruments, School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin 300072, PR China; Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| |
Collapse
|
32
|
Wehrkamp CJ, Gutwein AR, Natarajan SK, Phillippi MA, Mott JL. XIAP antagonist embelin inhibited proliferation of cholangiocarcinoma cells. PLoS One 2014; 9:e90238. [PMID: 24603802 PMCID: PMC3946004 DOI: 10.1371/journal.pone.0090238] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/26/2014] [Indexed: 01/07/2023] Open
Abstract
Cholangiocarcinoma cells are dependent on antiapoptotic signaling for survival and resistance to death stimuli. Recent mechanistic studies have revealed that increased cellular expression of the E3 ubiquitin-protein ligase X-linked inhibitor of apoptosis (XIAP) impairs TRAIL- and chemotherapy-induced cytotoxicity, promoting survival of cholangiocarcinoma cells. This study was undertaken to determine if pharmacologic antagonism of XIAP protein was sufficient to sensitize cholangiocarcinoma cells to cell death. We employed malignant cholangiocarcinoma cell lines and used embelin to antagonize XIAP protein. Embelin treatment resulted in decreased XIAP protein levels by 8 hours of treatment with maximal effect at 16 hours in KMCH and Mz-ChA-1 cells. Assessment of nuclear morphology demonstrated a concentration-dependent increase in nuclear staining. Interestingly, embelin induced nuclear morphology changes as a single agent, independent of the addition of TNF-related apoptosis inducing ligand (TRAIL). However, caspase activity assays revealed that increasing embelin concentrations resulted in slight inhibition of caspase activity, not activation. In addition, the use of a pan-caspase inhibitor did not prevent nuclear morphology changes. Finally, embelin treatment of cholangiocarcinoma cells did not induce DNA fragmentation or PARP cleavage. Apoptosis does not appear to contribute to the effects of embelin on cholangiocarcinoma cells. Instead, embelin caused inhibition of cell proliferation and cell cycle analysis indicated that embelin increased the number of cells in S and G2/M phase. Our results demonstrate that embelin decreased proliferation in cholangiocarcinoma cell lines. Embelin treatment resulted in decreased XIAP protein expression, but did not induce or enhance apoptosis. Thus, in cholangiocarcinoma cells the mechanism of action of embelin may not be dependent on apoptosis.
Collapse
Affiliation(s)
- Cody J. Wehrkamp
- Department of Biochemistry and Molecular Biology, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Ashley R. Gutwein
- Department of Biochemistry and Molecular Biology, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Sathish Kumar Natarajan
- Department of Biochemistry and Molecular Biology, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Mary Anne Phillippi
- Department of Biochemistry and Molecular Biology, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Justin L. Mott
- Department of Biochemistry and Molecular Biology, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
| |
Collapse
|
33
|
Thermal inactivation reaction rates for ricin are influenced by pH and carbohydrates. Food Chem Toxicol 2013; 58:116-23. [DOI: 10.1016/j.fct.2013.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/05/2013] [Indexed: 11/20/2022]
|
34
|
Choi JH, San A, Ostermeier M. Non-allosteric enzyme switches possess larger effector-induced changes in thermodynamic stability than their non-switch analogs. Protein Sci 2013; 22:475-85. [PMID: 23400970 DOI: 10.1002/pro.2234] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 02/05/2013] [Accepted: 02/07/2013] [Indexed: 11/11/2022]
Abstract
The ability to regulate cellular protein activity offers a broad range of biotechnological and biomedical applications. Such protein regulation can be achieved by modulating the specific protein activity or through processes that regulate the amount of protein in the cell. We have previously demonstrated that the nonhomologous recombination of the genes encoding maltose binding protein (MBP) and TEM1 β-lactamase (BLA) can result in genes that confer maltose-dependent resistance to β-lactam antibiotics even though the encoded proteins are not allosteric enzymes. We showed that these phenotypic switches-named based on their conferral of a switching phenotype to cells-resulted from a specific interaction with maltose in the cell that increased the switches cellular accumulation. Since phenotypic switches represent an important class of engineered proteins for basic science and biotechnological applications in vivo, we sought to elucidate the phenomena behind the increased accumulation and switching properties. Here, we demonstrate the key role for the linker region between the two proteins. Experimental evidence supports the hypothesis that in the absence of their effector, some phenotypic switches possess an increased rate of unfolding, decreased conformational stability, and increased protease susceptibility. These factors alone or in combination serve to decrease cellular accumulation. The effector functions to increase cellular accumulation by alleviating one or more of these defects. This perspective on the mechanism for phenotypic switching will aid the development of design rules for switch construction for applications and inform the study of the regulatory mechanisms of natural cellular proteins.
Collapse
Affiliation(s)
- Jay H Choi
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21212, USA
| | | | | |
Collapse
|
35
|
Systematic interaction analysis of human lipocalin-type prostaglandin D synthase with small lipophilic ligands. Biochem J 2012; 446:279-89. [DOI: 10.1042/bj20120324] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
L-PGDS [lipocalin-type PG (prostaglandin) D synthase] is a multi-functional protein, acting as a PGD2-producing enzyme and a lipid-transporter. In the present study, we focus on the function of L-PGDS as an extracellular transporter for small lipophilic molecules. We characterize the binding mechanism of human L-PGDS for the molecules, especially binding affinity stoichiometry and driving force, using tryptophan fluorescence quenching, ICD (induced circular dichroism) and ITC (isothermal titration calorimetry). The tryptophan fluorescence quenching measurements revealed that haem metabolites such as haemin, biliverdin and bilirubin bind to L-PGDS with significantly higher affinities than the other small lipophilic ligands examined, showing dissociation constant (Kd) values from 17.0 to 20.9 nM. We focused particularly on the extra-specificities of haem metabolites and L-PGDS. The ITC and ICD data revealed that two molecules of the haem metabolites bind to L-PGDS with high and low affinities, showing Kd values from 2.8 to 18.1 nM and from 0.209 to 1.63 μM respectively. The thermodynamic parameters for the interactions revealed that the contributions of enthalpy and entropy change were considerably different for each haem metabolite even when the Gibbs energy change was the same. Thus we believe that the binding energy of haem metabolites to L-PGDS is optimized by balancing enthalpy and entropy change.
Collapse
|
36
|
Burgos MI, Fernández RA, Celej MS, Rossi LI, Fidelio GD, Dassie SA. Binding of the Highly Toxic Tetracycline Derivative, Anhydrotetracycline, to Bovine Serum Albumin. Biol Pharm Bull 2011; 34:1301-6. [DOI: 10.1248/bpb.34.1301] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Martha Ines Burgos
- Departamento de Química Biológica-Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria
| | - Ricardo Ariel Fernández
- Departamento de Fisicoquímica-Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria
| | - María Soledad Celej
- Departamento de Química Biológica-Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria
| | - Laura Isabel Rossi
- Departamento de Química Orgánica-Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria
| | - Gerardo Daniel Fidelio
- Departamento de Química Biológica-Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria
| | - Sergio Alberto Dassie
- Departamento de Fisicoquímica-Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria
| |
Collapse
|
37
|
de Souza TLF, Sanches D, Gonçalves RB, da RochaPita SS, Pascutti PG, Bianconi ML, de Almeida FCL, Silva JL, de Oliveira AC. Conformational selection, dynamic restriction and the hydrophobic effect coupled to stabilization of the BIR3 domain of the human X-linked inhibitor of apoptosis protein by the tetrapeptide AVPI. Biophys Chem 2010; 152:99-108. [DOI: 10.1016/j.bpc.2010.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 08/09/2010] [Accepted: 08/10/2010] [Indexed: 10/19/2022]
|
38
|
Pliska V. Thermodynamic descriptors, profiles and driving forces in membrane receptor-ligand interactions. J Recept Signal Transduct Res 2010; 30:454-68. [DOI: 10.3109/10799893.2010.515594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
39
|
Di Lella S, Martí MA, Croci DO, Guardia CMA, Díaz-Ricci JC, Rabinovich GA, Caramelo JJ, Estrin DA. Linking the structure and thermal stability of beta-galactoside-binding protein galectin-1 to ligand binding and dimerization equilibria. Biochemistry 2010; 49:7652-8. [PMID: 20666428 DOI: 10.1021/bi100356g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The stability of proteins involves a critical balance of interactions of different orders of magnitude. In this work, we present experimental evidence of an increased thermal stability of galectin-1, a multifunctional beta-galactoside-binding protein, upon binding to the disaccharide lactose. Analysis of structural changes occurring upon binding of lectin to its specific glycans and thermal denaturation of the protein and the complex were analyzed by circular dichroism. On the other hand, we studied dimerization as another factor that may induce structural and thermal stability changes. The results were then complemented with molecular dynamics simulations followed by a detailed computation of thermodynamic properties, including the internal energy, solvation free energy, and conformational entropy. In addition, an energetic profile of the binding and dimerization processes is also presented. Whereas binding and cross-linking of lactose do not alter galectin-1 structure, this interaction leads to substantial changes in the flexibility and internal energy of the protein which confers increased thermal stability to this endogenous lectin. Given that an improved understanding of the physicochemical properties of galectin-glycan lattices may contribute to the dissection of their biological functions and prediction of their therapeutic applications, our study suggests that galectin binding to specific disaccharide ligands may increase the thermal stability of this glycan-binding protein, an effect that could influence its critical biological functions.
Collapse
Affiliation(s)
- Santiago Di Lella
- Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Valerio-Lepiniec M, Aumont-Nicaise M, Roux C, Raynal B, England P, Badet B, Badet-Denisot MA, Desmadril M. Analysis of the Escherichia coli glucosamine-6-phosphate synthase activity by isothermal titration calorimetry and differential scanning calorimetry. Arch Biochem Biophys 2010; 498:95-104. [PMID: 20416269 DOI: 10.1016/j.abb.2010.04.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 04/14/2010] [Accepted: 04/14/2010] [Indexed: 11/25/2022]
Abstract
Glucosamine-6-phosphate synthase (GlmS) is responsible for the first and rate-limiting step in the hexosamine biosynthetic pathway. It catalyzes the conversion of D-fructose-6P (F6P) into D-glucosamine-6P (GlcN6P) using L-glutamine (Gln) as nitrogen donor (synthase activity) according to an ordered bi-bi process where F6P binds first. In the absence of F6P, the enzyme exhibits a weak hydrolyzing activity of Gln into Glu and ammonia (glutaminase activity), whereas the presence of F6P strongly stimulates it (hemi-synthase activity). Until now, these different activities were indirectly measured using either coupled enzyme or colorimetric methods. In this work, we have developed a direct assay monitoring the heat released by the reaction. Isothermal titration calorimetry and differential scanning calorimetry were used to determine kinetic and thermodynamic parameters of GlmS. The direct determination at 37 degrees C of kinetic parameters and affinity constants for both F6P and Gln demonstrated that part of the ammonia produced by Gln hydrolysis in the presence of both substrates is not used for the formation of the GlcN6P. The full characterization of this phenomenon allowed to identify experimental conditions where this leak of ammonia is negligible. Enthalpy measurements at 25 degrees C in buffers of various heats of protonation demonstrated that no proton exchange with the medium occurred during the enzyme-catalyzed glutaminase or synthase reaction suggesting for the first time that both products are released as a globally neutral pair composed by the Glu carboxylic side chain and the GlcN6P amine function. Finally we showed that the oligomerization state of GlmS is concentration-dependent.
Collapse
Affiliation(s)
- Marie Valerio-Lepiniec
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, Université de Paris-Sud 11, Orsay, France.
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Quesada-Soriano I, Parker LJ, Primavera A, Casas-Solvas JM, Vargas-Berenguel A, Barón C, Morton CJ, Mazzetti AP, Lo Bello M, Parker MW, García-Fuentes L. Influence of the H-site residue 108 on human glutathione transferase P1-1 ligand binding: structure-thermodynamic relationships and thermal stability. Protein Sci 2010; 18:2454-70. [PMID: 19780048 DOI: 10.1002/pro.253] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The effect of the Y108V mutation of human glutathione S-transferase P1-1 (hGST P1-1) on the binding of the diuretic drug ethacrynic acid (EA) and its glutathione conjugate (EASG) was investigated by calorimetric, spectrofluorimetric, and crystallographic studies. The mutation Tyr 108 --> Val resulted in a 3D-structure very similar to the wild type (wt) enzyme, where both the hydrophobic ligand binding site (H-site) and glutathione binding site (G-site) are unchanged except for the mutation itself. However, due to a slight increase in the hydrophobicity of the H-site, as a consequence of the mutation, an increase in the entropy was observed. The Y108V mutation does not affect the affinity of EASG for the enzyme, which has a higher affinity (K(d) approximately 0.5 microM) when compared with those of the parent compounds, K(d) (EA) approximately 13 microM, K(d) (GSH) approximately 25 microM. The EA moiety of the conjugate binds in the H-site of Y108V mutant in a fashion completely different to those observed in the crystal structures of the EA or EASG wt complex structures. We further demonstrate that the Delta C(p) values of binding can also be correlated with the potential stacking interactions between ligand and residues located in the binding sites as predicted from crystal structures. Moreover, the mutation does not significantly affect the global stability of the enzyme. Our results demonstrate that calorimetric measurements maybe useful in determining the preference of binding (the binding mode) for a drug to a specific site of the enzyme, even in the absence of structural information.
Collapse
Affiliation(s)
- Indalecio Quesada-Soriano
- Physical Chemistry, Faculty of Experimental Sciences, University of Almería, La Cañada de San Urbano, 04120 Almería, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Varshney A, Sen P, Ahmad E, Rehan M, Subbarao N, Khan RH. Ligand binding strategies of human serum albumin: how can the cargo be utilized? Chirality 2010; 22:77-87. [PMID: 19319989 DOI: 10.1002/chir.20709] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human serum albumin (HSA), being the most abundant carrier protein in blood and a modern day clinical tool for drug delivery, attracts high attention among biologists. Hence, its unfolding/refolding strategies and exogenous/endogenous ligand binding preference are of immense use in therapeutics and clinical biochemistry. Among its fellow proteins albumin is known to carry almost every small molecule. Thus, it is a potential contender for being a molecular cargo/or nanovehicle for clinical, biophysical and industrial purposes. Nonetheless, its structure and function are largely regulated by various chemical and physical factors to accommodate HSA to its functional purpose. This multifunctional protein also possesses enzymatic properties which may be used to convert prodrugs to active therapeutics. This review aims to highlight current overview on the binding strategies of protein to various ligands that may be expected to lead to significant clinical applications.
Collapse
Affiliation(s)
- Ankita Varshney
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | | | | | | | | | | |
Collapse
|
43
|
Kavitha M, Bobbili KB, Swamy MJ. Differential scanning calorimetric and spectroscopic studies on the unfolding of Momordica charantia lectin. Similar modes of thermal and chemical denaturation. Biochimie 2010; 92:58-64. [DOI: 10.1016/j.biochi.2009.09.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Accepted: 09/17/2009] [Indexed: 11/15/2022]
|
44
|
Lieberman RL, D'aquino JA, Ringe D, Petsko GA. Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability. Biochemistry 2009; 48:4816-27. [PMID: 19374450 PMCID: PMC2699628 DOI: 10.1021/bi9002265] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Human lysosomal enzymes acid-beta-glucosidase (GCase) and acid-alpha-galactosidase (alpha-Gal A) hydrolyze the sphingolipids glucosyl- and globotriaosylceramide, respectively, and mutations in these enzymes lead to the lipid metabolism disorders Gaucher and Fabry disease, respectively. We have investigated the structure and stability of GCase and alpha-Gal A in a neutral-pH environment reflective of the endoplasmic reticulum and an acidic-pH environment reflective of the lysosome. These details are important for the development of pharmacological chaperone therapy for Gaucher and Fabry disease, in which small molecules bind mutant enzymes in the ER to enable the mutant enzyme to meet quality control requirements for lysosomal trafficking. We report crystal structures of apo GCase at pH 4.5, at pH 5.5, and in complex with the pharmacological chaperone isofagomine (IFG) at pH 7.5. We also present thermostability analysis of GCase at pH 7.4 and 5.2 using differential scanning calorimetry. We compare our results with analogous experiments using alpha-Gal A and the chaperone 1-deoxygalactonijirimycin (DGJ), including the first structure of alpha-Gal A with DGJ. Both GCase and alpha-Gal A are more stable at lysosomal pH with and without their respective iminosugars bound, and notably, the stability of the GCase-IFG complex is pH sensitive. We show that the conformations of the active site loops in GCase are sensitive to ligand binding but not pH, whereas analogous galactose- or DGJ-dependent conformational changes in alpha-Gal A are not seen. Thermodynamic parameters obtained from alpha-Gal A unfolding indicate two-state, van't Hoff unfolding in the absence of the iminosugar at neutral and lysosomal pH, and non-two-state unfolding in the presence of DGJ. Taken together, these results provide insight into how GCase and alpha-Gal A are thermodynamically stabilized by iminosugars and suggest strategies for the development of new pharmacological chaperones for lysosomal storage disorders.
Collapse
Affiliation(s)
- Raquel L Lieberman
- Structural Neurology Lab at the Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.
| | | | | | | |
Collapse
|
45
|
Spectroscopic and differential scanning calorimetric studies on the unfolding of Trichosanthes dioica seed lectin. Similar modes of thermal and chemical denaturation. Glycoconj J 2009; 26:1075-84. [DOI: 10.1007/s10719-009-9228-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 01/03/2009] [Accepted: 01/12/2009] [Indexed: 10/21/2022]
|
46
|
Abstract
The thermodynamics of the stacking to unstacking transitions of 24 single-stranded DNA sequences (ssDNA), 10-12 bases in length, in sodium phosphate buffer were determined from 10 to 95 degrees C, using differential scanning calorimetry (DSC). An additional 22 ssDNA sequences did not exhibit an S<=>U transition in this temperature range. The transition properties of the ssDNA sequences with <or=60% self-complementarily in the reverse direction were independent of concentration with transition temperatures ranging from 15 to 70 degrees C, van't Hoff transition enthalpies from 92 to 201 kJ mol(-1) and transition enthalpies from 5 to 75% of the corresponding van't Hoff transition enthalpies. Since all the 16 doublets and 60 of the 64 triplets are present in both the transition and the non-transition ssDNA sequences, it is unlikely that the nucleation subset initiating stacking of the sequence is a specific doublet or triplet subset. Of the 141 quadruplet subsets of the 46 sequences, each transition ssDNA sequence contained at least one or more quadruplets not found in the non-transition ssDNA sequences. It could be concluded that the thermal stability of the stacked conformation was dependent on the presence of a possible nucleation quadruplet and the length of the ssDNA sequence and not on the G or C content of the ssDNA sequence, nor on the number of purine bases in the sequence.
Collapse
Affiliation(s)
- Jayanthi Ramprakash
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | | | | |
Collapse
|
47
|
Gordo S, Martos V, Santos E, Menéndez M, Bo C, Giralt E, de Mendoza J. Stability and structural recovery of the tetramerization domain of p53-R337H mutant induced by a designed templating ligand. Proc Natl Acad Sci U S A 2008; 105:16426-31. [PMID: 18940924 PMCID: PMC2575436 DOI: 10.1073/pnas.0805658105] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Indexed: 11/18/2022] Open
Abstract
Protein p53 is a transcription factor crucial for cell cycle and genome integrity. It is able to induce both cell arrest when DNA is damaged and the expression of DNA repair machinery. When the damage is irreversible, it triggers apoptosis. Indeed, the protein, which is a homotetramer, is mutated in most human cancers. For instance, the inherited mutation p53-R337H results in destabilization of the tetramer and, consequently, leads to an organism prone to tumor setup. We describe herein a rational designed molecule capable of holding together the four monomers of the mutated p53-R337H protein, recovering the tetramer integrity as in the wild-type structure. Two ligand molecules, based on a conical calix[4]arene with four cationic guanidiniomethyl groups at the wider edge (upper rim) and hydrophobic loops at the narrower edge (lower rim), fit nicely and cooperatively into the hydrophobic clefts between two of the monomers at each side of the protein and keep the tetrameric structure, like molecular templates, by both ion-pair and hydrophobic interactions. We found a good agreement between the structure of the complex and the nature of the interactions involved by a combination of theory (molecular dynamics) and experiments (circular dichroism, differential scanning calorimetry and (1)H saturation transfer difference NMR).
Collapse
Affiliation(s)
- Susana Gordo
- *Institute for Research in Biomedicine, Parc Científic de Barcelona, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Vera Martos
- Institute of Chemical Research of Catalonia, Avgda. Països Catalans, 16, 43007 Tarragona, Spain
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Eva Santos
- Institute of Chemical Research of Catalonia, Avgda. Països Catalans, 16, 43007 Tarragona, Spain
| | - Margarita Menéndez
- Instituto Rocasolano, Consejo Superior de Investigaciones Científicas and Ciber of Respiratory Diseases (Ciberes), Serrano 119, 28006 Madrid, Spain
| | - Carles Bo
- Institute of Chemical Research of Catalonia, Avgda. Països Catalans, 16, 43007 Tarragona, Spain
- Department of Inorganic and Physical Chemistry, Universitat Rovira i Virgili, 43997 Tarragona, Spain; and
| | - Ernest Giralt
- *Institute for Research in Biomedicine, Parc Científic de Barcelona, Baldiri Reixac, 10, 08028 Barcelona, Spain
- **Department of Organic Chemistry, Universitat de Barcelona, Martí i Franquès, 1, 08028 Barcelona, Spain
| | - Javier de Mendoza
- Institute of Chemical Research of Catalonia, Avgda. Països Catalans, 16, 43007 Tarragona, Spain
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
48
|
Cushing PR, Fellows A, Villone D, Boisguérin P, Madden DR. The relative binding affinities of PDZ partners for CFTR: a biochemical basis for efficient endocytic recycling. Biochemistry 2008; 47:10084-98. [PMID: 18754678 DOI: 10.1021/bi8003928] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is an epithelial chloride channel mutated in patients with cystic fibrosis. Its expression and functional interactions in the apical membrane are regulated by several PDZ (PSD-95, discs large, zonula occludens-1) proteins, which mediate protein-protein interactions, typically by binding C-terminal recognition motifs. In particular, the CFTR-associated ligand (CAL) limits cell-surface levels of the most common disease-associated mutant DeltaF508-CFTR. CAL also mediates degradation of wild-type CFTR, targeting it to lysosomes following endocytosis. Nevertheless, wild-type CFTR survives numerous cycles of uptake and recycling. In doing so, how does it repeatedly avoid CAL-mediated degradation? One mechanism may involve competition between CAL and other PDZ proteins including Na (+)/H (+) exchanger-3 regulatory factors 1 and 2 (NHERF1 and NHERF2), which functionally stabilize cell-surface CFTR. Thus, to understand the biochemical basis of WT-CFTR persistence, we need to know the relative affinities of these partners. However, no quantitative binding data are available for CAL or the individual NHERF2 PDZ domains, and published estimates for the NHERF1 PDZ domains conflict. Here we demonstrate that the affinity of the CAL PDZ domain for the CFTR C-terminus is much weaker than those of NHERF1 and NHERF2 domains, enabling wild-type CFTR to avoid premature entrapment in the lysosomal pathway. At the same time, CAL's affinity is evidently sufficient to capture and degrade more rapidly cycling mutants, such as DeltaF508-CFTR. The relatively weak affinity of the CAL:CFTR interaction may provide a pharmacological window for stabilizing rescued DeltaF508-CFTR in patients with cystic fibrosis.
Collapse
Affiliation(s)
- Patrick R Cushing
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
| | | | | | | | | |
Collapse
|
49
|
Hill AD, Reilly PJ. A Gibbs free energy correlation for automated docking of carbohydrates. J Comput Chem 2008; 29:1131-41. [PMID: 18074341 DOI: 10.1002/jcc.20873] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Thermodynamic information can be inferred from static atomic configurations. To model the thermodynamics of carbohydrate binding to proteins accurately, a large binding data set has been assembled from the literature. The data set contains information from 262 unique protein-carbohydrate crystal structures for which experimental binding information is known. Hydrogen atoms were added to the structures and training conformations were generated with the automated docking program AutoDock 3.06, resulting in a training set of 225,920 all-atom conformations. In all, 288 formulations of the AutoDock 3.0 free energy model were trained against the data set, testing each of four alternate methods of computing the van der Waals, solvation, and hydrogen-bonding energetic components. The van der Waals parameters from AutoDock 1 produced the lowest errors, and an entropic model derived from statistical mechanics produced the only models with five physically and statistically significant coefficients. Eight models predict the Gibbs free energy of binding with an error of less than 40% of the error of any similar models previously published.
Collapse
Affiliation(s)
- Anthony D Hill
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
| | | |
Collapse
|
50
|
Singh SK, Kishore N. Calorimetric and Spectroscopic Studies on the Interaction of Methimazole with Bovine Serum Albumin. J Pharm Sci 2008; 97:2362-72. [PMID: 17879290 DOI: 10.1002/jps.21140] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The potential binding interaction(s) of the anti-thyroid drug methimazole (MMZ) with the protein bovine serum albumin (BSA) has been studied using isothermal titration calorimetry (ITC) and UV-Visible, fluorescence and circular dichroism (CD) spectroscopic techniques. The binding of MMZ to BSA has been studied in both the presence and absence of added surfactants. Since, the ITC thermograms show the molar enthalpy of binding of MMZ and BSA to be zero within experimental error, either the enthalpy change of the binding interaction is zero or there is no binding occurring. The CD and the intrinsic fluorescence and life time spectra of BSA were unchanged by the addition of MMZ. This is also indicative of the absence of any significant interaction of MMZ with BSA.
Collapse
Affiliation(s)
- Sreelekha K Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | |
Collapse
|