1
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Charbonneau AA, Reicks EJ, Cambria JF, Inman J, Danley D, Shockley EA, Davion R, Salgado I, Norton EG, Corbett LJ, Hanacek LE, Jensen JG, Kibodeaux MA, Kirkpatrick TK, Rausch KM, Roth SR, West B, Wilson KE, Lawrence CM, Cloninger MJ. CUREs for high-level Galectin-3 expression. Protein Expr Purif 2024; 221:106516. [PMID: 38801985 DOI: 10.1016/j.pep.2024.106516] [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: 02/06/2024] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 05/29/2024]
Abstract
Galectins are a large and diverse protein family defined by the presence of a carbohydrate recognition domain (CRD) that binds β-galactosides. They play important roles in early development, tissue regeneration, immune homeostasis, pathogen recognition, and cancer. In many cases, studies that examine galectin biology and the effect of manipulating galectins are aided by, or require the ability to express and purify, specific members of the galectin family. In many cases, E. coli is employed as a heterologous expression system, and galectin expression is induced with isopropyl β-galactoside (IPTG). Here, we show that galectin-3 recognizes IPTG with micromolar affinity and that as IPTG induces expression, newly synthesized galectin can bind and sequester cytosolic IPTG, potentially repressing further expression. To circumvent this putative inhibitory feedback loop, we utilized an autoinduction protocol that lacks IPTG, leading to significantly increased yields of galectin-3. Much of this work was done within the context of a course-based undergraduate research experience, indicating the ease and reproducibility of the resulting expression and purification protocols.
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Affiliation(s)
| | - Elizabeth J Reicks
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - John F Cambria
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Jacob Inman
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Daria Danley
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Emmie A Shockley
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Ravenor Davion
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Isabella Salgado
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Erienne G Norton
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Lucy J Corbett
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Lucy E Hanacek
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Jordan G Jensen
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Marguerite A Kibodeaux
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Tess K Kirkpatrick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Keilen M Rausch
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Samantha R Roth
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Bernadette West
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Kenai E Wilson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - C Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Mary J Cloninger
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
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2
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Kalabekova R, Quinn CM, Movellan KT, Gronenborn AM, Akke M, Polenova T. 19F Fast Magic-Angle Spinning NMR Spectroscopy on Microcrystalline Complexes of Fluorinated Ligands and the Carbohydrate Recognition Domain of Galectin-3. Biochemistry 2024. [PMID: 39008798 DOI: 10.1021/acs.biochem.4c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Structural characterization of protein-ligand binding interfaces at atomic resolution is essential for improving the design of specific and potent inhibitors. Herein, we explored fast 19F- and 1H-detected magic angle spinning NMR spectroscopy to investigate the interaction between two fluorinated ligand diastereomers with the microcrystalline galectin-3 carbohydrate recognition domain. The detailed environment around the fluorine atoms was mapped by 2D 13C-19F and 1H-19F dipolar correlation experiments and permitted characterization of the binding interface. Our results demonstrate that 19F MAS NMR is a powerful tool for detailed characterization of protein-ligand interfaces and protein interactions at the atomic level.
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Affiliation(s)
- Roza Kalabekova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Kumar Tekwani Movellan
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Angela M Gronenborn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261, United States
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, Lund SE-22100, Sweden
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261, United States
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3
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Verteramo ML, Ignjatović MM, Kumar R, Wernersson S, Ekberg V, Wallerstein J, Carlström G, Chadimová V, Leffler H, Zetterberg F, Logan DT, Ryde U, Akke M, Nilsson UJ. Interplay of halogen bonding and solvation in protein-ligand binding. iScience 2024; 27:109636. [PMID: 38633000 PMCID: PMC11021960 DOI: 10.1016/j.isci.2024.109636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/13/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Halogen bonding is increasingly utilized in efforts to achieve high affinity and selectivity of molecules designed to bind proteins, making it paramount to understand the relationship between structure, dynamics, and thermodynamic driving forces. We present a detailed analysis addressing this problem using a series of protein-ligand complexes involving single halogen substitutions - F, Cl, Br, and I - and nearly identical structures. Isothermal titration calorimetry reveals an increasingly favorable binding enthalpy from F to I that correlates with the halogen size and σ-hole electropositive character, but is partially counteracted by unfavorable entropy, which is constant from F to Cl and Br, but worse for I. Consequently, the binding free energy is roughly equal for Cl, Br, and I. QM and solvation-free-energy calculations reflect an intricate balance between halogen bonding, hydrogen bonds, and solvation. These advances have the potential to aid future drug design initiatives involving halogenated compounds.
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Affiliation(s)
| | | | - Rohit Kumar
- Department of Chemistry, Lund University, Lund, Sweden
| | | | | | | | | | | | - Hakon Leffler
- Microbiology, Immunology, and Glycobiology, Department of Experimental Medicine, Lund University, Lund, Sweden
| | | | | | - Ulf Ryde
- Department of Chemistry, Lund University, Lund, Sweden
| | - Mikael Akke
- Department of Chemistry, Lund University, Lund, Sweden
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4
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Stenström O, Diehl C, Modig K, Akke M. Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit. Proc Natl Acad Sci U S A 2024; 121:e2317747121. [PMID: 38527204 PMCID: PMC10998626 DOI: 10.1073/pnas.2317747121] [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: 10/22/2023] [Accepted: 02/29/2024] [Indexed: 03/27/2024] Open
Abstract
Protein-ligand complex formation is fundamental to biological function. A central question is whether proteins spontaneously adopt binding-competent conformations to which ligands bind conformational selection (CS) or whether ligands induce the binding-competent conformation induced fit (IF). Here, we resolve the CS and IF binding pathways by characterizing protein conformational dynamics over a wide range of ligand concentrations using NMR relaxation dispersion. We determined the relative flux through the two pathways using a four-state binding model that includes both CS and IF. Experiments conducted without ligand show that galectin-3 exchanges between the ground-state conformation and a high-energy conformation similar to the ligand-bound conformation, demonstrating that CS is a plausible pathway. Near-identical crystal structures of the apo and ligand-bound states suggest that the high-energy conformation in solution corresponds to the apo crystal structure. Stepwise additions of the ligand lactose induce progressive changes in the relaxation dispersions that we fit collectively to the four-state model, yielding all microscopic rate constants and binding affinities. The ligand affinity is higher for the bound-like conformation than for the ground state, as expected for CS. Nonetheless, the IF pathway contributes greater than 70% of the total flux even at low ligand concentrations. The higher flux through the IF pathway is explained by considerably higher rates of exchange between the two protein conformations in the ligand-associated state. Thus, the ligand acts to decrease the activation barrier between protein conformations in a manner reciprocal to enzymatic transition-state stabilization of reactions involving ligand transformation.
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Affiliation(s)
- Olof Stenström
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Carl Diehl
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Kristofer Modig
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
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5
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Nam K, Shao Y, Major DT, Wolf-Watz M. Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS OMEGA 2024; 9:7393-7412. [PMID: 38405524 PMCID: PMC10883025 DOI: 10.1021/acsomega.3c09084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
Abstract
Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Dan T. Major
- Department
of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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6
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Dhurua S, Jana M. Sulfation Effects of Chondroitin Sulfate to Bind a Chemokine in Aqueous Medium: Conformational Heterogeneity and Dynamics from Molecular Simulation. J Chem Inf Model 2023; 63:5660-5675. [PMID: 37611186 DOI: 10.1021/acs.jcim.3c00668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
The sulfation patterns and degree of sulfation of chondroitin sulfate (CS), an important class of glycosaminoglycans (GAG), and their interactions with chemokines are accountable for various diseases. To realize the underlying mechanism of such complex biological phenomena at a molecular level and their application in rational drug design, a study on conformations and dynamics of CSs is necessary. To explore this, in this study, we performed a series of atomistic molecular dynamics (MD) simulations with different sulfated variants of octadecasaccharide CS, like CS-C, CS-E, and CS-T, in their free forms and when bound to the protein chemokine CXCL8 dimer in an aqueous medium. The calculated binding free energy of CSs with the CXCL8 dimer is favorable, and the degree of sulfation favors the complexation process further with prominent hydrophobic and hydrogen-bonded interactions. We find that the recognition is associated with the configurational entropy loss of the CS molecules as calculated from the Gaussian mixture approach, which supports that the degree of sulfation regulates the process. Cluster analysis through the k-means algorithm and end-to-end distance measurement revealed that although the free CS molecules adopted linear conformations, the nonlinear conformations during binding with protein were noted. Adaptation of nonlinear forms in the bound forms is noteworthy for the less-sulfated CS-C and CS-E. Apart from favorable 4C1 conformations, the occasional appearance of skew-boat forms from the free-energy map of ring pucker for the GlcUA unit was observed, which remains unaffected by the sulfation. We find that during recognition, the average relaxation time of intra-CS and inter-CS-CXCL8 hydrogen bonds (HBs) is about a magnitude lesser than that of CS-water HBs, most prominent on the involvement of higher sulfated CS-T analogues. The translational motion of surrounded water molecules in CSs exhibited sublinear diffusion, and the degree of sublinearity increases around the heavily sulfated molecules due to the hindrance created by them as well as the presence of the chemokine and exhibited markedly slow heterogeneous diffusion.
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Affiliation(s)
- Shakuntala Dhurua
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
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7
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Wernersson S, Birgersson S, Akke M. Cosolvent Dimethyl Sulfoxide Influences Protein-Ligand Binding Kinetics via Solvent Viscosity Effects: Revealing the Success Rate of Complex Formation Following Diffusive Protein-Ligand Encounter. Biochemistry 2023; 62:44-52. [PMID: 36542811 DOI: 10.1021/acs.biochem.2c00507] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein-ligand-exchange kinetics determines the duration of biochemical signals and consequently plays an important role in drug design. Binding studies commonly require solubilization of designed ligands in solvents such as dimethyl sulfoxide (DMSO), resulting in residual amounts of DMSO following titration of solubilized ligands into aqueous protein samples. Therefore, it is critical to establish whether DMSO influences protein-ligand binding. Here, we address the general and indirect effect of DMSO on protein-ligand binding caused by solvent viscosity, which is strongly dependent on the relative concentrations of DMSO and water. As a model system, we studied the binding of a drug-like ligand to the carbohydrate recognition domain of galectin-3 in the presence of variable amounts of DMSO. We used isothermal titration calorimetry to characterize binding thermodynamics and 15N NMR relaxation to monitor kinetics. The binding enthalpy is not affected, but we observe a subtle trend of increasingly unfavorable entropy of binding, and consequently decreased affinity, with increasing DMSO concentration. The increasing concentration of DMSO results in a reduced association rate of binding, while the dissociation rate is less affected. The observed association rate is inversely proportional to the viscosity of the DMSO-water mixture, as expected from theory, but significantly reduced from the diffusion-controlled limit. By comparing the viscosity dependence of the observed association rate with that of the theoretical diffusion-controlled association rate, we estimate the success rate of productive complex formation following an initial encounter of proteins and ligands, showing that only one out of several hundred binding "attempts" are successful.
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Affiliation(s)
- Sven Wernersson
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00Lund, Sweden
| | - Simon Birgersson
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00Lund, Sweden
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00Lund, Sweden
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8
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Abstract
Carbohydrate recognition is crucial for biological processes ranging from development to immune system function to host-pathogen interactions. The proteins that bind glycans are faced with a daunting task: to coax these hydrophilic species out of water and into a binding site. Here, we examine the forces underlying glycan recognition by proteins. Our previous bioinformatic study of glycan-binding sites indicated that the most overrepresented side chains are electron-rich aromatic residues, including tyrosine and tryptophan. These findings point to the importance of CH-π interactions for glycan binding. Studies of CH-π interactions show a strong dependence on the presence of an electron-rich π system, and the data indicate binding is enhanced by complementary electronic interactions between the electron-rich aromatic ring and the partial positive charge of the carbohydrate C-H protons. This electronic dependence means that carbohydrate residues with multiple aligned highly polarized C-H bonds, such as β-galactose, form strong CH-π interactions, whereas less polarized residues such as α-mannose do not. This information can guide the design of proteins to recognize sugars and the generation of ligands for proteins, small molecules, or catalysts that bind sugars.
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Affiliation(s)
- Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Roger C. Diehl
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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9
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Gabius HJ, Cudic M, Diercks T, Kaltner H, Kopitz J, Mayo KH, Murphy PV, Oscarson S, Roy R, Schedlbauer A, Toegel S, Romero A. What is the Sugar Code? Chembiochem 2021; 23:e202100327. [PMID: 34496130 PMCID: PMC8901795 DOI: 10.1002/cbic.202100327] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/07/2021] [Indexed: 12/18/2022]
Abstract
A code is defined by the nature of the symbols, which are used to generate information‐storing combinations (e. g. oligo‐ and polymers). Like nucleic acids and proteins, oligo‐ and polysaccharides are ubiquitous, and they are a biochemical platform for establishing molecular messages. Of note, the letters of the sugar code system (third alphabet of life) excel in coding capacity by making an unsurpassed versatility for isomer (code word) formation possible by variability in anomery and linkage position of the glycosidic bond, ring size and branching. The enzymatic machinery for glycan biosynthesis (writers) realizes this enormous potential for building a large vocabulary. It includes possibilities for dynamic editing/erasing as known from nucleic acids and proteins. Matching the glycome diversity, a large panel of sugar receptors (lectins) has developed based on more than a dozen folds. Lectins ‘read’ the glycan‐encoded information. Hydrogen/coordination bonding and ionic pairing together with stacking and C−H/π‐interactions as well as modes of spatial glycan presentation underlie the selectivity and specificity of glycan‐lectin recognition. Modular design of lectins together with glycan display and the nature of the cognate glycoconjugate account for the large number of post‐binding events. They give an entry to the glycan vocabulary its functional, often context‐dependent meaning(s), hereby building the dictionary of the sugar code.
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Affiliation(s)
- Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539, Munich, Germany
| | - Maré Cudic
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida, 33431, USA
| | - Tammo Diercks
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160, Derio, Bizkaia, Spain
| | - Herbert Kaltner
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539, Munich, Germany
| | - Jürgen Kopitz
- Institute of Pathology, Department of Applied Tumor Biology, Faculty of Medicine, Ruprecht-Karls-University Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Kevin H Mayo
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul V Murphy
- CÚRAM - SFI Research Centre for Medical Devices and the, School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - René Roy
- Département de Chimie et Biochimie, Université du Québec à Montréal, Case Postale 888, Succ. Centre-Ville Montréal, Québec, H3C 3P8, Canada
| | - Andreas Schedlbauer
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160, Derio, Bizkaia, Spain
| | - Stefan Toegel
- Karl Chiari Lab for Orthopaedic Biology, Department of Orthopedics and Trauma Surgery, Medical University of Vienna, Vienna, Austria
| | - Antonio Romero
- Department of Structural and Chemical Biology, CIB Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
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10
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Caldararu O, Ekberg V, Logan DT, Oksanen E, Ryde U. Exploring ligand dynamics in protein crystal structures with ensemble refinement. Acta Crystallogr D Struct Biol 2021; 77:1099-1115. [PMID: 34342282 PMCID: PMC8329865 DOI: 10.1107/s2059798321006513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/21/2021] [Indexed: 11/10/2022] Open
Abstract
Understanding the dynamics of ligands bound to proteins is an important task in medicinal chemistry and drug design. However, the dominant technique for determining protein-ligand structures, X-ray crystallography, does not fully account for dynamics and cannot accurately describe the movements of ligands in protein binding sites. In this article, an alternative method, ensemble refinement, is used on six protein-ligand complexes with the aim of understanding the conformational diversity of ligands in protein crystal structures. The results show that ensemble refinement sometimes indicates that the flexibility of parts of the ligand and some protein side chains is larger than that which can be described by a single conformation and atomic displacement parameters. However, since the electron-density maps are comparable and Rfree values are slightly increased, the original crystal structure is still a better model from a statistical point of view. On the other hand, it is shown that molecular-dynamics simulations and automatic generation of alternative conformations in crystallographic refinement confirm that the flexibility of these groups is larger than is observed in standard refinement. Moreover, the flexible groups in ensemble refinement coincide with groups that give high atomic displacement parameters or non-unity occupancy if optimized in standard refinement. Therefore, the conformational diversity indicated by ensemble refinement seems to be qualitatively correct, indicating that ensemble refinement can be an important complement to standard crystallographic refinement as a tool to discover which parts of crystal structures may show extensive flexibility and therefore are poorly described by a single conformation. However, the diversity of the ensembles is often exaggerated (probably partly owing to the rather poor force field employed) and the ensembles should not be trusted in detail.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Vilhelm Ekberg
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Derek T. Logan
- Biochemistry and Structural Biology, Centre for Molecular Protein Science, Department of Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source Consortium ESS ERIC, PO Box 176, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
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11
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Ali HS, Chakravorty A, Kalayan J, de Visser SP, Henchman RH. Energy-entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host-guest challenge. J Comput Aided Mol Des 2021; 35:911-921. [PMID: 34264476 PMCID: PMC8367938 DOI: 10.1007/s10822-021-00406-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/22/2021] [Indexed: 11/29/2022]
Abstract
Free energy drives a wide range of molecular processes such as solvation, binding, chemical reactions and conformational change. Given the central importance of binding, a wide range of methods exist to calculate it, whether based on scoring functions, machine-learning, classical or electronic structure methods, alchemy, or explicit evaluation of energy and entropy. Here we present a new energy-entropy (EE) method to calculate the host-guest binding free energy directly from molecular dynamics (MD) simulation. Entropy is evaluated using Multiscale Cell Correlation (MCC) which uses force and torque covariance and contacts at two different length scales. The method is tested on a series of seven host-guest complexes in the SAMPL8 (Statistical Assessment of the Modeling of Proteins and Ligands) "Drugs of Abuse" Blind Challenge. The EE-MCC binding free energies are found to agree with experiment with an average error of 0.9 kcal mol-1. MCC makes clear the origin of the entropy changes, showing that the large loss of positional, orientational, and to a lesser extent conformational entropy of each binding guest is compensated for by a gain in orientational entropy of water released to bulk, combined with smaller decreases in vibrational entropy of the host, guest and contacting water.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Arghya Chakravorty
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jas Kalayan
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Samuel P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.
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12
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Wernersson S, Carlström G, Jakobsson A, Akke M. Rapid measurement of heteronuclear transverse relaxation rates using non-uniformly sampled R1ρ accordion experiments. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:571-587. [PMID: 37905216 PMCID: PMC10539792 DOI: 10.5194/mr-2-571-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/28/2021] [Indexed: 11/01/2023]
Abstract
Multidimensional, heteronuclear NMR relaxation methods are used extensively to characterize the dynamics of biological macromolecules. Acquisition of relaxation datasets on proteins typically requires significant measurement time, often several days. Accordion spectroscopy offers a powerful means to shorten relaxation rate measurements by encoding the "relaxation dimension" into the indirect evolution period in multidimensional experiments. Time savings can also be achieved by non-uniform sampling (NUS) of multidimensional NMR data, which is used increasingly to improve spectral resolution or increase sensitivity per unit time. However, NUS is not commonly implemented in relaxation experiments, because most reconstruction algorithms are inherently nonlinear, leading to problems when estimating signal intensities, relaxation rate constants and their error bounds. We have previously shown how to avoid these shortcomings by combining accordion spectroscopy with NUS, followed by data reconstruction using sparse exponential mode analysis, thereby achieving a dramatic decrease in the total length of longitudinal relaxation experiments. Here, we present the corresponding transverse relaxation experiment, taking into account the special considerations required for its successful implementation in the framework of the accordion-NUS approach. We attain the highest possible precision in the relaxation rate constants by optimizing the NUS scheme with respect to the Cramér-Rao lower bound of the variance of the estimated parameter, given the total number of sampling points and the spectrum-specific signal characteristics. The resulting accordion-NUS R 1 ρ relaxation experiment achieves comparable precision in the parameter estimates compared to conventional CPMG (Carr-Purcell-Meiboom-Gill) R 2 or spin-lock R 1 ρ experiments while saving an order of magnitude in experiment time.
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Affiliation(s)
- Sven Wernersson
- Biophysical Chemistry, Center for Molecular Protein Science,
Department of Chemistry, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Göran Carlström
- Centre for Analysis and Synthesis, Department of Chemistry, Lund
University, P.O. Box 124, 22100 Lund, Sweden
| | - Andreas Jakobsson
- Department of Mathematical Statistics, Lund University, P.O. Box 118,
22100 Lund, Sweden
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science,
Department of Chemistry, Lund University, P.O. Box 124, 22100 Lund, Sweden
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13
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Wallerstein J, Ekberg V, Ignjatović MM, Kumar R, Caldararu O, Peterson K, Wernersson S, Brath U, Leffler H, Oksanen E, Logan DT, Nilsson UJ, Ryde U, Akke M. Entropy-Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C. JACS AU 2021; 1:484-500. [PMID: 34467311 PMCID: PMC8395690 DOI: 10.1021/jacsau.0c00094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Indexed: 06/13/2023]
Abstract
Molecular recognition is fundamental to biological signaling. A central question is how individual interactions between molecular moieties affect the thermodynamics of ligand binding to proteins and how these effects might propagate beyond the immediate neighborhood of the binding site. Here, we investigate this question by introducing minor changes in ligand structure and characterizing the effects of these on ligand affinity to the carbohydrate recognition domain of galectin-3, using a combination of isothermal titration calorimetry, X-ray crystallography, NMR relaxation, and computational approaches including molecular dynamics (MD) simulations and grid inhomogeneous solvation theory (GIST). We studied a congeneric series of ligands with a fluorophenyl-triazole moiety, where the fluorine substituent varies between the ortho, meta, and para positions (denoted O, M, and P). The M and P ligands have similar affinities, whereas the O ligand has 3-fold lower affinity, reflecting differences in binding enthalpy and entropy. The results reveal surprising differences in conformational and solvation entropy among the three complexes. NMR backbone order parameters show that the O-bound protein has reduced conformational entropy compared to the M and P complexes. By contrast, the bound ligand is more flexible in the O complex, as determined by 19F NMR relaxation, ensemble-refined X-ray diffraction data, and MD simulations. Furthermore, GIST calculations indicate that the O-bound complex has less unfavorable solvation entropy compared to the other two complexes. Thus, the results indicate compensatory effects from ligand conformational entropy and water entropy, on the one hand, and protein conformational entropy, on the other hand. Taken together, these different contributions amount to entropy-entropy compensation among the system components involved in ligand binding to a target protein.
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Affiliation(s)
- Johan Wallerstein
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Vilhelm Ekberg
- Theoretical
Chemistry, Department of Chemistry, Lund
University, 221 00 Lund, Sweden
| | | | - Rohit Kumar
- Biochemistry
and Structural Biology, Center for Molecular Protein Science, Department
of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Octav Caldararu
- Theoretical
Chemistry, Department of Chemistry, Lund
University, 221 00 Lund, Sweden
| | - Kristoffer Peterson
- Centre
for Analysis and Synthesis, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Sven Wernersson
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ulrika Brath
- The
Swedish NMR Center, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Hakon Leffler
- Microbiology,
Immunology, and Glycobiology, Department of Experimental Medicine, Lund University, 221 00 Lund, Sweden
| | - Esko Oksanen
- European
Spallation Source ESS ERIC, 225 92 Lund, Sweden
| | - Derek T. Logan
- Biochemistry
and Structural Biology, Center for Molecular Protein Science, Department
of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ulf J. Nilsson
- Centre
for Analysis and Synthesis, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ulf Ryde
- Theoretical
Chemistry, Department of Chemistry, Lund
University, 221 00 Lund, Sweden
| | - Mikael Akke
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
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14
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Stenström O, Diehl C, Modig K, Nilsson UJ, Akke M. Mapping the energy landscape of protein-ligand binding via linear free energy relationships determined by protein NMR relaxation dispersion. RSC Chem Biol 2021; 2:259-265. [PMID: 34458786 PMCID: PMC8341105 DOI: 10.1039/d0cb00229a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 12/16/2020] [Indexed: 11/22/2022] Open
Abstract
Biochemical signaling is mediated by complexes between macromolecular receptors and their ligands, with the duration of the signal being directly related to the lifetime of the ligand-receptor complex. In the field of drug design, the recognition that drug efficacy in vivo depends on the lifetime of the drug-protein complex has spawned the concept of designing drugs with particular binding kinetics. To advance this field it is critical to investigate how the molecular details of designed ligands might affect the binding kinetics, as well as the equilibrium binding constant. Here we use protein NMR relaxation dispersion to determine linear free energy relationships involving the on- and off-rates and the affinity for a series of congeneric ligands targeting the carbohydrate recognition domain of galectin-3. Using this approach we determine the energy landscape and the position of the transition state along the reaction coordinate of protein-ligand binding. The results show that ligands exhibiting reduced off-rates achieve this by primarily stabilizing the bound state, but do not affect the transition state to any greater extent. The transition state forms early, that is, it is located significantly closer to the free state than to the bound state, suggesting a critical role of desolvation. Furthermore, the data suggest that different subclasses of ligands show different behavior with respect to these characteristics.
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Affiliation(s)
- Olof Stenström
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University Box 124 SE-22100 Lund Sweden
| | - Carl Diehl
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University Box 124 SE-22100 Lund Sweden
| | - Kristofer Modig
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University Box 124 SE-22100 Lund Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University Box 124 SE-22100 Lund Sweden
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University Box 124 SE-22100 Lund Sweden
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15
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Kraus J, Gupta R, Lu M, Gronenborn AM, Akke M, Polenova T. Accurate Backbone 13 C and 15 N Chemical Shift Tensors in Galectin-3 Determined by MAS NMR and QM/MM: Details of Structure and Environment Matter. Chemphyschem 2020; 21:1436-1443. [PMID: 32363727 PMCID: PMC8080305 DOI: 10.1002/cphc.202000249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/27/2020] [Indexed: 01/07/2023]
Abstract
Chemical shift tensors obtained from solid-state NMR spectroscopy are very sensitive reporters of structure and dynamics in proteins. While accurate 13 C and 15 N chemical shift tensors are accessible by magic angle spinning (MAS) NMR, their quantum mechanical calculations remain challenging, particularly for 15 N atoms. Here we compare experimentally determined backbone 13 Cα and 15 NH chemical shift tensors by MAS NMR with hybrid quantum mechanics/molecular mechanics/molecular dynamics (MD-QM/MM) calculations for the carbohydrate-binding domain of galectin-3. Excellent agreement between experimental and computed 15 NH chemical shift anisotropy values was obtained using the Amber ff15ipq force field when solvent dynamics was taken into account in the calculation. Our results establish important benchmark conditions for improving the accuracy of chemical shift calculations in proteins and may aid in the validation of protein structure models derived by MAS NMR.
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Affiliation(s)
- Jodi Kraus
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Rupal Gupta
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Department of Chemistry, The College of Staten Island, 2800 Victory Blvd, Staten Island, NY 10314
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
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16
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Spotlight on the Ballet of Proteins: The Structural Dynamic Properties of Proteins Illuminated by Solution NMR. Int J Mol Sci 2020; 21:ijms21051829. [PMID: 32155847 PMCID: PMC7084655 DOI: 10.3390/ijms21051829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 12/22/2022] Open
Abstract
Solution NMR spectroscopy is a unique and powerful technique that has the ability to directly connect the structural dynamics of proteins in physiological conditions to their activity and function. Here, we summarize recent studies in which solution NMR contributed to the discovery of relationships between key dynamic properties of proteins and functional mechanisms in important biological systems. The capacity of NMR to quantify the dynamics of proteins over a range of time scales and to detect lowly populated protein conformations plays a critical role in its power to unveil functional protein dynamics. This analysis of dynamics is not only important for the understanding of biological function, but also in the design of specific ligands for pharmacologically important proteins. Thus, the dynamic view of structure provided by NMR is of importance in both basic and applied biology.
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17
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Caldararu O, Misini Ignjatović M, Oksanen E, Ryde U. Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures. RSC Adv 2020; 10:8435-8443. [PMID: 35497843 PMCID: PMC9049968 DOI: 10.1039/c9ra09601a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/18/2020] [Indexed: 01/13/2023] Open
Abstract
The function of proteins is influenced not only by the atomic structure but also by the detailed structure of the solvent surrounding it. Computational studies of protein structure also critically depend on the water structure around the protein. Herein we compare the water structure obtained from molecular dynamics (MD) simulations of galectin-3 in complex with two ligands to crystallographic water molecules observed in the corresponding crystal structures. We computed MD trajectories both in a water box, which mimics a protein in solution, and in a crystallographic unit cell, which mimics a protein in a crystal. The calculations were compared to crystal structures obtained at both cryogenic and room temperature. Two types of analyses of the MD simulations were performed. First, the positions of the crystallographic water molecules were compared to peaks in the MD density after alignment of the protein in each snapshot. The results of this analysis indicate that all simulations reproduce the crystallographic water structure rather poorly. However, if we define the crystallographic water sites based on their distances to nearby protein atoms and follow these sites throughout the simulations, the MD simulations reproduce the crystallographic water sites much better. This shows that the failure of MD simulations to reproduce the water structure around proteins in crystal structures observed both in this and previous studies is caused by the problem of identifying water sites for a flexible and dynamic protein (traditionally done by overlaying the structures). Our local clustering approach solves the problem and shows that the MD simulations reasonably reproduce the water structure observed in crystals. Furthermore, analysis of the crystal MD simulations indicates a few water molecules that are close to unmodeled electron density peaks in the crystal structures, suggesting that crystal MD could be used as a complementary tool for identifying and modelling water in protein crystallography.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre P. O. Box 124 SE-221 00 Lund Sweden +46-46-2228648 +46-46-2224502
| | - Majda Misini Ignjatović
- Department of Theoretical Chemistry, Lund University, Chemical Centre P. O. Box 124 SE-221 00 Lund Sweden +46-46-2228648 +46-46-2224502
| | - Esko Oksanen
- Instruments Division, European Spallation Source Consortium ESS ERIC P. O. Box 176 SE-221 00 Lund Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre P. O. Box 124 SE-221 00 Lund Sweden +46-46-2228648 +46-46-2224502
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18
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Carlström G, Elvander F, Swärd J, Jakobsson A, Akke M. Rapid NMR Relaxation Measurements Using Optimal Nonuniform Sampling of Multidimensional Accordion Data Analyzed by a Sparse Reconstruction Method. J Phys Chem A 2019; 123:5718-5723. [PMID: 31194551 DOI: 10.1021/acs.jpca.9b04152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nonuniform sampling (NUS) of multidimensional NMR data offers significant time savings while improving spectral resolution or increasing sensitivity per unit time. However, NUS has not been widely used for quantitative analysis because of the nonlinearity of most methods used to model NUS data, which leads to problems in estimating signal intensities, relaxation rate constants, and their error bounds. Here, we present an approach that avoids these limitations by combining accordion spectroscopy and NUS in the indirect dimensions of multidimensional spectra and then applying sparse exponential mode analysis, which is well suited for analyzing accordion-type relaxation data in a NUS context. By evaluating the Cramér-Rao lower bound of the variances of the estimated relaxation rate constants, we achieve a robust benchmark for the underlying reconstruction model. Furthermore, we design NUS schemes optimized with respect to the information theoretical lower bound of the error in the parameters of interest, given a specified number of sampling points. The accordion-NUS method compares favorably with conventional relaxation experiments in that it produces identical results, within error, while shortening the length of the experiment by an order of magnitude. Thus, our approach enables rapid acquisition of NMR relaxation data for optimized use of spectrometer time or accurate measurements on samples of limited lifetime.
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Affiliation(s)
| | - Filip Elvander
- Department of Mathematical Statistics , Lund University , Box 118, SE-22100 Lund , Sweden
| | - Johan Swärd
- Department of Mathematical Statistics , Lund University , Box 118, SE-22100 Lund , Sweden
| | - Andreas Jakobsson
- Department of Mathematical Statistics , Lund University , Box 118, SE-22100 Lund , Sweden
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19
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Verteramo ML, Stenström O, Ignjatović MM, Caldararu O, Olsson MA, Manzoni F, Leffler H, Oksanen E, Logan DT, Nilsson UJ, Ryde U, Akke M. Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding. J Am Chem Soc 2019; 141:2012-2026. [PMID: 30618244 DOI: 10.1021/jacs.8b11099] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Understanding the driving forces underlying molecular recognition is of fundamental importance in chemistry and biology. The challenge is to unravel the binding thermodynamics into separate contributions and to interpret these in molecular terms. Entropic contributions to the free energy of binding are particularly difficult to assess in this regard. Here we pinpoint the molecular determinants underlying differences in ligand affinity to the carbohydrate recognition domain of galectin-3, using a combination of isothermal titration calorimetry, X-ray crystallography, NMR relaxation, and molecular dynamics simulations followed by conformational entropy and grid inhomogeneous solvation theory (GIST) analyses. Using a pair of diastereomeric ligands that have essentially identical chemical potential in the unbound state, we reduced the problem of dissecting the thermodynamics to a comparison of the two protein-ligand complexes. While the free energies of binding are nearly equal for the R and S diastereomers, greater differences are observed for the enthalpy and entropy, which consequently exhibit compensatory behavior, ΔΔ H°(R - S) = -5 ± 1 kJ/mol and - TΔΔ S°(R - S) = 3 ± 1 kJ/mol. NMR relaxation experiments and molecular dynamics simulations indicate that the protein in complex with the S-stereoisomer has greater conformational entropy than in the R-complex. GIST calculations reveal additional, but smaller, contributions from solvation entropy, again in favor of the S-complex. Thus, conformational entropy apparently dominates over solvation entropy in dictating the difference in the overall entropy of binding. This case highlights an interplay between conformational entropy and solvation entropy, pointing to both opportunities and challenges in drug design.
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Affiliation(s)
- Maria Luisa Verteramo
- Centre for Analysis and Synthesis, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Olof Stenström
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | | | - Octav Caldararu
- Theoretical Chemistry, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Martin A Olsson
- Theoretical Chemistry, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Francesco Manzoni
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Hakon Leffler
- Microbiology, Immunology, and Glycobiology, Department of Laboratory Medicine , Lund University , 221 00 Lund , Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC , 225 92 Lund , Sweden
| | - Derek T Logan
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Ulf Ryde
- Theoretical Chemistry, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
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20
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Wallerstein J, Akke M. Minute Additions of DMSO Affect Protein Dynamics Measurements by NMR Relaxation Experiments through Significant Changes in Solvent Viscosity. Chemphyschem 2019; 20:326-332. [PMID: 30102005 PMCID: PMC6391962 DOI: 10.1002/cphc.201800626] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Indexed: 11/07/2022]
Abstract
Studies of protein-ligand binding often rely on dissolving the ligand in dimethyl sulfoxide (DMSO) to achieve sufficient solubility, and then titrating the ligand solution into the protein solution. As a result, the final protein-ligand solution contains small amounts of DMSO in the buffer. Here we report how the addition of DMSO impacts studies of protein conformational dynamics. We used 15 N NMR relaxation to compare the rotational diffusion correlation time (τC ) of proteins in aqueous buffer with and without DMSO. We found that τC scales with the viscosity of the water-DMSO mixture, which depends sensitively on the amount of DMSO and varies by a factor of 2 across the relevant concentration range. NMR relaxation studies of side chains dynamics are commonly interpreted using τC as a fixed parameter, obtained from backbone 15 N relaxation data acquired on a separate sample. Model-free calculations show that errors in τC , arising from mismatched DMSO concentration between samples, lead to significant errors in order parameters. Our results highlight the importance of determining τC for each sample or carefully matching the DMSO concentrations between samples.
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Affiliation(s)
- Johan Wallerstein
- Biophysical Chemistry, Center for Molecular Protein Science Department of ChemistryLund UniversityBox 124SE-221 00LundSweden
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science Department of ChemistryLund UniversityBox 124SE-221 00LundSweden
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21
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Caldararu O, Kumar R, Oksanen E, Logan DT, Ryde U. Are crystallographic B-factors suitable for calculating protein conformational entropy? Phys Chem Chem Phys 2019; 21:18149-18160. [DOI: 10.1039/c9cp02504a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It is not possible to obtain reliable entropy estimates from crystallographic B-factors even with re-refined or room-temperature crystal structures.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| | - Rohit Kumar
- Department of Biophysical Chemistry
- Centre for Molecular Protein Science
- Lund University
- Chemical Centre
- SE-221 00 Lund
| | - Esko Oksanen
- Department of Biophysical Chemistry
- Centre for Molecular Protein Science
- Lund University
- Chemical Centre
- SE-221 00 Lund
| | - Derek T. Logan
- Department of Biophysical Chemistry
- Centre for Molecular Protein Science
- Lund University
- Chemical Centre
- SE-221 00 Lund
| | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
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22
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Gavrilov Y, Dagan S, Reich Z, Scherf T, Levy Y. An NMR Confirmation for Increased Folded State Entropy Following Loop Truncation. J Phys Chem B 2018; 122:10855-10860. [PMID: 30411894 DOI: 10.1021/acs.jpcb.8b09658] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Previous studies conducted on flexible loop regions in proteins revealed that the energetic consequences of changing loop length predominantly arise from the entropic cost of ordering a loop during folding. However, in an earlier study of human acylphosphatase (hmAcP) using experimental and computational approaches, we showed that thermodynamic stabilization upon loop truncation can be attributed mainly to the increased entropy of the folded state. Here, using 15N NMR spectroscopy, we studied the effect of loop truncation on hmAcP backbone dynamics on the picosecond-nanosecond timescale with the aim of confirming the effect of folded state entropy on protein stability. NMR-relaxation-derived N-H squared generalized order parameters reveal that loop truncation results in a significant increase in protein conformational flexibility. Comparison of these results with previously acquired all-atom molecular dynamics simulation, analyzed here in terms of squared generalized NMR order parameters, demonstrates general agreement between the two methods. The NMR study not only provides direct evidence for the enhanced conformational entropy of the folded state of hmAcP upon loop truncation but also gives a quantitative measure of the observed effects.
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23
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Demetriou M, Nabi IR, Dennis JW. Galectins as Adaptors: Linking Glycosylation and Metabolism with Extracellular Cues. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1732.1se] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Ivan R. Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia
| | - James W. Dennis
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital
- Department of Molecular Genetics, & Department of Laboratory Medicine and Pathology, Department of Medicine, University of Toronto
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24
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Solomentsev G, Diehl C, Akke M. Conformational Entropy of FK506 Binding to FKBP12 Determined by Nuclear Magnetic Resonance Relaxation and Molecular Dynamics Simulations. Biochemistry 2018; 57:1451-1461. [DOI: 10.1021/acs.biochem.7b01256] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Gleb Solomentsev
- Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Carl Diehl
- Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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25
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Wiecikowski A, Cabral KMDS, Almeida MDS, Carvalho RS. Ligand-free method to produce the anti-angiogenic recombinant Galectin-3 carbohydrate recognition domain. Protein Expr Purif 2017; 144:19-24. [PMID: 29198976 DOI: 10.1016/j.pep.2017.11.006] [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: 08/09/2017] [Revised: 11/21/2017] [Accepted: 11/25/2017] [Indexed: 12/28/2022]
Abstract
Galectin-3 (Gal3) is involved in many physiological processes related to tumor growth, such as promoting angiogenesis, cell migration/invasion, resistance to apoptosis and immune response modulation. Usually the overexpression of Gal3 is a poor prognostic marker for cancer patients. Recombinant Gal3 carbohydrate domain (Gal3C) has been proposed as a useful tool to inhibit angiogenesis. So far, all production protocols reported for Gal3C production have used proteolytic cleavage of full length Gal3 and/or affinity-based purification. This involves dialysis, a time consuming step used to eliminate the elution ligand, usually lactose. In this report, we describe an alternative method to produce human recombinant Gal3C in E. coli, purified with cationic exchange and size exclusion chromatography. The recombinant protein was characterized using circular dichroism and nuclear magnetic resonance, showing a beta sheet enriched well-folded globular structure. The average yield obtained was 26 mg/L of broth and the purity was above 99%. The anti-angiogenic activity was assessed in vitro and showed a reduction of 70% and 77% in endothelial cells tubule formation upon treatment with 10 and 20 μg/mL, respectively and also had no impact on cell viability. The method described here is more suitable for both laboratory and industrial production of the potential anti-tumor Gal3C.
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Affiliation(s)
- Adalgisa Wiecikowski
- Laboratório de Alvos Moleculares, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, UFRJ, Brazil
| | - Katia Maria Dos Santos Cabral
- Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, UFRJ, Brazil; Faculdade de Medicina de Petrópolis/Faculdade Arthur Sá Earp, Brazil
| | - Marcius da Silva Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, UFRJ, Brazil; Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, UFRJ, Brazil
| | - Renato Sampaio Carvalho
- Laboratório de Alvos Moleculares, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, UFRJ, Brazil.
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Yang EH, Rode J, Howlader MA, Eckermann M, Santos JT, Hernandez Armada D, Zheng R, Zou C, Cairo CW. Galectin-3 alters the lateral mobility and clustering of β1-integrin receptors. PLoS One 2017; 12:e0184378. [PMID: 29016609 PMCID: PMC5634555 DOI: 10.1371/journal.pone.0184378] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/22/2017] [Indexed: 01/25/2023] Open
Abstract
Glycoprotein receptors are influenced by myriad intermolecular interactions at the cell surface. Specific glycan structures may interact with endogenous lectins that enforce or disrupt receptor-receptor interactions. Glycoproteins bound by multivalent lectins may form extended oligomers or lattices, altering the lateral mobility of the receptor and influencing its function through endocytosis or changes in activation. In this study, we have examined the interaction of Galectin-3 (Gal-3), a human lectin, with adhesion receptors. We measured the effect of recombinant Gal-3 added exogenously on the lateral mobility of the α5β1 integrin on HeLa cells. Using single-particle tracking (SPT) we detected increased lateral mobility of the integrin in the presence of Gal-3, while its truncated C-terminal domain (Gal-3C) showed only minor reductions in lateral mobility. Treatment of cells with Gal-3 increased β1-integrin mediated migration with no apparent changes in viability. In contrast, Gal-3C decreased both cell migration and viability. Fluorescence microscopy allowed us to confirm that exogenous Gal-3 resulted in reorganization of the integrin into larger clusters. We used a proteomics analysis to confirm that cells expressed endogenous Gal-3, and found that addition of competitive oligosaccharide ligands for the lectin altered the lateral mobility of the integrin. Together, our results are consistent with a Gal-3-integrin lattice model of binding and confirm that the lateral mobility of integrins is natively regulated, in part, by galectins.
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Affiliation(s)
- Esther H. Yang
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton Alberta, Canada
| | - Julia Rode
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton Alberta, Canada
| | - Md. Amran Howlader
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton Alberta, Canada
| | - Marina Eckermann
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton Alberta, Canada
| | - Jobette T. Santos
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton Alberta, Canada
| | - Daniel Hernandez Armada
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton Alberta, Canada
| | - Ruixiang Zheng
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton Alberta, Canada
| | - Chunxia Zou
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton Alberta, Canada
| | - Christopher W. Cairo
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton Alberta, Canada
- * E-mail:
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Lin YH, Qiu DC, Chang WH, Yeh YQ, Jeng US, Liu FT, Huang JR. The intrinsically disordered N-terminal domain of galectin-3 dynamically mediates multisite self-association of the protein through fuzzy interactions. J Biol Chem 2017; 292:17845-17856. [PMID: 28893908 DOI: 10.1074/jbc.m117.802793] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 08/23/2017] [Indexed: 12/28/2022] Open
Abstract
Galectins are a family of lectins that bind β-galactosides through their conserved carbohydrate recognition domain (CRD) and can induce aggregation with glycoproteins or glycolipids on the cell surface and thereby regulate cell activation, migration, adhesion, and signaling. Galectin-3 has an intrinsically disordered N-terminal domain and a canonical CRD. Unlike the other 14 known galectins in mammalian cells, which have dimeric or tandem-repeated CRDs enabling multivalency for various functions, galectin-3 is monomeric, and its functional multivalency therefore is somewhat of a mystery. Here, we used NMR spectroscopy, mutagenesis, small-angle X-ray scattering, and computational modeling to study the self-association-related multivalency of galectin-3 at the residue-specific level. We show that the disordered N-terminal domain (residues ∼20-100) interacts with itself and with a part of the CRD not involved in carbohydrate recognition (β-strands 7-9; residues ∼200-220), forming a fuzzy complex via inter- and intramolecular interactions, mainly through hydrophobicity. These fuzzy interactions are characteristic of intrinsically disordered proteins to achieve liquid-liquid phase separation, and we demonstrated that galectin-3 can also undergo liquid-liquid phase separation. We propose that galectin-3 may achieve multivalency through this multisite self-association mechanism facilitated by fuzzy interactions.
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Affiliation(s)
- Yu-Hao Lin
- From the Institute of Biochemistry and Molecular Biology and
| | - De-Chen Qiu
- From the Institute of Biochemistry and Molecular Biology and
| | - Wen-Han Chang
- From the Institute of Biochemistry and Molecular Biology and
| | - Yi-Qi Yeh
- the National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - U-Ser Jeng
- the National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan.,the Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, and
| | - Fu-Tong Liu
- the Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Jie-Rong Huang
- From the Institute of Biochemistry and Molecular Biology and .,the Institute of Biomedical Informatics, National Yang-Ming University, Number 155 Section 2 Li-nong Street, Taipei 11221, Taiwan
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Diniz A, Dias JS, Jiménez-Barbero J, Marcelo F, Cabrita EJ. Protein-Glycan Quinary Interactions in Crowding Environment Unveiled by NMR Spectroscopy. Chemistry 2017. [PMID: 28649731 DOI: 10.1002/chem.201702800] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein-glycan interactions as modulators for quinary structures in crowding environments were explored. The interaction between human galectin 3 (Gal-3) and distinct macromolecular crowders, such as bovine and human serum albumin (BSA and HSA), Ficoll 70 and PEG3350, was scrutinized. The molecular recognition event of the specific ligand, lactose, by Gal-3 in crowding conditions was evaluated. Gal-3 interactions were monitored by NMR analysing chemical shift perturbation (CSP) and line broadening of 1 H15 N-HSQC signals. The intensity of the Gal-3 1 H15 N-HSQC signals decreased in the presence of all crowders, due to the increase in the solution viscosity and to the formation of large protein complexes. When glycosylated containing samples of BSA and HSA were used, signal broadening was more severe than that observed in the presence of the more viscous solutions of PEG3350 and Ficoll 70. However, for the samples containing glycoproteins, the signal intensity of 1 H15 N-HSQC recovered upon addition of lactose. We show that serum proteins interact with Gal-3, through their α2,3-linked sialylgalactose moieties exposed at their surfaces, competing with lactose for the same binding site. The quinary interaction between Gal-3 and serum glycoproteins, could help to co-localize Gal-3 at the cell surface, and may play a role in adhesion and signalling functions of this protein.
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Affiliation(s)
- Ana Diniz
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Jorge S Dias
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Jesús Jiménez-Barbero
- CIC-bioGUNE Bizkaia, 48160, Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48005, Bilbao, Spain.,Departament Organic Chemistry II, EHU-UPV, 48040, Leioa, Spain
| | - Filipa Marcelo
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Eurico J Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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Towse CL, Akke M, Daggett V. The Dynameomics Entropy Dictionary: A Large-Scale Assessment of Conformational Entropy across Protein Fold Space. J Phys Chem B 2017; 121:3933-3945. [PMID: 28375008 DOI: 10.1021/acs.jpcb.7b00577] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular dynamics (MD) simulations contain considerable information with regard to the motions and fluctuations of a protein, the magnitude of which can be used to estimate conformational entropy. Here we survey conformational entropy across protein fold space using the Dynameomics database, which represents the largest existing data set of protein MD simulations for representatives of essentially all known protein folds. We provide an overview of MD-derived entropies accounting for all possible degrees of dihedral freedom on an unprecedented scale. Although different side chains might be expected to impose varying restrictions on the conformational space that the backbone can sample, we found that the backbone entropy and side chain size are not strictly coupled. An outcome of these analyses is the Dynameomics Entropy Dictionary, the contents of which have been compared with entropies derived by other theoretical approaches and experiment. As might be expected, the conformational entropies scale linearly with the number of residues, demonstrating that conformational entropy is an extensive property of proteins. The calculated conformational entropies of folding agree well with previous estimates. Detailed analysis of specific cases identifies deviations in conformational entropy from the average values that highlight how conformational entropy varies with sequence, secondary structure, and tertiary fold. Notably, α-helices have lower entropy on average than do β-sheets, and both are lower than coil regions.
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Affiliation(s)
- Clare-Louise Towse
- Department of Bioengineering, University of Washington , Box 355013, Seattle, Washington 98195-5013, United States
| | - Mikael Akke
- Department of Biophysical Chemistry, Lund University , PO Box 124, SE-22100 Lund, Sweden
| | - Valerie Daggett
- Department of Bioengineering, University of Washington , Box 355013, Seattle, Washington 98195-5013, United States
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Shams-Ud-Doha K, Kitova EN, Kitov PI, St-Pierre Y, Klassen JS. Human Milk Oligosaccharide Specificities of Human Galectins. Comparison of Electrospray Ionization Mass Spectrometry and Glycan Microarray Screening Results. Anal Chem 2017; 89:4914-4921. [PMID: 28345865 DOI: 10.1021/acs.analchem.6b05169] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The affinities of thirty-two free human milk oligosaccharides (HMOs) for four human galectin proteins, a stable mutant of hGal1 (hGal-1), a C-terminal fragment of hGal-3 (hGal-3C), hGal-7, and an N-terminal fragment of hGal-9 (hGal-9N), were measured using electrospray ionization mass spectrometry (ESI-MS). The binding data show that each of the four galectins recognize the majority of the HMOs tested (hGal-1 binds thirty-two HMOs, hGal-3C binds twenty-six, hGal-7 binds thirty-one, and hGal-9N binds twenty-six). Twenty-five of the HMOs tested bind all four galectins, with affinities ranging from 103 to 105 M-1. The reliability of the ESI-MS assay for quantifying the affinities of HMOs for lectins was established from the agreement found between the ESI-MS data and affinities of a small number of HMOs for hGal-1, hGal-3C, and hGal-7 measured by isothermal titration calorimetry (ITC). Comparison of the relative affinities (of 14 HMOs) measured by ESI-MS with the reported specificities of hGal-1, hGal-3, hGal-7, and hGal-9 for these same HMOs established using the shotgun human milk glycan microarray (HM-SGM-v2) showed fair-to-poor correlation, with evidence of false positives and false negatives in the microarray data. The results of this study suggest that HMO specificities of lectins established using microarrays may not accurately reflect their true HMO-binding properties and that the use of "in solution" assays such as ESI-MS and ITC is to be preferred.
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Affiliation(s)
- Km Shams-Ud-Doha
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2
| | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2
| | - Pavel I Kitov
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2
| | - Yves St-Pierre
- INRS-Institut Armand-Frappier , Laval, Québec Canada H7 V 1B7
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2
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31
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Effect of solvent model when probing protein dynamics with molecular dynamics. J Mol Graph Model 2017; 71:80-87. [DOI: 10.1016/j.jmgm.2016.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
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Abstract
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.
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33
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Han L, Shams-Ud-Doha K, Kitova EN, Klassen JS. Screening Oligosaccharide Libraries against Lectins Using the Proxy Protein Electrospray Ionization Mass Spectrometry Assay. Anal Chem 2016; 88:8224-31. [DOI: 10.1021/acs.analchem.6b02044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Ling Han
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G
2G2
| | - Km Shams-Ud-Doha
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G
2G2
| | - Elena N. Kitova
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G
2G2
| | - John S. Klassen
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G
2G2
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34
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Characterization of the conformational fluctuations in the Josephin domain of ataxin-3. Biophys J 2016; 107:2932-2940. [PMID: 25517158 PMCID: PMC4269769 DOI: 10.1016/j.bpj.2014.10.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/10/2014] [Accepted: 10/10/2014] [Indexed: 11/24/2022] Open
Abstract
As for a variety of other molecular recognition processes, conformational fluctuations play an important role in the cleavage of polyubiquitin chains by the Josephin domain of ataxin-3. The interaction between Josephin and ubiquitin appears to be mediated by the motions of α-helical hairpin that is unusual among deubiquitinating enzymes. Here, we characterized the conformational fluctuations of the helical hairpin by incorporating NMR measurements as replica-averaged restraints in molecular dynamics simulations, and by validating the results by small-angle x-ray scattering measurements. This approach allowed us to define the extent of the helical hairpin motions and suggest a role of such motions in the recognition of ubiquitin.
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35
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Gabius HJ, Manning JC, Kopitz J, André S, Kaltner H. Sweet complementarity: the functional pairing of glycans with lectins. Cell Mol Life Sci 2016; 73:1989-2016. [PMID: 26956894 PMCID: PMC11108359 DOI: 10.1007/s00018-016-2163-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 02/07/2023]
Abstract
Carbohydrates establish the third alphabet of life. As part of cellular glycoconjugates, the glycans generate a multitude of signals in a minimum of space. The presence of distinct glycotopes and the glycome diversity are mapped by sugar receptors (antibodies and lectins). Endogenous (tissue) lectins can read the sugar-encoded information and translate it into functional aspects of cell sociology. Illustrated by instructive examples, each glycan has its own ligand properties. Lectins with different folds can converge to target the same epitope, while intrafamily diversification enables functional cooperation and antagonism. The emerging evidence for the concept of a network calls for a detailed fingerprinting. Due to the high degree of plasticity and dynamics of the display of genes for lectins the validity of extrapolations between different organisms of the phylogenetic tree yet is inevitably limited.
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Affiliation(s)
- H-J Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539, Munich, Germany.
| | - J C Manning
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539, Munich, Germany
| | - J Kopitz
- Institute of Pathology, Department of Applied Tumor Biology, Ruprecht-Karls-University Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - S André
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539, Munich, Germany
| | - H Kaltner
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539, Munich, Germany
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36
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Genheden S, Diehl C, Akke M, Ryde U. Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations. J Chem Theory Comput 2015; 6:2176-90. [PMID: 26615944 DOI: 10.1021/ct900696z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We have studied how backbone N-H S(2) order parameters calculated from molecular dynamics simulations depend on the method used to calculate them, the starting conditions, and the length of the simulations. Using the carbohydrate binding domain of galectin-3 in the free and lactose-bound states as a test case, we compared the calculated order parameters with experimental data from NMR relaxation. The results indicate that the sampling can be improved by using several starting structures, taking into account conformational heterogeneity reported in crystal structures. However, the improvement is rather limited, and for 93% of the dihedrals that have alternative conformations in the crystal structures, the conformational space is well sampled even if a single conformation is used as the starting structure. Moreover, the agreement with experimental data is improved when using several short simulations, rather than a single long simulation. In the present case, we find that ∼10 independent simulations provide sufficient sampling, and the ideal length of the simulations is ∼10 ns, which is ∼25% longer than the global correlation time for rotational diffusion. On the other hand, the equilibration time appears to be less important, and our results suggest that an equilibration time of 0.25 ns is sufficient. We have also compared four different methods to extract the order parameters from the simulations, namely, the autocorrelation function and isotropic reorientational eigenmode dynamics using three different window sizes. Overall, the four methods yield comparable results, but large differences between the methods may serve to pinpoint cases for which the calculated parameters are unreliable.
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Affiliation(s)
- Samuel Genheden
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden and Center for Molecular Protein Science, Biophysical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Carl Diehl
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden and Center for Molecular Protein Science, Biophysical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mikael Akke
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden and Center for Molecular Protein Science, Biophysical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden and Center for Molecular Protein Science, Biophysical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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Ruiz FM, Gilles U, Lindner I, André S, Romero A, Reusch D, Gabius HJ. Combining Crystallography and Hydrogen-Deuterium Exchange to Study Galectin-Ligand Complexes. Chemistry 2015; 21:13558-68. [DOI: 10.1002/chem.201501961] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Indexed: 01/25/2023]
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38
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Xiao X, He H, Ding X, Yang Q, Liu X, Liu S, Rang J, Wang T, Zuo M, Xia L. Purification and cloning of lectin that induce cell apoptosis from Allium chinense. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2015; 22:238-244. [PMID: 25765828 DOI: 10.1016/j.phymed.2014.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 10/20/2014] [Accepted: 12/14/2014] [Indexed: 06/04/2023]
Abstract
A 8.7 kDa lectin with high agglutin activity was isolated by affinity chromatography and cloned from Allium chinense in this study. For the MTT assay, approximately 60 µg/ml A. chinense lectin (ACL) inhibited 50% of the human hepatoma Hep-3B cells grown after 48 h. In addition, no antiproliferative effect was observed on normal human umbilical vein endothelial cells (HUVEC) even at 100 µg/ml concentration. After treatments with ACL on Hep-3B cells, morphologic changes in the nucleus and cytoskeleton were observed under laser scanning confocal microscopy with 4',6-diamidino-2-phenylindole and tubulin Alexa Fluor 488 staining; whereas, the mitochondrial membrane potential was observed through Mito Tracker Red CMXRos staining. The results showed that ACL led to cell morphology and structure change (e.g., round cell shrinkage). Moreover, ACL resulted in significant change in the shape of the nucleus, damaged the cytoskeleton when tubulin was degraded, and reduced the mitochondrial transmembrane potential. By contrast, no changes were observed on HUVEC cells under the same treatment conditions. DNA fragmentation analysis was used to detect DNA damage. Western blot showed that ACL upregulated caspase-3 and Bax expression during apoptosis and cloned the structural gene of ACL with an open reading frame of 456 bp encoding 151 amino acid residues. The results showed that ACL is a potential anticancer drug.
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Affiliation(s)
- Xiuqing Xiao
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha 410081, China
| | - Hao He
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha 410081, China
| | - Xuezhi Ding
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha 410081, China.
| | - Qi Yang
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha 410081, China
| | - Xuemei Liu
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha 410081, China
| | - Shuang Liu
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha 410081, China
| | - Jie Rang
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha 410081, China
| | - Ting Wang
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha 410081, China
| | - Mingxing Zuo
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha 410081, China
| | - Liqiu Xia
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha 410081, China.
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40
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Rauthu SR, Shiao TC, André S, Miller MC, Madej É, Mayo KH, Gabius HJ, Roy R. Defining the Potential of Aglycone Modifications for Affinity/Selectivity Enhancement against Medically Relevant Lectins: Synthesis, Activity Screening, and HSQC-Based NMR Analysis. Chembiochem 2014; 16:126-39. [DOI: 10.1002/cbic.201402474] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Indexed: 12/28/2022]
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41
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Solís D, Bovin NV, Davis AP, Jiménez-Barbero J, Romero A, Roy R, Smetana K, Gabius HJ. A guide into glycosciences: How chemistry, biochemistry and biology cooperate to crack the sugar code. Biochim Biophys Acta Gen Subj 2014; 1850:186-235. [PMID: 24685397 DOI: 10.1016/j.bbagen.2014.03.016] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 01/17/2023]
Abstract
BACKGROUND The most demanding challenge in research on molecular aspects within the flow of biological information is posed by the complex carbohydrates (glycan part of cellular glycoconjugates). How the 'message' encoded in carbohydrate 'letters' is 'read' and 'translated' can only be unraveled by interdisciplinary efforts. SCOPE OF REVIEW This review provides a didactic step-by-step survey of the concept of the sugar code and the way strategic combination of experimental approaches characterizes structure-function relationships, with resources for teaching. MAJOR CONCLUSIONS The unsurpassed coding capacity of glycans is an ideal platform for generating a broad range of molecular 'messages'. Structural and functional analyses of complex carbohydrates have been made possible by advances in chemical synthesis, rendering production of oligosaccharides, glycoclusters and neoglycoconjugates possible. This availability facilitates to test the glycans as ligands for natural sugar receptors (lectins). Their interaction is a means to turn sugar-encoded information into cellular effects. Glycan/lectin structures and their spatial modes of presentation underlie the exquisite specificity of the endogenous lectins in counterreceptor selection, that is, to home in on certain cellular glycoproteins or glycolipids. GENERAL SIGNIFICANCE Understanding how sugar-encoded 'messages' are 'read' and 'translated' by lectins provides insights into fundamental mechanisms of life, with potential for medical applications.
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Affiliation(s)
- Dolores Solís
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), 07110 Bunyola, Mallorca, Illes Baleares, Spain.
| | - Nicolai V Bovin
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul Miklukho-Maklaya 16/10, 117871 GSP-7, V-437, Moscow, Russian Federation.
| | - Anthony P Davis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - Antonio Romero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - René Roy
- Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada.
| | - Karel Smetana
- Charles University, 1st Faculty of Medicine, Institute of Anatomy, U nemocnice 3, 128 00 Prague 2, Czech Republic.
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 München, Germany.
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42
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Genheden S, Akke M, Ryde U. Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability. J Chem Theory Comput 2013; 10:432-8. [DOI: 10.1021/ct400747s] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Samuel Genheden
- Department
of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mikael Akke
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department
of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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43
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Vugmeyster L, Do T, Ostrovsky D, Fu R. Effect of subdomain interactions on methyl group dynamics in the hydrophobic core of villin headpiece protein. Protein Sci 2013; 23:145-56. [PMID: 24243806 DOI: 10.1002/pro.2398] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/16/2013] [Accepted: 11/06/2013] [Indexed: 11/06/2022]
Abstract
Thermostable villin headpiece protein (HP67) consists of the N-terminal subdomain (residues 10-41) and the autonomously folding C-terminal subdomain (residues 42-76) which pack against each other to form a structure with a unified hydrophobic core. The X-ray structures of the isolated C-terminal subdomain (HP36) and its counterpart in HP67 are very similar for the hydrophobic core residues. However, fine rearrangements of the free energy landscape are expected to occur because of the interactions between the two subdomains. We detect and characterize these changes by comparing the µs-ms time scale dynamics of the methyl-bearing side chains in isolated HP36 and in HP67. Specifically, we probe three hydrophobic side chains at the interface of the two subdomains (L42, V50, and L75) as well as at two residues far from the interface (L61 and L69). Solid-state deuteron NMR techniques are combined with computational modeling for the detailed characterization of motional modes in terms of their kinetic and thermodynamic parameters. The effect of interdomain interactions on side chain dynamics is seen for all residues but L75. Thus, changes in dynamics because of subdomain interactions are not confined to the site of perturbation. One of the main results is a two- to threefold increase in the value of the activation energies for the rotameric mode of motions in HP67 compared with HP36. Detailed analysis of configurational entropies and heat capacities complement the kinetic view of the degree of the disorder in the folded state.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska
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44
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Martin SF, Clements JH. Correlating structure and energetics in protein-ligand interactions: paradigms and paradoxes. Annu Rev Biochem 2013; 82:267-93. [PMID: 23746256 DOI: 10.1146/annurev-biochem-060410-105819] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Predicting protein-binding affinities of small molecules, even closely related ones, is a formidable challenge in biomolecular recognition and medicinal chemistry. A thermodynamic approach to optimizing affinity in protein-ligand interactions requires knowledge and understanding of how altering the structure of a small molecule will be manifested in protein-binding enthalpy and entropy changes; however, there is a relative paucity of such detailed information. In this review, we examine two strategies commonly used to increase ligand potency. The first of these involves introducing a cyclic constraint to preorganize a small molecule in its biologically active conformation, and the second entails adding nonpolar groups to a molecule to increase the amount of hydrophobic surface that is buried upon binding. Both of these approaches are motivated by paradigms suggesting that protein-binding entropy changes should become more favorable, but paradoxes can emerge that defy conventional wisdom.
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Affiliation(s)
- Stephen F Martin
- Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
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45
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Veglia G, Cembran A. Role of conformational entropy in the activity and regulation of the catalytic subunit of protein kinase A. FEBS J 2013; 280:5608-15. [PMID: 23902454 DOI: 10.1111/febs.12462] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/19/2013] [Accepted: 06/24/2013] [Indexed: 12/01/2022]
Abstract
Protein kinase A (PKA) is the archetypical phosphokinase, sharing a catalytic core with the entire protein kinase superfamily. In eukaryotes, the ubiquitous location of PKA makes it one of the most important cellular signaling molecules, involved in a myriad of events. The catalytic subunit of PKA (PKA-C) is one of the most studied enzymes and was the first kinase to be crystallized; however, the effects of ligand binding, post-translational modifications and mutations on the activity of the kinase have been difficult to understand with only structural data. Here, we review our latest NMR studies on PKA-C, the results of which underscore the role of fast and slow conformational dynamics in the activation and inhibition of the kinase.
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Affiliation(s)
- Gianluigi Veglia
- Department of Biochemistry, Biophysics & Molecular Biology, University of Minnesota, Jackson Hall, MN, USA; Department of Chemistry, University of Minnesota, Smith Hall, MN, USA
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46
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Ruiz FM, Fernández IS, López-Merino L, Lagartera L, Kaltner H, Menéndez M, André S, Solís D, Gabius HJ, Romero A. Fine-tuning of prototype chicken galectins: structure of CG-2 and structure-activity correlations. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1665-76. [PMID: 23999290 DOI: 10.1107/s0907444913011773] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 04/30/2013] [Indexed: 11/11/2022]
Abstract
The comparatively small number of members of the family of adhesion/growth-regulatory galectins in chicken predestines this system as an attractive model to study the divergence of these lectins after gene duplication. Expression profiling of the three homodimeric (prototype) chicken galectins (CG-1A, CG-1B and CG-2) has raised evidence of distinct functionalities, explaining the interest in a detailed crystallographic analysis of CG-2. As revealed here, marked differences are found in the ligand-binding site and in the contact pattern within the homodimer interface, underlying a characteristic orientation of the two subunits. Notably, a distinctive trimer of dimers that is unique in all galectin crystal structures reported to date forms the core unit of the crystallographic assembly. Combination with spectroscopic and thermodynamic measurements, and comparisons with CG-1A and CG-1B, identify differential changes in the circular-dichroism spectra in the presence of lactose, reflecting the far-reaching impact of the ligand on hydrodynamic behaviour, and inter-galectin differences in both the entropy and the enthalpy of binding. This structural information is a salient step to complete the analysis of the full set of galectins from this model organism.
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Affiliation(s)
- Federico M Ruiz
- Departamento de Biología Físico-Química, Centro de Investigaciones Biológicas - CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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47
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Yegorova S, Chavaroche AE, Rodriguez MC, Minond D, Cudic M. Development of an AlphaScreen assay for discovery of inhibitors of low-affinity glycan–lectin interactions. Anal Biochem 2013; 439:123-31. [DOI: 10.1016/j.ab.2013.04.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/25/2013] [Accepted: 04/29/2013] [Indexed: 12/31/2022]
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48
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Ermakova E, Miller MC, Nesmelova IV, López-Merino L, Berbís MA, Nesmelov Y, Tkachev YV, Lagartera L, Daragan VA, André S, Cañada FJ, Jiménez-Barbero J, Solís D, Gabius HJ, Mayo KH. Lactose binding to human galectin-7 (p53-induced gene 1) induces long-range effects through the protein resulting in increased dimer stability and evidence for positive cooperativity. Glycobiology 2013; 23:508-23. [PMID: 23376190 DOI: 10.1093/glycob/cwt005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The product of p53-induced gene 1 is a member of the galectin family, i.e., galectin-7 (Gal-7). To move beyond structural data by X-ray diffraction, we initiated the study of the lectin by nuclear magnetic resonance (NMR) and circular dichroism spectroscopies, and molecular dynamics (MD) simulations. In concert, our results indicate that lactose binding to human Gal-7 induces long-range effects (minor conformational shifts and changes in structural dynamics) throughout the protein that result in stabilization of the dimer state, with evidence for positive cooperativity. Monte Carlo fits of (15)N-Gal-7 HSQC titrations with lactose using a two-site model yield K1 = 0.9 ± 0.6 × 10(3) M(-1) and K2 = 3.4 ± 0.8 × 10(3) M(-1). Ligand binding-induced stabilization of the Gal-7 dimer was supported by several lines of evidence: MD-based calculations of interaction energies between ligand-loaded and ligand-free states, gel filtration data and hetero-FRET spectroscopy that indicate a highly reduced tendency for dimer dissociation in the presence of lactose, CD-based thermal denaturation showing that the transition temperature of the lectin is significantly increased in the presence of lactose, and saturation transfer difference (STD) NMR using a molecular probe of the monomer state whose presence is diminished in the presence of lactose. MD simulations with the half-loaded ligand-bound state also provided insight into how allosteric signaling may occur. Overall, our results reveal long-range effects on Gal-7 structure and dynamics, which factor into entropic contributions to ligand binding and allow further comparisons with other members of the galectin family.
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Affiliation(s)
- Elena Ermakova
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street, Minneapolis, MN 55455, USA
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49
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Suárez E, Suárez D. Multibody local approximation: application to conformational entropy calculations on biomolecules. J Chem Phys 2013; 137:084115. [PMID: 22938226 DOI: 10.1063/1.4748104] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Multibody type expansions like mutual information expansions are widely used for computing or analyzing properties of large composite systems. The power of such expansions stems from their generality. Their weaknesses, however, are the large computational cost of including high order terms due to the combinatorial explosion and the fact that truncation errors do not decrease strictly with the expansion order. Herein, we take advantage of the redundancy of multibody expansions in order to derive an efficient reformulation that captures implicitly all-order correlation effects within a given cutoff, avoiding the combinatory explosion. This approach, which is cutoff dependent rather than order dependent, keeps the generality of the original expansions and simultaneously mitigates their limitations provided that a reasonable cutoff can be used. An application of particular interest can be the computation of the conformational entropy of flexible peptide molecules from molecular dynamics trajectories. By combining the multibody local estimations of conformational entropy with average values of the rigid-rotor and harmonic-oscillator entropic contributions, we obtain by far a tighter upper bound of the absolute entropy than the one obtained by the broadly used quasi-harmonic method.
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Affiliation(s)
- Ernesto Suárez
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
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50
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Yongye AB, Calle L, Ardá A, Jiménez-Barbero J, André S, Gabius HJ, Martínez-Mayorga K, Cudic M. Molecular Recognition of the Thomsen-Friedenreich Antigen–Threonine Conjugate by Adhesion/Growth Regulatory Galectin-3: Nuclear Magnetic Resonance Studies and Molecular Dynamics Simulations. Biochemistry 2012; 51:7278-89. [DOI: 10.1021/bi300761s] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Austin B. Yongye
- Torrey Pines Institute for Molecular Studies, Port Saint Lucie, Florida 34987-2352,
United States
| | - Luis Calle
- Chemical
and Physical Biology, CIB-CSIC, Madrid,
Spain
| | - Ana Ardá
- Chemical
and Physical Biology, CIB-CSIC, Madrid,
Spain
| | | | - Sabine André
- Institute of Physiological
Chemistry,
Faculty of Veterinary Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Hans-Joachim Gabius
- Institute of Physiological
Chemistry,
Faculty of Veterinary Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Karina Martínez-Mayorga
- Torrey Pines Institute for Molecular Studies, Port Saint Lucie, Florida 34987-2352,
United States
| | - Mare Cudic
- Torrey Pines Institute for Molecular Studies, Port Saint Lucie, Florida 34987-2352,
United States
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