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Thole JF, Waudby CA, Pielak GJ. Disordered proteins mitigate the temperature dependence of site-specific binding free energies. J Biol Chem 2023; 299:102984. [PMID: 36739945 PMCID: PMC10027511 DOI: 10.1016/j.jbc.2023.102984] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/12/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Biophysical characterization of protein-protein interactions involving disordered proteins is challenging. A common simplification is to measure the thermodynamics and kinetics of disordered site binding using peptides containing only the minimum residues necessary. We should not assume, however, that these few residues tell the whole story. Son of sevenless, a multidomain signaling protein from Drosophila melanogaster, is critical to the mitogen-activated protein kinase pathway, passing an external signal to Ras, which leads to cellular responses. The disordered 55 kDa C-terminal domain of Son of sevenless is an autoinhibitor that blocks guanidine exchange factor activity. Activation requires another protein, Downstream of receptor kinase (Drk), which contains two Src homology 3 domains. Here, we utilized NMR spectroscopy and isothermal titration calorimetry to quantify the thermodynamics and kinetics of the N-terminal Src homology 3 domain binding to the strongest sites incorporated into the flanking disordered sequences. Comparing these results to those for isolated peptides provides information about how the larger domain affects binding. The affinities of sites on the disordered domain are like those of the peptides at low temperatures but less sensitive to temperature. Our results, combined with observations showing that intrinsically disordered proteins become more compact with increasing temperature, suggest a mechanism for this effect.
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Affiliation(s)
- Joseph F Thole
- Department of Chemistry, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Molecular and Cellular Biophysics Program, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Gary J Pielak
- Department of Chemistry, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Molecular and Cellular Biophysics Program, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry & Biophysics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Cancer Center, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Integrative Program for Biological and Genome Sciences, UNC - Chapel Hill, Chapel Hill, North Carolina, USA.
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2
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Studying the Interactions of U24 from HHV-6 in Order to Further Elucidate Its Potential Role in MS. Viruses 2022; 14:v14112384. [PMID: 36366483 PMCID: PMC9696605 DOI: 10.3390/v14112384] [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: 09/20/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 01/31/2023] Open
Abstract
A number of studies have suggested that human herpesvirus 6A (HHV-6A) may play a role in multiple sclerosis (MS). Three possible hypotheses have been investigated: (1) U24 from HHV-6A (U24-6A) mimics myelin basic protein (MBP) through analogous phosphorylation and interaction with Fyn-SH3; (2) U24-6A affects endocytic recycling by binding human neural precursor cell (NPC) expressed developmentally down-regulated protein 4-like WW3* domain (hNedd4L-WW3*); and (3) MS patients who express Killer Cell Immunoglobulin Like Receptor 2DL2 (KIR2DL2) on natural killer (NK) cells are more susceptible to HHV-6 infection. In this contribution, we examined the validity of these propositions by investigating the interactions of U24 from HHV-6B (U24-6B), a variant less commonly linked to MS, with Fyn-SH3 and hNedd4L-WW3* using heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) titrations and isothermal titration calorimetry (ITC). In addition, the importance of phosphorylation and the specific role of U24 in NK cell activation in MS patients were examined. Overall, the findings allowed us to shed light into the models linking HHV-6 to MS and the involvement of U24.
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Shen SK, Bu QY, Yu WT, Chen YW, Liu FJ, Ding ZW, Mao JL. Interaction and binding mechanism of lipid oxidation products to sturgeon myofibrillar protein in low temperature vacuum heating conditions: Multispectroscopic and molecular docking approaches. Food Chem X 2022; 15:100389. [PMID: 36211750 PMCID: PMC9532714 DOI: 10.1016/j.fochx.2022.100389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 11/27/2022] Open
Abstract
A comparative study of the effects of malondialdehyde and 4-hydroxy-2-nonenal on protein oxidation. Interaction mechanism between lipid oxidation production and protein at temperatures were firstly studied. Hydrogen bonding was the main driving force for bonding. Malondialdehyde had a strong ability to bind MP and accelerated protein oxidation.
In this work, the binding mechanism of myofibrillar protein (MP) with malondialdehyde and 4-hydroxy-2-nonenal under low temperature vacuum heating was investigated via multispectroscopic and molecular docking. The results showed that binding interaction and increasing temperature caused significant changes in the conformations as well as a decrease in the value of protein intrinsic fluorescence, surface hydrophobicity, and fluorescence excitation-emission matrix spectra. Furthermore, the decrease in α-helix and β-turn, increase in β-sheet and a random coil of MP, imply the MP molecules to be more unfolded. Isothermal titration calorimetry and molecular docking results showed that main driving force for binding with MP was hydrogen bond, and the binding ability of malondialdehyde was superior to that of 4-hydroxy-2-nonenal. Moreover, increasing the heating temperature was beneficial to the binding reaction and intensified the conformational transition of MP. These results will provide a reference for further studies on the lipid and protein interaction of sturgeon.
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4
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Chen JN, Jiang F, Wu YD. Accurate Prediction for Protein-Peptide Binding Based on High-Temperature Molecular Dynamics Simulations. J Chem Theory Comput 2022; 18:6386-6395. [PMID: 36149394 DOI: 10.1021/acs.jctc.2c00743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural characterization of protein-peptide interactions is fundamental to elucidating biological processes and designing peptide drugs. Molecular dynamics (MD) simulations are extensively used to study biomolecular systems. However, simulating the protein-peptide binding process is usually quite expensive. Based on our previous studies, herein, we propose a simple and effective method to predict the binding site and pose of the peptide simultaneously using high-temperature (high-T) MD simulations with the RSFF2C force field. Thousands of binding events (nonspecific or specific) can be sampled during microseconds of high-T MD. From density-based clustering analysis, the structures of all of the 12 complexes (nine with linear peptides and three with cyclic peptides) can be successfully predicted with root-mean-square deviation (RMSD) < 2.5 Å. By directly simulating the process of the ligand binding onto the receptor, our method approaches experimental precision for the first time, significantly surpassing previous protein-peptide docking methods in terms of accuracy.
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Affiliation(s)
- Jia-Nan Chen
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Fan Jiang
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,Shenzhen Bay Laboratory, Shenzhen 518132, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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5
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Daniloski D, McCarthy NA, Auldist MJ, Vasiljevic T. Properties of sodium caseinate as affected by the β-casein phenotypes. J Colloid Interface Sci 2022; 626:939-950. [PMID: 35835044 DOI: 10.1016/j.jcis.2022.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/15/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
The aim of the study was to investigate the properties of sodium caseinate dispersions and oil-in-water emulsions obtained from cows' milk of either A1/A1, A1/A2, or A2/A2 β-casein phenotype. Protein structural characterisation was examined using Fourier Transform Infrared and Nuclear Magnetic Resonance spectroscopies, with physicochemical and interfacial properties assessed by analysing adsorbed protein content, hydrophobicity, solubility, and emulsion stability of the samples. Results showed variations in the secondary structure of all samples dependent of the presence of A1 or A2 β-caseins. The main differences included greater amounts of α-helix and β-sheet in A1/A1 and A1/A2 sodium caseinate dispersions that influenced their lower solubility, while random coils/polyproline II helixes were found only in A2/A2 sodium caseinate dispersion. In contrast, upon adsorption on the interface of A2/A2 sodium caseinate emulsion, the protein adopted ordered conformational motifs. This conformational shift supposedly arose from structural differences between the two β-casein proteoforms, which most likely enhanced the emulsion properties of A2/A2 sodium caseinate compared to either A1/A1 or A1/A2 sodium caseinates. The A2 β-casein in both, A1/A2 and A2/A2 sodium caseinates, appears to be able to more rapidly reach the oil droplet surface and was more efficient as emulsifying agent. The current results demonstrated that the conformational rearrangement of proteins upon adsorption to emulsion interfaces was dependent not only on hydrophobicity and on solubility, but also on the conformational flexibility of A1/A1, A1/A2, and A2/A2 β-casein phenotypes. These findings can assist in predicting the behaviour of sodium caseinates during relevant industrial processing.
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Affiliation(s)
- Davor Daniloski
- Victoria University, Advanced Food Systems Research Unit, Institute for Sustainable Industries and Liveable Cities and College of Health and Biomedicine, Melbourne, Victoria 8001, Australia; Teagasc Food Research Centre, Food Chemistry and Technology Department, Moorepark, Fermoy, P61 C996, Cork, Ireland
| | - Noel A McCarthy
- Teagasc Food Research Centre, Food Chemistry and Technology Department, Moorepark, Fermoy, P61 C996, Cork, Ireland
| | - Martin J Auldist
- Agriculture Victoria, Department of Jobs, Precincts and Regions, Ellinbank, Victoria 3821, Australia; University of Melbourne, Centre for Agricultural Innovation, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, Melbourne, Victoria 3010, Australia
| | - Todor Vasiljevic
- Victoria University, Advanced Food Systems Research Unit, Institute for Sustainable Industries and Liveable Cities and College of Health and Biomedicine, Melbourne, Victoria 8001, Australia.
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6
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Viral Proteins with PxxP and PY Motifs May Play a Role in Multiple Sclerosis. Viruses 2022; 14:v14020281. [PMID: 35215874 PMCID: PMC8879583 DOI: 10.3390/v14020281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/19/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Multiple sclerosis (MS) is a debilitating disease that arises from immune system attacks to the protective myelin sheath that covers nerve fibers and ensures optimal communication between brain and body. Although the cause of MS is unknown, a number of factors, which include viruses, have been identified as increasing the risk of displaying MS symptoms. Specifically, the ubiquitous and highly prevalent Epstein–Barr virus, human herpesvirus 6, cytomegalovirus, varicella–zoster virus, and other viruses have been identified as potential triggering agents. In this review, we examine the specific role of proline-rich proteins encoded by these viruses and their potential role in MS at a molecular level.
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7
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Dreydoppel M, Lichtenecker RJ, Akke M, Weininger U. 1H R 1ρ relaxation dispersion experiments in aromatic side chains. JOURNAL OF BIOMOLECULAR NMR 2021; 75:383-392. [PMID: 34510298 PMCID: PMC8642340 DOI: 10.1007/s10858-021-00382-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Aromatic side chains are attractive probes of protein dynamic, since they are often key residues in enzyme active sites and protein binding sites. Dynamic processes on microsecond to millisecond timescales can be studied by relaxation dispersion experiments that attenuate conformational exchange contributions to the transverse relaxation rate by varying the refocusing frequency of applied radio-frequency fields implemented as either CPMG pulse trains or continuous spin-lock periods. Here we present an aromatic 1H R1ρ relaxation dispersion experiment enabling studies of two to three times faster exchange processes than achievable by existing experiments for aromatic side chains. We show that site-specific isotope labeling schemes generating isolated 1H-13C spin pairs with vicinal 2H-12C moieties are necessary to avoid anomalous relaxation dispersion profiles caused by Hartmann-Hahn matching due to the 3JHH couplings and limited chemical shift differences among 1H spins in phenylalanine, tyrosine and the six-ring moiety of tryptophan. This labeling pattern is sufficient in that remote protons do not cause additional complications. We validated the approach by measuring ring-flip kinetics in the small protein GB1. The determined rate constants, kflip, agree well with previous results from 13C R1ρ relaxation dispersion experiments, and yield 1H chemical shift differences between the two sides of the ring in good agreement with values measured under slow-exchange conditions. The aromatic1H R1ρ relaxation dispersion experiment in combination with the site-selective 1H-13C/2H-12C labeling scheme enable measurement of exchange rates up to kex = 2kflip = 80,000 s-1, and serve as a useful complement to previously developed 13C-based methods.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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8
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Kuruba B, Kaczmarek M, Kęsik-Brodacka M, Fojutowska M, Śliwinska M, Kostyukova AS, Moraczewska J. Structural Effects of Disease-Related Mutations in Actin-Binding Period 3 of Tropomyosin. Molecules 2021; 26:6980. [PMID: 34834072 PMCID: PMC8622905 DOI: 10.3390/molecules26226980] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
Tropomyosin (Tpm) is an actin-binding coiled-coil protein. In muscle, it regulates contractions in a troponin/Ca2+-dependent manner and controls the thin filament lengths at the pointed end. Due to its size and periodic structure, it is difficult to observe small local structural changes in the coiled coil caused by disease-related mutations. In this study, we designed 97-residue peptides, Tpm1.164-154 and Tpm3.1265-155, focusing on the actin-binding period 3 of two muscle isoforms. Using these peptides, we evaluated the effects of cardiomyopathy mutations: I92T and V95A in Tpm1.1, and congenital myopathy mutations R91P and R91C in Tpm3.12. We introduced a cysteine at the N-terminus of each fragment to promote the formation of the coiled-coil structure by disulfide bonds. Dimerization of the designed peptides was confirmed by gel electrophoresis in the presence and absence of dithiothreitol. Using circular dichroism, we showed that all mutations decreased coiled coil stability, with Tpm3.1265-155R91P and Tpm1.164-154I92T having the most drastic effects. Our experiments also indicated that adding the N-terminal cysteine increased coiled coil stability demonstrating that our design can serve as an effective tool in studying the coiled-coil fragments of various proteins.
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Affiliation(s)
- Balaganesh Kuruba
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99163, USA; (B.K.); (A.S.K.)
| | - Marta Kaczmarek
- Department of Biochemistry and Cell Biology, Faculty of Biological Sciences, Kazimierz Wielki University, 85-671 Bydgoszcz, Poland; (M.K.); (M.F.); (M.Ś.)
| | | | - Magdalena Fojutowska
- Department of Biochemistry and Cell Biology, Faculty of Biological Sciences, Kazimierz Wielki University, 85-671 Bydgoszcz, Poland; (M.K.); (M.F.); (M.Ś.)
| | - Małgorzata Śliwinska
- Department of Biochemistry and Cell Biology, Faculty of Biological Sciences, Kazimierz Wielki University, 85-671 Bydgoszcz, Poland; (M.K.); (M.F.); (M.Ś.)
| | - Alla S. Kostyukova
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99163, USA; (B.K.); (A.S.K.)
| | - Joanna Moraczewska
- Department of Biochemistry and Cell Biology, Faculty of Biological Sciences, Kazimierz Wielki University, 85-671 Bydgoszcz, Poland; (M.K.); (M.F.); (M.Ś.)
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9
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Wang J, Miao Y. Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding. J Chem Phys 2021; 153:154109. [PMID: 33092378 DOI: 10.1063/5.0021399] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play an important role in cellular signaling. However, it is challenging to simulate both binding and unbinding of peptides and calculate peptide binding free energies through conventional molecular dynamics, due to long biological timescales and extremely high flexibility of the peptides. Based on the Gaussian accelerated molecular dynamics (GaMD) enhanced sampling technique, we have developed a new computational method "Pep-GaMD," which selectively boosts essential potential energy of the peptide in order to effectively model its high flexibility. In addition, another boost potential is applied to the remaining potential energy of the entire system in a dual-boost algorithm. Pep-GaMD has been demonstrated on binding of three model peptides to the SH3 domains. Independent 1 µs dual-boost Pep-GaMD simulations have captured repetitive peptide dissociation and binding events, which enable us to calculate peptide binding thermodynamics and kinetics. The calculated binding free energies and kinetic rate constants agreed very well with available experimental data. Furthermore, the all-atom Pep-GaMD simulations have provided important insights into the mechanism of peptide binding to proteins that involves long-range electrostatic interactions and mainly conformational selection. In summary, Pep-GaMD provides a highly efficient, easy-to-use approach for unconstrained enhanced sampling and calculations of peptide binding free energies and kinetics.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, USA
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10
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Reid Alderson T, Adriaenssens E, Asselbergh B, Pritišanac I, Van Lent J, Gastall HY, Wälti MA, Louis JM, Timmerman V, Baldwin AJ, LP Benesch J. A weakened interface in the P182L variant of HSP27 associated with severe Charcot-Marie-Tooth neuropathy causes aberrant binding to interacting proteins. EMBO J 2021; 40:e103811. [PMID: 33644875 PMCID: PMC8047445 DOI: 10.15252/embj.2019103811] [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: 11/05/2019] [Revised: 01/10/2021] [Accepted: 01/14/2021] [Indexed: 01/18/2023] Open
Abstract
HSP27 is a human molecular chaperone that forms large, dynamic oligomers and functions in many aspects of cellular homeostasis. Mutations in HSP27 cause Charcot-Marie-Tooth (CMT) disease, the most common inherited disorder of the peripheral nervous system. A particularly severe form of CMT disease is triggered by the P182L mutation in the highly conserved IxI/V motif of the disordered C-terminal region, which interacts weakly with the structured core domain of HSP27. Here, we observed that the P182L mutation disrupts the chaperone activity and significantly increases the size of HSP27 oligomers formed in vivo, including in motor neurons differentiated from CMT patient-derived stem cells. Using NMR spectroscopy, we determined that the P182L mutation decreases the affinity of the HSP27 IxI/V motif for its own core domain, leaving this binding site more accessible for other IxI/V-containing proteins. We identified multiple IxI/V-bearing proteins that bind with higher affinity to the P182L variant due to the increased availability of the IxI/V-binding site. Our results provide a mechanistic basis for the impact of the P182L mutation on HSP27 and suggest that the IxI/V motif plays an important, regulatory role in modulating protein-protein interactions.
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Affiliation(s)
- T Reid Alderson
- Chemistry Research LaboratoryUniversity of OxfordOxfordUK
- Laboratory of Chemical PhysicsNational Institutes of HealthBethesdaMDUSA
- Present address:
Department of BiochemistryTorontoONCanada
| | - Elias Adriaenssens
- Peripheral Neuropathy Research GroupDepartment of Biomedical SciencesInstitute Born BungeUniversity of AntwerpAntwerpenBelgium
| | - Bob Asselbergh
- Neuromics Support FacilityVIB Center for Molecular NeurologyVIBAntwerpenBelgium
- Neuromics Support Facility, Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | - Iva Pritišanac
- Molecular Medicine ProgramThe Hospital for Sick ChildrenTorontoONCanada
| | - Jonas Van Lent
- Peripheral Neuropathy Research GroupDepartment of Biomedical SciencesInstitute Born BungeUniversity of AntwerpAntwerpenBelgium
| | | | - Marielle A Wälti
- Laboratory of Chemical PhysicsNational Institutes of HealthBethesdaMDUSA
| | - John M Louis
- Laboratory of Chemical PhysicsNational Institutes of HealthBethesdaMDUSA
| | - Vincent Timmerman
- Peripheral Neuropathy Research GroupDepartment of Biomedical SciencesInstitute Born BungeUniversity of AntwerpAntwerpenBelgium
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11
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Oh KI, Lee AR, Choi SR, Go Y, Ryu KS, Kim EH, Lee JH. Systematic Approach to Find the Global Minimum of Relaxation Dispersion Data for Protein-Induced B-Z Transition of DNA. Int J Mol Sci 2021; 22:3517. [PMID: 33805331 PMCID: PMC8037647 DOI: 10.3390/ijms22073517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 11/17/2022] Open
Abstract
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion spectroscopy is commonly used for quantifying conformational changes of protein in μs-to-ms timescale transitions. To elucidate the dynamics and mechanism of protein binding, parameters implementing CPMG relaxation dispersion results must be appropriately determined. Building an analytical model for multi-state transitions is particularly complex. In this study, we developed a new global search algorithm that incorporates a random search approach combined with a field-dependent global parameterization method. The robust inter-dependence of the parameters carrying out the global search for individual residues (GSIR) or the global search for total residues (GSTR) provides information on the global minimum of the conformational transition process of the Zα domain of human ADAR1 (hZαADAR1)-DNA complex. The global search results indicated that a α-helical segment of hZαADAR1 provided the main contribution to the three-state conformational changes of a hZαADAR1-DNA complex with a slow B-Z exchange process. The two global exchange rate constants, kex and kZB, were found to be 844 and 9.8 s-1, respectively, in agreement with two regimes of residue-dependent chemical shift differences-the "dominant oscillatory regime" and "semi-oscillatory regime". We anticipate that our global search approach will lead to the development of quantification methods for conformational changes not only in Z-DNA binding protein (ZBP) binding interactions but also in various protein binding processes.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea; (K.-I.O.); (A.-R.L.); (S.-R.C.); (Y.G.)
| | - Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea; (K.-I.O.); (A.-R.L.); (S.-R.C.); (Y.G.)
| | - Seo-Ree Choi
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea; (K.-I.O.); (A.-R.L.); (S.-R.C.); (Y.G.)
| | - Youyeon Go
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea; (K.-I.O.); (A.-R.L.); (S.-R.C.); (Y.G.)
| | - Kyoung-Seok Ryu
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chungbuk 28119, Korea;
| | - Eun-Hee Kim
- Center for Research Equipment, Korea Basic Science Institute, Ochang, Chungbuk 28119, Korea;
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea; (K.-I.O.); (A.-R.L.); (S.-R.C.); (Y.G.)
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12
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Cao L, Wang Z, Zhang D, Li X, Hou C, Ren C. Phosphorylation of myosin regulatory light chain at Ser17 regulates actomyosin dissociation. Food Chem 2021; 356:129655. [PMID: 33831832 DOI: 10.1016/j.foodchem.2021.129655] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 11/19/2022]
Abstract
Phosphorylation of myosin regulatory light chain (MRLC) can regulate muscle contraction and thus affect actomyosin dissociation and meat quality. The objective of this study was to explore the mechanism by how MRLC phosphorylation regulates actomyosin dissociation and thus develop strategies for improving meat quality. Here, the phosphorylation status of MRLC was modulated by myosin light chain kinase and myosin light chain kinase inhibitor. MRLC phosphorylation at Ser17 decreased the kinetic energy and total energy of actomyosin, thus stabilized the structure, facilitating the interaction between myosin and actin; this was one possible way that MRLC phosphorylation at Ser17 negatively affects actomyosin dissociation. Moreover, MRLC phosphorylation at Ser17 was beneficial to the formation of ionic bonds, hydrogen bonds, and hydrophobic interaction between myosin and actin, and was the second possible way that MRLC phosphorylation at Ser17 negatively affects actomyosin dissociation.
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Affiliation(s)
- Lichuang Cao
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China; Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg C, Denmark.
| | - Zhenyu Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China.
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China.
| | - Xin Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Chengli Hou
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Chi Ren
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
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13
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Hong JKY, Schwendeman SP. Characterization of Octreotide-PLGA Binding by Isothermal Titration Calorimetry. Biomacromolecules 2020; 21:4087-4093. [PMID: 32885949 DOI: 10.1021/acs.biomac.0c00885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Cationic peptides are well known to readily bind poly(lactic-co-glycolic acids) (PLGAs) with a carboxylic acid (-COOH) end group, which poses a significant challenge to develop PLGA-based delivery systems for peptide therapeutics. This binding has been considered as a critical step leading to the peptide acylation within PLGA-based formulations, which is also known to affect microencapsulation and release. Herein, we utilized nano isothermal titration calorimetry (NanoITC) to investigate the thermodynamics of peptide-PLGA binding in dimethyl sulfoxide (DMSO) using a model cationic octapeptide, octreotide, which contains two primary amino groups located at its N-terminus and lysine side chain at position five. ITC results of PLGAs with different lactic acid to glycolic acid ratios (50:50 to 100:0) revealed that the extent of the interaction with the octreotide was solely dependent on the availability of the acid end group of the PLGA. The binding constants (Ka) at 37 °C were determined in a narrow range from 1.33 to 1.72 × 104 M-1 with 0.59 to 0.66 binding stoichiometries irrespective of the lactic/glycolic acid ratio in the PLGA-COOH. Over 25-65 °C, the octreotide-PLGA-COOH interactions were found to be enthalpically favored (ΔH < 0) and entropically unfavorable (ΔS < 0). Hence, the interactions were characterized as enthalpically driven. At different sodium chloride (NaCl) levels, the sensitivity of thermodynamics of the interactions to the charge screening effect contributed by the NaCl unveiled the actual driving force of the octreotide-PLGA-COOH interactions is simple ion-pairing.
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Affiliation(s)
- Justin K Y Hong
- Department of Pharmaceutical Sciences, The Biointerfaces Institute, University of Michigan, 2800 Plymouth Rd, Ann Arbor, Michigan 48109, United States
| | - Steven P Schwendeman
- Department of Pharmaceutical Sciences, The Biointerfaces Institute, University of Michigan, 2800 Plymouth Rd, Ann Arbor, Michigan 48109, United States.,Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel Blvd, Ann Arbor, Michigan 48109, United States
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14
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Stadmiller SS, Aguilar JS, Parnham S, Pielak GJ. Protein–Peptide Binding Energetics under Crowded Conditions. J Phys Chem B 2020; 124:9297-9309. [DOI: 10.1021/acs.jpcb.0c05578] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Samantha S. Stadmiller
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Jhoan S. Aguilar
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Stuart Parnham
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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15
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Gerlach GJ, Carrock R, Stix R, Stollar EJ, Ball KA. A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway. PLoS Comput Biol 2020; 16:e1007815. [PMID: 32925900 PMCID: PMC7514057 DOI: 10.1371/journal.pcbi.1007815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 09/24/2020] [Accepted: 08/15/2020] [Indexed: 12/20/2022] Open
Abstract
Protein-protein interactions are involved in a wide range of cellular processes. These interactions often involve intrinsically disordered proteins (IDPs) and protein binding domains. However, the details of IDP binding pathways are hard to characterize using experimental approaches, which can rarely capture intermediate states present at low populations. SH3 domains are common protein interaction domains that typically bind proline-rich disordered segments and are involved in cell signaling, regulation, and assembly. We hypothesized, given the flexibility of SH3 binding peptides, that their binding pathways include multiple steps important for function. Molecular dynamics simulations were used to characterize the steps of binding between the yeast Abp1p SH3 domain (AbpSH3) and a proline-rich IDP, ArkA. Before binding, the N-terminal segment 1 of ArkA is pre-structured and adopts a polyproline II helix, while segment 2 of ArkA (C-terminal) adopts a 310 helix, but is far less structured than segment 1. As segment 2 interacts with AbpSH3, it becomes more structured, but retains flexibility even in the fully engaged state. Binding simulations reveal that ArkA enters a flexible encounter complex before forming the fully engaged bound complex. In the encounter complex, transient nonspecific hydrophobic and long-range electrostatic contacts form between ArkA and the binding surface of SH3. The encounter complex ensemble includes conformations with segment 1 in both the forward and reverse orientation, suggesting that segment 2 may play a role in stabilizing the correct binding orientation. While the encounter complex forms quickly, the slow step of binding is the transition from the disordered encounter ensemble to the fully engaged state. In this transition, ArkA makes specific contacts with AbpSH3 and buries more hydrophobic surface. Simulating the binding between ApbSH3 and ArkA provides insight into the role of encounter complex intermediates and nonnative hydrophobic interactions for other SH3 domains and IDPs in general.
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Affiliation(s)
- Gabriella J. Gerlach
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
| | - Rachel Carrock
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
| | - Robyn Stix
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
| | - Elliott J. Stollar
- School of Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - K. Aurelia Ball
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
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16
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Li X, Bai Y, Ji H, Jin Z. The binding mechanism between cyclodextrins and pullulanase: A molecular docking, isothermal titration calorimetry, circular dichroism and fluorescence study. Food Chem 2020; 321:126750. [DOI: 10.1016/j.foodchem.2020.126750] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 02/06/2023]
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17
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Zhao L, Cai J, Li Y, Wei J, Duan C. A host-guest approach to combining enzymatic and artificial catalysis for catalyzing biomimetic monooxygenation. Nat Commun 2020; 11:2903. [PMID: 32518257 PMCID: PMC7283336 DOI: 10.1038/s41467-020-16714-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
Direct transfer of protons and electrons between two tandem reactions is still a great challenge, because overall reaction kinetics is seriously affected by diffusion rate of the proton and electron carriers. We herein report a host–guest supramolecular strategy based on the incorporation of NADH mimics onto the surface of a metal-organic capsule to encapsulate flavin analogues for catalytic biomimetic monooxygenations in conjunction with enzymes. Coupling an artificial catalysis and a natural enzymatic catalysis in the pocket of an enzyme, this host–guest catalyst–enzyme system allows direct proton and electron transport between two catalytic processes via NADH mimics for the monooxygenation of both cyclobutanones and thioethers. This host–guest approach, which involves the direct coupling of abiotic and biotic catalysts via a NADH-containing host, is quite promising compared to normal catalyst–enzyme systems, as it offers the key advantages of supramolecular catalysis in integrated chemical and biological synthetic sequences. Combining artificial and natural enzymes is a strategy to mimic biocatalytic processes with high efficiency and selectivity. This study reports a dual catalytic system composed of flavin adenine dinucleotide model and NADH mimics to catalyze the monooxygenation of cyclobutanones and thioethers.
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Affiliation(s)
- Liang Zhao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 116024, Dalian, People's Republic of China
| | - Junkai Cai
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 116024, Dalian, People's Republic of China
| | - Yanan Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 116024, Dalian, People's Republic of China
| | - Jianwei Wei
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 116024, Dalian, People's Republic of China
| | - Chunying Duan
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 116024, Dalian, People's Republic of China. .,Zhang Dayu School of Chemistry, Dalian University of Technology, 116024, Dalian, People's Republic of China.
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18
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Stadmiller SS, Aguilar JS, Waudby CA, Pielak GJ. Rapid Quantification of Protein-Ligand Binding via 19F NMR Lineshape Analysis. Biophys J 2020; 118:2537-2548. [PMID: 32348722 PMCID: PMC7231920 DOI: 10.1016/j.bpj.2020.03.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
Fluorine incorporation is ideally suited to many NMR techniques, and incorporation of fluorine into proteins and fragment libraries for drug discovery has become increasingly common. Here, we use one-dimensional 19F NMR lineshape analysis to quantify the kinetics and equilibrium thermodynamics for the binding of a fluorine-labeled Src homology 3 (SH3) protein domain to four proline-rich peptides. SH3 domains are one of the largest and most well-characterized families of protein recognition domains and have a multitude of functions in eukaryotic cell signaling. First, we showe that fluorine incorporation into SH3 causes only minor structural changes to both the free and bound states using amide proton temperature coefficients. We then compare the results from lineshape analysis of one-dimensional 19F spectra to those from two-dimensional 1H-15N heteronuclear single quantum coherence spectra. Their agreement demonstrates that one-dimensional 19F lineshape analysis is a robust, low-cost, and fast alternative to traditional heteronuclear single quantum coherence-based experiments. The data show that binding is diffusion limited and indicate that the transition state is highly similar to the free state. We also measured binding as a function of temperature. At equilibrium, binding is enthalpically driven and arises from a highly positive activation enthalpy for association with small entropic contributions. Our results agree with those from studies using different techniques, providing additional evidence for the utility of 19F NMR lineshape analysis, and we anticipate that this analysis will be an effective tool for rapidly characterizing the energetics of protein interactions.
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Affiliation(s)
| | - Jhoan S Aguilar
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Christopher A Waudby
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina.
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19
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Nishizawa M, Walinda E, Morimoto D, Sugase K. Pinpoint analysis of a protein in slow exchange using F 1F 2-selective ZZ-exchange spectroscopy: assignment and kinetic analysis. JOURNAL OF BIOMOLECULAR NMR 2020; 74:205-211. [PMID: 32236785 DOI: 10.1007/s10858-020-00309-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
ZZ-exchange spectroscopy is widely used to study slow exchange processes in biomolecules, especially determination of exchange rates and assignment of minor peaks. However, if the exchange cross peaks overlap or the populations are skewed, kinetic analysis is hindered. In order to analyze slow exchange protein dynamics under such conditions, here we have developed a new method by combining ZZ-exchange and F1F2-selective NMR spectroscopy. We demonstrate the utility of this method by examining the monomer-dimer transition of the ubiquitin-associated domain of p62, successfully assigning the minor (monomeric) peaks and obtaining the exchange rates, which cannot be achieved by ZZ-exchange alone.
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Affiliation(s)
- Mayu Nishizawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Sakyo-ku Yoshida Konoe-cho, Kyoto, 606-8501, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan.
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20
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Li S, Lu G, Fang X, Ramelot TA, Kennedy MA, Zhou X, Gong P, Zhang X, Liu M, Zhu J, Yang Y. Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins. Nucleic Acids Res 2020; 48:432-444. [PMID: 31713614 PMCID: PMC7145681 DOI: 10.1093/nar/gkz1045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/30/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022] Open
Abstract
SP_0782 from Streptococcus pneumoniae is a dimeric protein that potentially binds with single-stranded DNA (ssDNA) in a manner similar to human PC4, the prototype of PC4-like proteins, which plays roles in transcription and maintenance of genome stability. In a previous NMR study, SP_0782 exhibited an ssDNA-binding property different from YdbC, a prokaryotic PC4-like protein from Lactococcus lactis, but the underlying mechanism remains unclear. Here, we show that although SP_0782 adopts an overall fold similar to those of PC4 and YdbC, the ssDNA length occupied by SP_0782 is shorter than those occupied by PC4 and YdbC. SP_0782 exhibits varied binding patterns for different lengths of ssDNA, and tends to form large complexes with ssDNA in a potential high-density binding manner. The structures of SP_0782 complexed with different ssDNAs reveal that the varied binding patterns are associated with distinct capture of nucleotides in two major DNA-binding regions of SP_0782. Moreover, a comparison of known structures of PC4-like proteins complexed with ssDNA reveals a divergence in the binding interface between prokaryotic and eukaryotic PC4-like proteins. This study provides insights into the ssDNA-binding mechanism of PC4-like proteins, and benefits further study regarding the biological function of SP_0782, probably in DNA protection and natural transformation.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Binding Sites
- Crystallography, X-Ray
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Humans
- Kinetics
- Lactococcus lactis/genetics
- Lactococcus lactis/metabolism
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Folding
- Protein Interaction Domains and Motifs
- Streptococcus pneumoniae/genetics
- Streptococcus pneumoniae/metabolism
- Thermodynamics
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription Factors/metabolism
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Affiliation(s)
- Shuangli Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoliang Lu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Fang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH 45056, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH 45056, USA
| | - Xin Zhou
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
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21
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Biophysical prediction of protein-peptide interactions and signaling networks using machine learning. Nat Methods 2020; 17:175-183. [PMID: 31907444 PMCID: PMC7004877 DOI: 10.1038/s41592-019-0687-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022]
Abstract
In mammalian cells, much of signal transduction is mediated by weak protein-protein interactions between globular peptide-binding domains (PBDs) and unstructured peptidic motifs in partner proteins. The number and diversity of these PBDs (over 1,800 are known), low binding affinities, and sensitivity of binding properties to minor sequence variation represent a substantial challenge to experimental and computational analysis of PBD specificity and the networks PBDs create. Here we introduce a bespoke machine learning approach, hierarchical statistical mechanical modelling (HSM), capable of accurately predicting the affinities of PBD-peptide interactions across multiple protein families. By synthesizing biophysical priors within a modern machine learning framework, HSM outperforms existing computational methods and high-throughput experimental assays. HSM models are interpretable in familiar biophysical terms at three spatial scales: the energetics of protein-peptide binding, the multi-dentate organization of protein-protein interactions, and the global architecture of signaling networks.
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22
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Raum HN, Schörghuber J, Dreydoppel M, Lichtenecker RJ, Weininger U. Site-selective 1H/ 2H labeling enables artifact-free 1H CPMG relaxation dispersion experiments in aromatic side chains. JOURNAL OF BIOMOLECULAR NMR 2019; 73:633-639. [PMID: 31506857 PMCID: PMC6859156 DOI: 10.1007/s10858-019-00275-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Aromatic side chains are often key residues in enzyme active sites and protein binding sites, making them attractive probes of protein dynamics on the millisecond timescale. Such dynamic processes can be studied by aromatic 13C or 1H CPMG relaxation dispersion experiments. Aromatic 1H CPMG relaxation dispersion experiments in phenylalanine, tyrosine and the six-ring moiety of tryptophan, however, are affected by 3J 1H-1H couplings which are causing anomalous relaxation dispersion profiles. Here we show that this problem can be addressed by site-selective 1H/2H labeling of the aromatic side chains and that artifact-free relaxation dispersion profiles can be acquired. The method has been further validated by measuring folding-unfolding kinetics of the small protein GB1. The determined rate constants and populations agree well with previous results from 13C CPMG relaxation dispersion experiments. Furthermore, the CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained directly from the spectra. In summary, site-selective 1H/2H labeling enables artifact-free aromatic 1H CPMG relaxation dispersion experiments in phenylalanine and the six-ring moiety of tryptophan, thereby extending the available methods for studying millisecond dynamics in aromatic protein side chains.
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Affiliation(s)
- Heiner N Raum
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
| | - Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
| | | | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany.
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23
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Paquette DR, Tibble RW, Daifuku TS, Gross JD. Control of mRNA decapping by autoinhibition. Nucleic Acids Res 2019; 46:6318-6329. [PMID: 29618050 PMCID: PMC6158755 DOI: 10.1093/nar/gky233] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/19/2018] [Indexed: 12/11/2022] Open
Abstract
5′ mediated cytoplasmic RNA decay is a conserved cellular process in eukaryotes. While the functions of the structured core domains in this pathway are well-studied, the role of abundant intrinsically disordered regions (IDRs) is lacking. Here we reconstitute the Dcp1:Dcp2 complex containing a portion of the disordered C-terminus and show its activity is autoinhibited by linear interaction motifs. Enhancers of decapping (Edc) 1 and 3 cooperate to activate decapping by different mechanisms: Edc3 alleviates autoinhibition by binding IDRs and destabilizing an inactive form of the enzyme, whereas Edc1 stabilizes the transition state for catalysis. Both activators are required to fully stimulate an autoinhibited Dcp1:Dcp2 as Edc1 alone cannot overcome the decrease in activity attributed to the C-terminal extension. Our data provide a mechanistic framework for combinatorial control of decapping by protein cofactors, a principle that is likely conserved in multiple 5′ mRNA decay pathways.
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Affiliation(s)
- David R Paquette
- Integrative Program in Quantitative Biology, Graduate Group in Biophysics, University of California, San Francisco, CA 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Ryan W Tibble
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.,Program in Chemistry and Chemical Biology, University of California, San Francisco, CA 94158, USA
| | - Tristan S Daifuku
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - John D Gross
- Integrative Program in Quantitative Biology, Graduate Group in Biophysics, University of California, San Francisco, CA 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.,Program in Chemistry and Chemical Biology, University of California, San Francisco, CA 94158, USA
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24
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Aloui G, Bouabdallah S, Baltaze JP, Pucheta JEH, Touil S, Farjon J, Giraud N. Monitoring Conformational Changes in an Enzyme Conversion Inhibitor Using Pure Shift Exchange NMR Spectroscopy. Chemphyschem 2019; 20:1738-1746. [PMID: 31033157 DOI: 10.1002/cphc.201900244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/25/2019] [Indexed: 11/06/2022]
Abstract
We report the acquisition of 2D NMR EXSY spectra with ultrahigh resolution, which allows for probing the slow conformational exchange process in a pharmaceutical compound. The resolution enhancement is achieved by implementing interferogram based PSYCHE homonuclear decoupling to generate a pure shift proton spectrum along the direct domain of the resulting data. The performance of this pure shift EXSY pulse sequence is compared to the standard experiment recorded under identical conditions. It is found that although being less sensitive and requiring a longer acquisition time, the quality of pure shift spectra allows for extracting exchange rates values that are coherent with the ones determined by standard approach, on a temperature range that demonstrates the robustness of the chosen homonuclear decoupling method. The resolution enhancement provided by the simplification of proton line shape allows for probing a higher number of proton sites whose analysis would have been biased using a standard method. These results open the way to a thorough and accurate study of chemical exchange processes based on a multi-site analysis of 2D pure shift EXSY spectra.
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Affiliation(s)
- G Aloui
- Université Paris Saclay, Institut de Chimie Moléculaire et des Matériaux d'Orsay Equipe RMN en Milieu Orienté UMR CNRS-UPS 8182, 91405, Orsay, France.,Laboratory of Hetero-Organic Compounds and Nanostructured Materials, University of Carthage, Faculty of Sciences of Bizerte, 7021, Jarzouna, Tunisia
| | - S Bouabdallah
- Laboratory of Hetero-Organic Compounds and Nanostructured Materials, University of Carthage, Faculty of Sciences of Bizerte, 7021, Jarzouna, Tunisia
| | - J P Baltaze
- Université Paris Saclay, Institut de Chimie Moléculaire et des Matériaux d'Orsay Equipe RMN en Milieu Orienté UMR CNRS-UPS 8182, 91405, Orsay, France
| | - J E H Pucheta
- Consejo Nacional de Ciencia y Tecnología - Laboratorio Nacional de Investigación y Servicio Agroalimentario y Forestal, Universidad Autónoma Chapingo, Km. 38.5 Carretera México-Texcoco, Chapingo, 56230, Estado de México, México
| | - S Touil
- Laboratory of Hetero-Organic Compounds and Nanostructured Materials, University of Carthage, Faculty of Sciences of Bizerte, 7021, Jarzouna, Tunisia
| | - J Farjon
- CEISAM UMR CNRS 6230, Faculté des Sciences et Techniques, 2 rue de la Houssinière, BP, 92208, 44322 Nantes cedex 3, France
| | - N Giraud
- Université Paris Saclay, Institut de Chimie Moléculaire et des Matériaux d'Orsay Equipe RMN en Milieu Orienté UMR CNRS-UPS 8182, 91405, Orsay, France.,Laboratory of Pharmacological and Toxicological Chemistry and Biochemistry, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints Pères, 75006, Paris, France
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25
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Phage tail fibre assembly proteins employ a modular structure to drive the correct folding of diverse fibres. Nat Microbiol 2019; 4:1645-1653. [DOI: 10.1038/s41564-019-0477-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 05/01/2019] [Indexed: 12/18/2022]
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26
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Consensus sequence design as a general strategy to create hyperstable, biologically active proteins. Proc Natl Acad Sci U S A 2019; 116:11275-11284. [PMID: 31110018 DOI: 10.1073/pnas.1816707116] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Consensus sequence design offers a promising strategy for designing proteins of high stability while retaining biological activity since it draws upon an evolutionary history in which residues important for both stability and function are likely to be conserved. Although there have been several reports of successful consensus design of individual targets, it is unclear from these anecdotal studies how often this approach succeeds and how often it fails. Here, we attempt to assess generality by designing consensus sequences for a set of six protein families with a range of chain lengths, structures, and activities. We characterize the resulting consensus proteins for stability, structure, and biological activities in an unbiased way. We find that all six consensus proteins adopt cooperatively folded structures in solution. Strikingly, four of six of these consensus proteins show increased thermodynamic stability over naturally occurring homologs. Each consensus protein tested for function maintained at least partial biological activity. Although peptide binding affinity by a consensus-designed SH3 is rather low, K m values for consensus enzymes are similar to values from extant homologs. Although consensus enzymes are slower than extant homologs at low temperature, they are faster than some thermophilic enzymes at high temperature. An analysis of sequence properties shows consensus proteins to be enriched in charged residues, and rarified in uncharged polar residues. Sequence differences between consensus and extant homologs are predominantly located at weakly conserved surface residues, highlighting the importance of these residues in the success of the consensus strategy.
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27
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Liu Q, Chen X, Guo Y, Han C, Li J, Jia L, Liu J, Wei X. Thermodynamic study of the aqueous two-phase systems of 1-butyl-3-methylimidazolium tetrafluoroborate and sodium dodecylbenzenesulfonate. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Cai J, Zhao L, Wei J, He C, Long S, Duan C. Negatively charged metal–organic hosts with cobalt dithiolene species: improving PET processes for light-driven proton reduction through host–guest electrostatic interactions. Chem Commun (Camb) 2019; 55:8524-8527. [PMID: 31257393 DOI: 10.1039/c9cc03871j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Negatively charged metal–organic hosts combined with cationic Ru-based photosensitizers by electrostatic interactions to improve PET processes for efficient photocatalytic proton reduction.
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Affiliation(s)
- Junkai Cai
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian
- P. R. China
| | - Liang Zhao
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian
- P. R. China
| | - Jianwei Wei
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian
- P. R. China
| | - Cheng He
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian
- P. R. China
| | - Saran Long
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian
- P. R. China
| | - Chunying Duan
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian
- P. R. China
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29
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Pandya MJ, Schiffers S, Hounslow AM, Baxter NJ, Williamson MP. Why the Energy Landscape of Barnase Is Hierarchical. Front Mol Biosci 2018; 5:115. [PMID: 30619881 PMCID: PMC6306431 DOI: 10.3389/fmolb.2018.00115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/07/2018] [Indexed: 01/29/2023] Open
Abstract
We have used NMR and computational methods to characterize the dynamics of the ribonuclease barnase over a wide range of timescales in free and inhibitor-bound states. Using temperature- and denaturant-dependent measurements of chemical shift, we show that barnase undergoes frequent and highly populated hinge bending. Using relaxation dispersion, we characterize a slower and less populated motion with a rate of 750 ± 200 s−1, involving residues around the lip of the active site, which occurs in both free and bound states and therefore suggests conformational selection. Normal mode calculations characterize correlated hinge bending motions on a very rapid timescale. These three measurements are combined with previous measurements and molecular dynamics calculations on barnase to characterize its dynamic landscape on timescales from picoseconds to milliseconds and length scales from 0.1 to 2.5 nm. We show that barnase has two different large-scale fluctuations: one on a timescale of 10−9−10−6 s that has no free energy barrier and is a hinge bending that is determined by the architecture of the protein; and one on a timescale of milliseconds (i.e., 750 s−1) that has a significant free energy barrier and starts from a partially hinge-bent conformation. These two motions can be described as hierarchical, in that the more highly populated faster motion provides a platform for the slower (less probable) motion. The implications are discussed. The use of temperature and denaturant is suggested as a simple and general way to characterize motions on the intermediate ns-μs timescale.
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Affiliation(s)
- Maya J Pandya
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Stefanie Schiffers
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
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30
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Raum HN, Dreydoppel M, Weininger U. Conformational exchange of aromatic side chains by 1H CPMG relaxation dispersion. JOURNAL OF BIOMOLECULAR NMR 2018; 72:105-114. [PMID: 30229369 PMCID: PMC6209042 DOI: 10.1007/s10858-018-0210-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
Aromatic side chains are attractive probes of protein dynamics on the millisecond time scale, because they are often key residues in enzyme active sites and protein binding sites. Further they allow to study specific processes, like histidine tautomerization and ring flips. Till now such processes have been studied by aromatic 13C CPMG relaxation dispersion experiments. Here we investigate the possibility of aromatic 1H CPMG relaxation dispersion experiments as a complementary method. Artifact-free dispersions are possible on uniformly 1H and 13C labeled samples for histidine δ2 and ε1, as well as for tryptophan δ1. The method has been validated by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined rate constants and populations agree well with previous results from 13C CPMG relaxation dispersion experiments. The CPMG-derived chemical shift differences between the folded and unfolded states are in good agreement with those obtained directly from the spectra. In contrast, the 1H relaxation dispersion profiles in phenylalanine, tyrosine and the six-ring moiety of tryptophan, display anomalous behavior caused by 3J 1H-1H couplings and, if present, strong 13C-13C couplings. Therefore they require site-selective 1H/2H and, in case of strong couplings, 13C/12C labeling. In summary, aromatic 1H CPMG relaxation dispersion experiments work on certain positions (His δ2, His ε1 and Trp δ1) in uniformly labeled samples, while other positions require site-selective isotope labeling.
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Affiliation(s)
- Heiner N Raum
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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31
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Optimization of a MT1-MMP-targeting Peptide and Its Application in Near-infrared Fluorescence Tumor Imaging. Sci Rep 2018; 8:10334. [PMID: 29985410 PMCID: PMC6037669 DOI: 10.1038/s41598-018-28493-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/08/2018] [Indexed: 01/11/2023] Open
Abstract
Membrane type 1 metalloproteinase (MT1-MMP) is an important regulator of cancer invasion, growth and angiogenesis, thus making it an attractive target for cancer imaging and therapy. A non-substrate peptide (MT1-AF7p) that bonded to the "MT-Loop" region of MT1-MMP was identified by using a phage-displayed peptide library and was used to image the MT1-MMP expression in vivo through optical imaging. However, the substrate in the screening did not have a 3D structure, thus resulting in a loose bonding of MT1-AF7p. To simulate the real conformation of the "MT-Loop" and improve the performance of MT1-AF7p, molecular simulations were performed, because this strategy provides multiple methods for predicting the conformation and interaction of proteinase in 3D. In view of the binding site of the receptor-ligand interactions, histidine 4 was selected for mutation to achieve an increased affinity effect. The optimized peptides were further identified and conformed by atomic force microscopy, isothermal titration calorimetry, cell fluorescence imaging in vitro, and near-infrared fluorescence tumor optical imaging in vivo. The results revealed that the optimized peptide with a mutation of histidine 4 to arginine has the highest affinity and specificity, and exhibited an increased fluorescence intensity in the tumor site in optical imaging.
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32
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Li Y, Lock LL, Wang Y, Ou SH, Stern D, Schön A, Freire E, Xu X, Ghose S, Li ZJ, Cui H. Bioinspired supramolecular engineering of self-assembling immunofibers for high affinity binding of immunoglobulin G. Biomaterials 2018; 178:448-457. [PMID: 29706234 DOI: 10.1016/j.biomaterials.2018.04.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/11/2018] [Accepted: 04/14/2018] [Indexed: 01/14/2023]
Abstract
Many one-dimensional (1D) nanostructures are constructed by self-assembly of peptides or peptide conjugates containing a short β-sheet sequence as the core building motif essential for the intermolecular hydrogen bonding that promotes directional, anisotropic growth of the resultant assemblies. While this molecular engineering strategy has led to the successful production of a plethora of bioactive filamentous β-sheet assemblies for interfacing with biomolecules and cells, concerns associated with effective presentation of α-helical epitopes and their function preservation have yet to be resolved. In this context, we report on the direct conjugation of the protein A mimicking peptide Z33, a motif containing two α-helices, to linear hydrocarbons to create self-assembling immuno-amphiphiles (IAs). Our results suggest that the resulting amphiphilic peptides can, despite lacking the essential β-sheet segment, effectively associate under physiological conditions into supramolecular immunofibers (IFs) while preserving their native α-helical conformation. Isothermal titration calorimetry (ITC) measurements confirmed that these self-assembling immunofibers can bind to the human immunoglobulin G class 1 (IgG1) with high specificity at pH 7.4, but with significantly weakened binding at pH 2.8. We further demonstrated the accessibility of Z33 ligand in the immunofibers using transmission electron microscopy (TEM) and confocal imaging. We believe these results shed important light into the supramolecular engineering of α-helical peptides into filamentous assemblies that may possess an important potential for antibody isolation.
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Affiliation(s)
- Yi Li
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Lye Lin Lock
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States
| | - Yuzhu Wang
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Shih-Hao Ou
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - David Stern
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Arne Schön
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Ernesto Freire
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Xuankuo Xu
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States.
| | - Sanchayita Ghose
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States
| | - Zheng Jian Li
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States
| | - Honggang Cui
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States; Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States.
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33
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Harris J, Shadrina M, Oliver C, Vogel J, Mittermaier A. Concerted millisecond timescale dynamics in the intrinsically disordered carboxyl terminus of γ-tubulin induced by mutation of a conserved tyrosine residue. Protein Sci 2018; 27:531-545. [PMID: 29127738 PMCID: PMC5775176 DOI: 10.1002/pro.3345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 12/30/2022]
Abstract
Tubulins are an ancient family of eukaryotic proteins characterized by an amino-terminal globular domain and disordered carboxyl terminus. These carboxyl termini play important roles in modulating the behavior of microtubules in living cells. However, the atomic-level basis of their function is not well understood. These regions contain multiple acidic residues and their overall charges are modulated in vivo by post-translational modifications, for example, phosphorylation. In this study, we describe an application of NMR and computer Monte Carlo simulations to investigate how the modification of local charge alters the conformational sampling of the γ-tubulin carboxyl terminus. We compared the dynamics of two 39-residue polypeptides corresponding to the carboxyl-terminus of yeast γ-tubulin. One polypeptide comprised the wild-type amino acid sequence while the second contained a Y > D mutation at Y11 in the polypeptide (Y445 in the full protein). This mutation introduces additional negative charge at a site that is phosphorylated in vivo and produces a phenotype with perturbed microtubule function. NMR relaxation measurements show that the Y11D mutation produces dramatic changes in the millisecond-timescale motions of the entire polypeptide. This observation is supported by Monte Carlo simulations that-similar to NMR-predict the WT γ-CT is largely unstructured and that the substitution of Tyr 11 with Asp causes the sampling of extended conformations that are unique to the Y11D polypeptide.
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Affiliation(s)
- Jason Harris
- Department of ChemistryMcGill University, 801 Sherbrooke St. WMontrealQuebecCanada
| | - Maria Shadrina
- Department of BiologyMcGill University, 3649 Promenade Sir William OslerMontrealQuebecCanada
| | - Carlos Oliver
- Department of BiologyMcGill University, 3649 Promenade Sir William OslerMontrealQuebecCanada
- The School of Computer ScienceMcGill University, 3480 University StMontrealQuebecCanada
| | - Jackie Vogel
- Department of BiologyMcGill University, 3649 Promenade Sir William OslerMontrealQuebecCanada
- The School of Computer ScienceMcGill University, 3480 University StMontrealQuebecCanada
| | - Anthony Mittermaier
- Department of ChemistryMcGill University, 801 Sherbrooke St. WMontrealQuebecCanada
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34
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Yang L, Jing X, An B, He C, Yang Y, Duan C. Binding of anions in triply interlocked coordination catenanes and dynamic allostery for dehalogenation reactions. Chem Sci 2018; 9:1050-1057. [PMID: 29675152 PMCID: PMC5883946 DOI: 10.1039/c7sc04070a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/30/2017] [Indexed: 01/17/2023] Open
Abstract
By synergistic combination of multicomponent self-assembly and template-directed approaches, triply interlocked metal organic catenanes that consist of two isolated chirally identical tetrahedrons were constructed and stabilized as thermodynamic minima. In the presence of suitable template anions, the structural conversion from the isolated tetrahedral conformers into locked catenanes occurred via the cleavage of an intrinsically reversible coordination bond in each of the tetrahedrons, followed by the reengineering and interlocking of two fragments with the regeneration of the broken coordination bonds. The presence of several kinds of individual pocket that were attributed to the triply interlocked patterns enabled the possibility of encapsulating different anions, allowing the dynamic allostery between the unlocked/locked conformers to promote the dehalogenation reaction of 3-bromo-cyclohexene efficiently, as with the use of dehalogenase enzymes. The interlocked structures could be unlocked into two individual tetrahedrons through removal of the well-matched anion templates. The stability and reversibility of the locked/unlocked structures were further confirmed by the catching/releasing process that accompanied emission switching, providing opportunities for the system to be a dynamic molecular logic system.
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Affiliation(s)
- Linlin Yang
- State Key Laboratory of Fine Chemicals , College of Zhang Dayu , Dalian University of Technology , Dalian , 116024 , P. R. China .
| | - Xu Jing
- State Key Laboratory of Fine Chemicals , College of Zhang Dayu , Dalian University of Technology , Dalian , 116024 , P. R. China .
| | - Bowen An
- State Key Laboratory of Fine Chemicals , College of Zhang Dayu , Dalian University of Technology , Dalian , 116024 , P. R. China .
| | - Cheng He
- State Key Laboratory of Fine Chemicals , College of Zhang Dayu , Dalian University of Technology , Dalian , 116024 , P. R. China .
| | - Yang Yang
- State Key Laboratory of Fine Chemicals , College of Zhang Dayu , Dalian University of Technology , Dalian , 116024 , P. R. China .
| | - Chunying Duan
- State Key Laboratory of Fine Chemicals , College of Zhang Dayu , Dalian University of Technology , Dalian , 116024 , P. R. China .
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35
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Mobbs JI, Di Paolo A, Metcalfe RD, Selig E, Stapleton DI, Griffin MDW, Gooley PR. Unravelling the Carbohydrate-Binding Preferences of the Carbohydrate-Binding Modules of AMP-Activated Protein Kinase. Chembiochem 2018; 19:229-238. [PMID: 29193585 DOI: 10.1002/cbic.201700589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Indexed: 01/24/2023]
Abstract
The β subunit of adenosine monophosphate (AMP)-activated protein kinase (AMPK), which exists as two isoforms (β1 and β2) in humans, has a carbohydrate-binding module (CBM) that interacts with glycogen. Although the β1- and β2-CBMs are structurally similar, with strictly conserved ligand-contact residues, they show different carbohydrate affinities. β2-CBM shows the strongest affinity for both branched and unbranched oligosaccharides and it has recently been shown that a Thr insertion into β2-CBM (Thr101) forms a pocket to accommodate branches. This insertion does not explain why β2-CBM binds all carbohydrates with stronger affinity. Herein, it is shown that residue 134 (Val for β2 and Thr for β1), which does not come into contact with a carbohydrate, appears to account for the affinity difference. Characterisation by NMR spectroscopy, however, suggests that mutant β2-Thr101Δ/Val134Thr differs from that of β1-CBM, and mutant β1-Thr101ins/Thr134Val differs from that of β2-CBM. Furthermore, these mutants are less stable to chemical denaturation, relative to that of wild-type β-CBMs, which confounds the affinity analyses. To support the importance of Thr101 and Val134, the ancestral CBM has been constructed. This CBM retains Thr101 and Val134, which suggests that the extant β1-CBM has a modest loss of function in carbohydrate binding. Because the ancestor bound carbohydrate with equal affinity to that of β2-CBM, it is concluded that residue 134 plays an indirect role in carbohydrate binding.
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Affiliation(s)
- Jesse I Mobbs
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.,Current Address: Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Alex Di Paolo
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.,Current Address: New Technologies Development Department, Kaneka Eurogentec S.A. Biologics Division, 14 Rue Bois Saint-Jean, 4102, Seraing, Belgium
| | - Riley D Metcalfe
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Emily Selig
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - David I Stapleton
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
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36
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Gooley PR, Koay A, Mobbs JI. Applications of NMR and ITC for the Study of the Kinetics of Carbohydrate Binding by AMPK β-Subunit Carbohydrate-Binding Modules. Methods Mol Biol 2018; 1732:87-98. [PMID: 29480470 DOI: 10.1007/978-1-4939-7598-3_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Understanding the kinetics of proteins interacting with their ligands is important for characterizing molecular mechanism. However, it can be difficult to determine the extent and nature of these interactions for weakly formed protein-ligand complexes that have lifetimes of micro- to milliseconds. Nuclear magnetic resonance (NMR) spectroscopy is a powerful solution-based method for the atomic-level analysis of molecular interactions on a wide range of timescales, including micro- to milliseconds. Recently the combination of thermodynamic experiments using isothermal titration calorimetry (ITC) with kinetic measurements using ZZ-exchange and CPMG relaxation dispersion NMR spectroscopy have been used to determine the kinetics of weakly interacting protein systems. This chapter describes the application of ITC and NMR to understand the differences in the kinetics of carbohydrate binding by the β1- and β2-carbohydrate-binding modules of AMP-activated protein kinase.
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Affiliation(s)
- Paul R Gooley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
| | - Ann Koay
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.,Experimental Therapeutics Centre, Agency for Science Technology and Research, Singapore, Singapore
| | - Jesse I Mobbs
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.,Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia
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37
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Liu M, Kim Y, Hilty C. Characterization of Chemical Exchange Using Relaxation Dispersion of Hyperpolarized Nuclear Spins. Anal Chem 2017; 89:9154-9158. [PMID: 28714674 DOI: 10.1021/acs.analchem.7b01896] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chemical exchange phenomena are ubiquitous in macromolecules, which undergo conformational change or ligand complexation. NMR relaxation dispersion (RD) spectroscopy based on a Carr-Purcell-Meiboom-Gill pulse sequence is widely applied to identify the exchange and measure the lifetime of intermediate states on the millisecond time scale. Advances in hyperpolarization methods improve the applicability of NMR spectroscopy when rapid acquisitions or low concentrations are required, through an increase in signal strength by several orders of magnitude. Here, we demonstrate the measurement of chemical exchange from a single aliquot of a ligand hyperpolarized by dissolution dynamic nuclear polarization (D-DNP). Transverse relaxation rates are measured simultaneously at different pulsing delays by dual-channel 19F NMR spectroscopy. This two-point measurement is shown to allow the determination of the exchange term in the relaxation rate expression. For the ligand 4-(trifluoromethyl)benzene-1-carboximidamide binding to the protein trypsin, the exchange term is found to be equal within error limits in neutral and acidic environments from D-DNP NMR spectroscopy, corresponding to a pre-equilibrium of trypsin deprotonation. This finding illustrates the capability for determination of binding mechanisms using D-DNP RD. Taking advantage of hyperpolarization, the ligand concentration in the exchange measurements can reach on the order of tens of μM and protein concentration can be below 1 μM, i.e., conditions typically accessible in drug discovery.
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Affiliation(s)
- Mengxiao Liu
- Department of Chemistry, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
| | - Yaewon Kim
- Department of Chemistry, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
| | - Christian Hilty
- Department of Chemistry, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
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38
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Zeng D, Bhatt VS, Shen Q, Cho JH. Kinetic Insights into the Binding between the nSH3 Domain of CrkII and Proline-Rich Motifs in cAbl. Biophys J 2017; 111:1843-1853. [PMID: 27806266 DOI: 10.1016/j.bpj.2016.09.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/13/2016] [Accepted: 09/22/2016] [Indexed: 10/20/2022] Open
Abstract
The interaction between CrkII and cAbl is implicated in diverse cellular processes. This interaction starts with the binding of the N-terminal Src homology 3 (nSH3) domain of CrkII to the proline-rich motifs of cAbl (PRMscAbl). Despite its critical importance, the detailed binding mechanism between the nSH3 domain and PRMs remains elusive. In this study, we used nuclear magnetic resonance Carr-Purcell-Meiboom-Gill relaxation dispersion experiment to study the binding kinetics between the nSH3 domain of CrkII and PRMscAbl. Our results highlight that the nSH3 domain binds to three PRMscAbl with very high on- and off-rate constants, indicating the transient nature of the binding. To further characterize the binding transition state, we conducted the Eyring and linear free energy relationship analyses using temperature-dependent kinetic data. These data indicate that the binding transition state of the nSH3 domain and PRM is accompanied by small activation enthalpy, owing to partial desolvation of the transition state. These results also highlight the similarity between the transition and free states, in terms of structure and energetics. Although the binding of the nSH3 domain and PRM displays the features consistent with a diffusion-limited process within our experimental conditions, further tests are necessary to determine if the binding is a true diffusion-limited process.
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Affiliation(s)
- Danyun Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Veer S Bhatt
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Qingliang Shen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Jae-Hyun Cho
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
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39
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Tressler CM, Zondlo NJ. Perfluoro-tert-butyl Homoserine Is a Helix-Promoting, Highly Fluorinated, NMR-Sensitive Aliphatic Amino Acid: Detection of the Estrogen Receptor·Coactivator Protein-Protein Interaction by 19F NMR. Biochemistry 2017; 56:1062-1074. [PMID: 28165218 PMCID: PMC5894335 DOI: 10.1021/acs.biochem.6b01020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Highly fluorinated amino acids can stabilize proteins and complexes with proteins, via enhanced hydrophobicity, and provide novel methods for identification of specific molecular events in complex solutions, via selective detection by 19F NMR and the absence of native 19F signals in biological contexts. However, the potential applications of 19F NMR in probing biological processes are limited both by the strong propensities of most highly fluorinated amino acids for the extended conformation and by the relatively modest sensitivity of NMR spectroscopy, which typically constrains measurements to mid-micromolar concentrations. Herein, we demonstrate that perfluoro-tert-butyl homoserine exhibits a propensity for compact conformations, including α-helix and polyproline helix (PPII), that is similar to that of methionine. Perfluoro-tert-butyl homoserine has nine equivalent fluorines that do not couple to any other nuclei, resulting in a sharp singlet that can be sensitively detected rapidly at low micromolar concentrations. Perfluoro-tert-butyl homoserine was incorporated at sites of leucine residues within the α-helical LXXLL short linear motif of estrogen receptor (ER) coactivator peptides. A peptide containing perfluoro-tert-butyl homoserine at position i + 3 of the ER coactivator LXXLL motif exhibited a Kd of 2.2 μM for the estradiol-bound estrogen receptor, similar to that of the native ligand. 19F NMR spectroscopy demonstrated the sensitive detection (5 μM concentration, 128 scans) of binding of the peptide to the ER and of inhibition of protein-protein interaction by the native ligand or by the ER antagonist tamoxifen. These results suggest diverse potential applications of perfluoro-tert-butyl homoserine in probing protein function and protein-protein interfaces in complex solutions.
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Affiliation(s)
- Caitlin M. Tressler
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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40
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Fenwick RB, Oyen D, Wright PE. Multi-probe relaxation dispersion measurements increase sensitivity to protein dynamics. Phys Chem Chem Phys 2017; 18:5789-98. [PMID: 26426424 DOI: 10.1039/c5cp04670j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion measurements are a valuable tool for the characterization of structural transitions on the micro-millisecond timescale. While the measurement of (15)N relaxation dispersion is now routine, the measurements with alternative nuclei remain limited. Here we report (15)N as well as (1)H R2 relaxation dispersion measurements of the N23PP/S148A "dynamic knockout" mutant of dihydrofolate reductase. The (1)H dispersion measurements are complementary to (15)N data as many additional residues are observed to have dispersive behavior for the (1)H nucleus. Simultaneous fitting of the dispersion profiles for the two nuclei increases the accuracy of exchange parameters determined for individual residues and clustered groups of residues. The different sensitivity of the two nuclei to changes in backbone torsional angles, ring currents, and hydrogen bonding effects provides important insights into the nature of the structural changes that take place during the exchange process. We observe clear evidence of direct and indirect hydrogen bond effects for the (15)N and (1)H chemical shift changes in the active-site, modulation of ring current shielding in the CD-loop and backbone torsional changes in a cluster of residues associated with the C-terminus. This work demonstrates the power of combined (1)H and (15)N probes for the study of backbone dynamics on the micro-millisecond timescale though the analysis of chemical shift changes.
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Affiliation(s)
- R Bryn Fenwick
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
| | - David Oyen
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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41
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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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42
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Hologne M, Cantrelle FX, Riviere G, Guillière F, Trivelli X, Walker O. NMR Reveals the Interplay among the AMSH SH3 Binding Motif, STAM2, and Lys63-Linked Diubiquitin. J Mol Biol 2016; 428:4544-4558. [PMID: 27725184 DOI: 10.1016/j.jmb.2016.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/30/2016] [Accepted: 10/01/2016] [Indexed: 01/31/2023]
Abstract
AMSH [associated molecule with a Src homology 3 domain of signal transducing adaptor molecule (STAM)] is one of the deubiquitinating enzymes associated in the regulation of endocytic cargo trafficking. It shows an exquisite selectivity for Lys63-linked polyubiquitin chains that are the main chains involved in cargo sorting. The first step requires the ESCRT-0 complex that comprises the STAM and hepatocyte growth factor-regulated substrate (Hrs) proteins. Previous studies have shown that the presence of the STAM protein increases the efficiency of Lys63-linked polyubiquitin chain cleavage by AMSH, one of the deubiquitinating enzyme involved in lysosomal degradation. In the present study, we are seeking to understand if a particular structural organization among these three key players is responsible for the stimulation of the catalytic activity of AMSH. To address this question, we first monitored the interaction between the ubiquitin interacting motif (UIM)-SH3 construct of STAM2 and the Lys63-linked diubiquitin (Lys63-Ub2) chains by means of NMR. We show that Lys63-Ub2 is able to bind either the UIM or the SH3 domain without any selectivity. We further demonstrate that the SH3 binding motif (SBM) of AMSH (AMSH-SBM) outcompetes Lys63-Ub2 for binding SH3. Additionally, we show how different AMSH-SBM variants, modified by their sequence and length, exhibit similar equilibrium dissociation constants when binding SH3 but significantly differ in their dissociation rate constants. Finally, we report the solution NMR structure of the AMSH-SBM/SH3 complex and propose a structural organization where the AMSH-SBM interacts with the STAM2-SH3 domain and contributes to the correct positioning of AMSH prior to polyubiquitin chains' cleavage.
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Affiliation(s)
- Maggy Hologne
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - François-Xavier Cantrelle
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Gwladys Riviere
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Florence Guillière
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Xavier Trivelli
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Olivier Walker
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France.
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43
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Camara-Artigas A, Ortiz-Salmeron E, Andujar-Sánchez M, Bacarizo J, Martin-Garcia JM. The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase. Acta Crystallogr F Struct Biol Commun 2016; 72:707-12. [PMID: 27599862 PMCID: PMC5012211 DOI: 10.1107/s2053230x16012310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 07/29/2016] [Indexed: 01/05/2023] Open
Abstract
Interactions of proline-rich motifs with SH3 domains are present in signal transduction and other important cell processes. Analysis of structural and thermodynamic data suggest a relevant role of water molecules in these protein-protein interactions. To determine whether or not the SH3 domain of the Fyn tyrosine kinase shows the same behaviour, the crystal structures of its complexes with two high-affinity synthetic peptides, VSL12 and APP12, which are class I and II peptides, respectively, have been solved. In the class I complexes two water molecules were found at the binding interface that were not present in the class II complexes. The structures suggest a role of these water molecules in facilitating conformational changes in the SH3 domain to allow the binding of the class I or II peptides. In the third binding pocket these changes modify the cation-π and salt-bridge interactions that determine the affinity of the binding. Comparison of the water molecules involved in the binding of the peptides with previous reported hydration spots suggests a different pattern for the SH3 domains of the Src tyrosine kinase family.
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Affiliation(s)
- Ana Camara-Artigas
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento, 04120 Almeria, Spain
| | - Emilia Ortiz-Salmeron
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento, 04120 Almeria, Spain
| | - Montserrrat Andujar-Sánchez
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento, 04120 Almeria, Spain
| | - Julio Bacarizo
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento, 04120 Almeria, Spain
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44
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Furukawa A, Konuma T, Yanaka S, Sugase K. Quantitative analysis of protein-ligand interactions by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:47-57. [PMID: 27573180 DOI: 10.1016/j.pnmrs.2016.02.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/21/2016] [Accepted: 02/21/2016] [Indexed: 06/06/2023]
Abstract
Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used to analyze population-averaged NMR quantities. Essentially, to apply NMR successfully, both the type of experiment and equation to fit the data must be carefully and specifically chosen for the protein-ligand interaction under analysis. In this review, we first explain the exchange regimes and kinetic models of protein-ligand interactions, and then describe the NMR methods that quantitatively analyze these specific interactions.
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Affiliation(s)
- Ayako Furukawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tsuyoshi Konuma
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan; Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Saeko Yanaka
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan; Department of Life and Coordination-Complex Molecular Science, Biomolecular Functions, Institute of Molecular Science, National Institute of Natural Sciences, Japan
| | - Kenji Sugase
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan; Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.
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45
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Yuwen T, Xue Y, Skrynnikov NR. Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets: 2. The Model of Encounter Complex Involving the Double Mutant of the c-Crk N-SH3 Domain and Peptide Sos. Biochemistry 2016; 55:1784-800. [PMID: 26910732 DOI: 10.1021/acs.biochem.5b01283] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tairan Yuwen
- Department
of Chemistry, Purdue University, West Lafayette Indiana 47907, United States
| | - Yi Xue
- Department
of Chemistry, Purdue University, West Lafayette Indiana 47907, United States
| | - Nikolai R. Skrynnikov
- Department
of Chemistry, Purdue University, West Lafayette Indiana 47907, United States
- Laboratory
of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
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46
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Dyson HJ, Wright PE. Role of Intrinsic Protein Disorder in the Function and Interactions of the Transcriptional Coactivators CREB-binding Protein (CBP) and p300. J Biol Chem 2016; 291:6714-22. [PMID: 26851278 DOI: 10.1074/jbc.r115.692020] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The transcriptional coactivators CREB-binding protein (CBP) and p300 undergo a particularly rich set of interactions with disordered and partly ordered partners, as a part of their ubiquitous role in facilitating transcription of genes. CBP and p300 contain a number of small structured domains that provide scaffolds for the interaction of disordered transactivation domains from a wide variety of partners, including p53, hypoxia-inducible factor 1α (HIF-1α), NF-κB, and STAT proteins, and are the targets for the interactions of disordered viral proteins that compete with cellular factors to disrupt signaling and subvert the cell cycle. The functional diversity of the CBP/p300 interactome provides an excellent example of the power of intrinsic disorder to facilitate the complexity of living systems.
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Affiliation(s)
- H Jane Dyson
- From the Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037-1000
| | - Peter E Wright
- From the Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037-1000
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47
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Yang C, Zhang S, Bai Z, Hou S, Wu D, Huang J, Zhou P. A two-step binding mechanism for the self-binding peptide recognition of target domains. MOLECULAR BIOSYSTEMS 2016; 12:1201-13. [DOI: 10.1039/c5mb00800j] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
By using state-of-the-art molecular dynamics to reconstruct the complete structural dynamics picture of self-binding peptides, a two-step binding mechanism was proposed, including a fast, nonspecific diffusive phase and a slow, specific organizational phase.
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Affiliation(s)
- Chao Yang
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Shilei Zhang
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Zhengya Bai
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Shasha Hou
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Di Wu
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Jian Huang
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Peng Zhou
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
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48
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Vohidov F, Knudsen SE, Leonard PG, Ohata J, Wheadon MJ, Popp BV, Ladbury JE, Ball ZT. Potent and selective inhibition of SH3 domains with dirhodium metalloinhibitors. Chem Sci 2015; 6:4778-4783. [PMID: 29142714 PMCID: PMC5667506 DOI: 10.1039/c5sc01602a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 06/03/2015] [Indexed: 01/23/2023] Open
Abstract
Src-family kinases (SFKs) play important roles in human biology and are key drug targets as well. However, achieving selective inhibition of individual Src-family kinases is challenging due to the high similarity within the protein family. We describe rhodium(ii) conjugates that deliver both potent and selective inhibition of Src-family SH3 domains. Rhodium(ii) conjugates offer dramatic affinity enhancements due to interactions with specific and unique Lewis-basic histidine residues near the SH3 binding interface, allowing predictable, structure-guided inhibition of SH3 targets that are recalcitrant to traditional inhibitors. In one example, a simple metallopeptide binds the Lyn SH3 domain with 6 nM affinity and exhibits functional activation of Lyn kinase under biologically relevant concentrations (EC50 ∼ 200 nM).
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Affiliation(s)
- Farrukh Vohidov
- Department of Chemistry , Rice University , 6100 Main St. , Houston , Texas , USA .
| | - Sarah E Knudsen
- Department of Chemistry , Rice University , 6100 Main St. , Houston , Texas , USA .
| | - Paul G Leonard
- Department of Genomic Medicine , Core for Biomolecular Structure and Function , University of Texas , M.D. Anderson Cancer Center , Houston , Texas , USA
| | - Jun Ohata
- Department of Chemistry , Rice University , 6100 Main St. , Houston , Texas , USA .
| | - Michael J Wheadon
- Department of Chemistry , Rice University , 6100 Main St. , Houston , Texas , USA .
| | - Brian V Popp
- Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia , USA
| | - John E Ladbury
- Department of Molecular and Cellular Biology , University of Leeds , LS2 9JT , UK
| | - Zachary T Ball
- Department of Chemistry , Rice University , 6100 Main St. , Houston , Texas , USA .
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49
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Determinants of oligosaccharide specificity of the carbohydrate-binding modules of AMP-activated protein kinase. Biochem J 2015; 468:245-57. [DOI: 10.1042/bj20150270] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We solved the structures of β1- and β2-carbohydrate-binding modules (CBMs) of AMP-activated protein kinase (AMPK) bound to a branched carbohydrate. The additional threonine within the β2-module allows it to bind single α1,6-branched carbohydrates, such as partially degraded glycogen, with greater affinity.
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50
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The proline-rich region of 18.5 kDa myelin basic protein binds to the SH3-domain of Fyn tyrosine kinase with the aid of an upstream segment to form a dynamic complex in vitro. Biosci Rep 2014; 34:e00157. [PMID: 25343306 PMCID: PMC4266924 DOI: 10.1042/bsr20140149] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The intrinsically disordered 18.5 kDa classic isoform of MBP (myelin basic protein) interacts with Fyn kinase during oligodendrocyte development and myelination. It does so primarily via a central proline-rich SH3 (Src homology 3) ligand (T92–R104, murine 18.5 kDa MBP sequence numbering) that is part of a molecular switch due to its high degree of conservation and modification by MAP (mitogen-activated protein) and other kinases, especially at residues T92 and T95. Here, we show using co-transfection experiments of an early developmental oligodendroglial cell line (N19) that an MBP segment upstream of the primary ligand is involved in MBP–Fyn–SH3 association in cellula. Using solution NMR spectroscopy in vitro, we define this segment to comprise MBP residues (T62–L68), and demonstrate further that residues (V83–P93) are the predominant SH3-target, assessed by the degree of chemical shift change upon titration. We show by chemical shift index analysis that there is no formation of local poly-proline type II structure in the proline-rich segment upon binding, and by NOE (nuclear Overhauser effect) and relaxation measurements that MBP remains dynamic even while complexed with Fyn–SH3. The association is a new example first of a non-canonical SH3-domain interaction and second of a fuzzy MBP complex. MBP interacts with Fyn kinase during oligodendrocyte development and myelination. We show that there is no binding-induced PPII formation in the primary ligand segment, and that a region upstream is required for in vitro interaction.
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