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Maiti S, Singh A, Maji T, Saibo NV, De S. Experimental methods to study the structure and dynamics of intrinsically disordered regions in proteins. Curr Res Struct Biol 2024; 7:100138. [PMID: 38707546 PMCID: PMC11068507 DOI: 10.1016/j.crstbi.2024.100138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 05/07/2024] Open
Abstract
Eukaryotic proteins often feature long stretches of amino acids that lack a well-defined three-dimensional structure and are referred to as intrinsically disordered proteins (IDPs) or regions (IDRs). Although these proteins challenge conventional structure-function paradigms, they play vital roles in cellular processes. Recent progress in experimental techniques, such as NMR spectroscopy, single molecule FRET, high speed AFM and SAXS, have provided valuable insights into the biophysical basis of IDP function. This review discusses the advancements made in these techniques particularly for the study of disordered regions in proteins. In NMR spectroscopy new strategies such as 13C detection, non-uniform sampling, segmental isotope labeling, and rapid data acquisition methods address the challenges posed by spectral overcrowding and low stability of IDPs. The importance of various NMR parameters, including chemical shifts, hydrogen exchange rates, and relaxation measurements, to reveal transient secondary structures within IDRs and IDPs are presented. Given the high flexibility of IDPs, the review outlines NMR methods for assessing their dynamics at both fast (ps-ns) and slow (μs-ms) timescales. IDPs exert their functions through interactions with other molecules such as proteins, DNA, or RNA. NMR-based titration experiments yield insights into the thermodynamics and kinetics of these interactions. Detailed study of IDPs requires multiple experimental techniques, and thus, several methods are described for studying disordered proteins, highlighting their respective advantages and limitations. The potential for integrating these complementary techniques, each offering unique perspectives, is explored to achieve a comprehensive understanding of IDPs.
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Affiliation(s)
| | - Aakanksha Singh
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Tanisha Maji
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Nikita V. Saibo
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
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Ashton NW, Jaiswal N, Moreno NC, Semenova IV, D'Orlando DA, Latancia MT, McIntyre J, Woodgate R, Bezsonova I. A Novel Interaction Between RAD23A/B and Y-family DNA Polymerases. J Mol Biol 2023; 435:168353. [PMID: 37935254 PMCID: PMC10842004 DOI: 10.1016/j.jmb.2023.168353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/17/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
The Y-family DNA polymerases - Pol ι, Pol η, Pol κ and Rev1 - are most well-known for their roles in the DNA damage tolerance pathway of translesion synthesis (TLS). They function to overcome replication barriers by bypassing DNA damage lesions that cannot be normally replicated, allowing replication forks to continue without stalling. In this work, we demonstrate a novel interaction between each Y-family polymerase and the nucleotide excision repair (NER) proteins, RAD23A and RAD23B. We initially focus on the interaction between RAD23A and Pol ι, and through a series of biochemical, cell-based, and structural assays, find that the RAD23A ubiquitin-binding domains (UBA1 and UBA2) interact with separate sites within the Pol ι catalytic domain. While this interaction involves the ubiquitin-binding cleft of UBA2, Pol ι interacts with a distinct surface on UBA1. We further find that mutating or deleting either UBA domain disrupts the RAD23A-Pol ι interaction, demonstrating that both interactions are necessary for stable binding. We also provide evidence that both RAD23 proteins interact with Pol ι in a similar manner, as well as with each of the Y-family polymerases. These results shed light on the interplay between the different functions of the RAD23 proteins and reveal novel binding partners for the Y-family TLS polymerases.
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Affiliation(s)
- Nicholas W Ashton
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Nancy Jaiswal
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06032, USA.
| | - Natália Cestari Moreno
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Irina V Semenova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06032, USA.
| | - Dana A D'Orlando
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Marcela Teatin Latancia
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Justyna McIntyre
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06032, USA.
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Nguyen K, Jin Y, Howell M, Hsiao CHC, Wiemer AJ, Vinogradova O. Mutations to the BTN2A1 Linker Region Impact Its Homodimerization and Its Cytoplasmic Interaction with Phospho-Antigen-Bound BTN3A1. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:23-33. [PMID: 37171180 PMCID: PMC10330345 DOI: 10.4049/jimmunol.2200949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/26/2023] [Indexed: 05/13/2023]
Abstract
Intracellular binding of small-molecule phospho-Ags to the HMBPP receptor complex in infected cells leads to extracellular detection by T cells expressing the Vγ9Vδ2 TCR, a noncanonical method of Ag detection. The butyrophilin proteins BTN2A1 and BTN3A1 are part of the complex; however, their precise roles are unclear. We suspected that BTN2A1 and BTN3A1 form a tetrameric (dimer of dimers) structure, and we wanted to probe the importance of the BTN2A1 homodimer. We analyzed mutations to human BTN2A1, using internal domain or full-length BTN2A1 constructs, expressed in Escherichia coli or human K562 cells, that might disrupt its structure and/or function. Although BTN2A1 is a disulfide-linked homodimer, mutation of cysteine residues C247 and C265 did not affect the ability to stimulate T cell IFN-γ production by ELISA. Two mutations of the juxtamembrane region (at EKE282) failed to impact BTN2A1 function. In contrast, single point mutations (L318G and L325G) near the BTN2A1 B30.2 domain blocked phospho-Ag response. Size exclusion chromatography and nuclear magnetic resonance (NMR) experiments showed that the isolated BTN2A1 B30.2 domain is a homodimer, even in the absence of its extracellular and transmembrane region. [31P]-NMR experiments confirmed that HMBPP binds to BTN3A1 but not BTN2A1, and binding abrogates signals from both phosphorus atoms. Furthermore, the BTN2A1 L325G mutation but not the L318G mutation prevents both homodimerization of BTN2A1 internal domain constructs in size exclusion chromatography (and NMR) experiments and their binding to HMBPP-bound BTN3A1 in isothermal titration calorimetry experiments. Together, these findings support the importance of homodimerization within the BTN2A1 internal domain for phospho-Ag detection.
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Affiliation(s)
- Khiem Nguyen
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT
| | - Yiming Jin
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT
| | - Matthew Howell
- Department of Chemistry, University of Connecticut, Storrs, CT
| | | | - Andrew J Wiemer
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT
- Institute for Systems Genomics, University of Connecticut, Storrs, CT
| | - Olga Vinogradova
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT
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Casado-Combreras MÁ, Rivero-Rodríguez F, Elena-Real CA, Molodenskiy D, Díaz-Quintana A, Martinho M, Gerbaud G, González-Arzola K, Velázquez-Campoy A, Svergun D, Belle V, De la Rosa MA, Díaz-Moreno I. PP2A is activated by cytochrome c upon formation of a diffuse encounter complex with SET/TAF-Iβ. Comput Struct Biotechnol J 2022; 20:3695-3707. [PMID: 35891793 PMCID: PMC9293736 DOI: 10.1016/j.csbj.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Intrinsic protein flexibility is of overwhelming relevance for intermolecular recognition and adaptability of highly dynamic ensemble of complexes, and the phenomenon is essential for the understanding of numerous biological processes. These conformational ensembles-encounter complexes-lack a unique organization, which prevents the determination of well-defined high resolution structures. This is the case for complexes involving the oncoprotein SET/template-activating factor-Iβ (SET/TAF-Iβ), a histone chaperone whose functions and interactions are significantly affected by its intrinsic structural plasticity. Besides its role in chromatin remodeling, SET/TAF-Iβ is an inhibitor of protein phosphatase 2A (PP2A), which is a key phosphatase counteracting transcription and signaling events controlling the activity of DNA damage response (DDR) mediators. During DDR, SET/TAF-Iβ is sequestered by cytochrome c (Cc) upon migration of the hemeprotein from mitochondria to the cell nucleus. Here, we report that the nuclear SET/TAF-Iβ:Cc polyconformational ensemble is able to activate PP2A. In particular, the N-end folded, globular region of SET/TAF-Iβ (a.k.a. SET/TAF-Iβ ΔC)-which exhibits an unexpected, intrinsically highly dynamic behavior-is sufficient to be recognized by Cc in a diffuse encounter manner. Cc-mediated blocking of PP2A inhibition is deciphered using an integrated structural and computational approach, combining small-angle X-ray scattering, electron paramagnetic resonance, nuclear magnetic resonance, calorimetry and molecular dynamics simulations.
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Key Words
- ANP32B, Acidic leucine-rich nuclear phosphoprotein family member B
- BTFA, 3-bromo-1,1,1-trifluoroacetone
- CD, Circular dichroism
- CDK9, Cyclin-dependent kinase 9
- CW, Continuous wave
- Cc, Cytochrome c
- Cytochrome c
- DDR, DNA damage response
- DEER, Double electron–electron resonance
- DLS, Dynamic light scattering
- DMEM, Dulbecco’s modified Eagle’s medium
- DNA, Deoxyribonucleic acid
- DTT, Dithiotreitol
- Dmax, Maximum dimension
- EDTA, Ethylenediamine tetraacetic acid
- EGTA, Ethyleneglycol tetraacetic acid
- EPR, Electron paramagnetic resonance
- Encounter complex
- FBS, Fetal bovine serum
- GUI, Graphical user interface
- HEK, Human embryonic kidney cells
- HRP, Horseradish peroxidase
- I2PP2A, Inhibitor 2 of the protein phosphatase 2A
- I3PP2A, Inhibitor 3 of the protein phosphatase 2A
- INTAC, Integrator-PP2A complex
- IPTG, Isopropyl-β-D-1-thiogalactopyranoside
- ITC, Isothermal titration calorimetry
- Ip/Id, Intensity ratio of NMR resonances between paramagnetic and diamagnetic samples
- LB, Luria-Bertani
- MD, Molecular dynamics
- MTS, (1-acetoxy-2,2,5,5-tetramethyl-δ-3-pyrroline-3-methyl) methanethiosulfonate
- MTSL, (1-oxyl-2,2,5,5-tetramethyl- δ −3-pyrroline-3-methyl) methanethiosulfonate
- MW, Molecular weight
- Molecular dynamics
- NAP1, Nucleosome assembly protein 1
- NAPL, Nucleosome assembly protein L
- NMA, Normal mode analysis
- NMR, Nuclear magnetic resonance
- NPT, Constant number, pressure and temperature
- NVT, Constant number, volume and temperature
- Nuclear magnetic resonance
- OD600, Optical density measured at 600 nm
- OPC, Optimal 3-charge, 4-point rigid water model
- PCR, Polymerase chain reaction
- PME, Particle mesh Ewald
- PMSF, Phenylmethylsulfonyl fluoride
- PP2A, Protein phosphatase 2A
- PRE, Paramagnetic relaxation enhancement
- PVDF, Polyvinylidene fluoride
- Protein phosphatase 2A
- RNA, Ribonucleic acid
- RNApol II, RNA polymerase II
- Rg, Radius of gyration
- SAXS, Small-angle X-ray scattering
- SC, Sample changer
- SDS-PAGE, Sodium dodecylsulfate-polyacrylamide gel electrophoresis
- SDSL, Site-directed spin labeling
- SEC, Size-exclusion chromatography
- SET/TAF-Iβ
- SET/TAF-Iβ ΔC, SET/template-activating factor-Iβ construct lacking its C-terminal domain
- SET/TAF-Iβ, SET/template-activating factor-Iβ
- SPRi, Surface plasmon resonance imaging
- TAF-Iα, Template-activating factor-Iα
- TPBS, Tween 20-phosphate buffered saline
- VPS75, Vacuolar protein sorting-associated protein 75
- WT, Wild type
- XRD, X-ray diffraction
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Affiliation(s)
- Miguel Á. Casado-Combreras
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Francisco Rivero-Rodríguez
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Carlos A. Elena-Real
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
- Centre de Biologie Structurale (CBS), INSERM, Centre National de la Recherche Scientifique (CNRS) and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Antonio Díaz-Quintana
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Marlène Martinho
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Katiuska González-Arzola
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physic of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza. C. de Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, C. Pedro Cerbuna, 12, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), C. de Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Valérie Belle
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Miguel A. De la Rosa
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Irene Díaz-Moreno
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
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Mureddu LG, Vuister GW. Fragment-Based Drug Discovery by NMR. Where Are the Successes and Where can It Be Improved? Front Mol Biosci 2022; 9:834453. [PMID: 35252355 PMCID: PMC8895297 DOI: 10.3389/fmolb.2022.834453] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Over the last century, the definitions of pharmaceutical drug and drug discovery have changed considerably. Evolving from an almost exclusively serendipitous approach, drug discovery nowadays involves several distinct, yet sometimes interconnected stages aimed at obtaining molecules able to interact with a defined biomolecular target, and triggering a suitable biological response. At each of the stages, a wide range of techniques are typically employed to obtain the results required to move the project into the next stage. High Throughput Screening (HTS) and Fragment Based Drug Design (FBDD) are the two main approaches used to identify drug-like candidates in the early stages of drug discovery. Nuclear Magnetic Resonance (NMR) spectroscopy has many applications in FBDD and is used extensively in industry as well as in academia. In this manuscript, we discuss the paths of both successful and unsuccessful molecules where NMR had a crucial part in their development. We specifically focus on the techniques used and describe strengths and weaknesses of each stage by examining several case studies. More precisely, we examine the development history from the primary screening to the final lead optimisation of AZD3839 interacting with BACE-1, ABT-199 interacting with BCL2/XL and S64315 interacting with MCL-1. Based on these studies, we derive observations and conclusions regarding the FBDD process by NMR and discuss its potential improvements.
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Affiliation(s)
| | - Geerten W. Vuister
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
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Caldovic L, Bhuvanendran S, Jaiswal J. Assessing Protein Interactions for Clustering of Mitochondrial Urea Cycle Enzymes. Methods Mol Biol 2022; 2487:73-92. [PMID: 35687230 PMCID: PMC11270477 DOI: 10.1007/978-1-0716-2269-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Enzyme clustering is a phenomenon that involves partitioning of proteins that function together in a common subcellular or sub-organellar compartment. Traditional genetic, biochemical, and biophysical approaches for studying protein-protein interactions in complexes with defined stoichiometry yield inconclusive results when applied to clustered proteins. This chapter describes a combination of approaches to study clustered proteins including co-immunoprecipitation, biochemical co-localization in purified mitochondria, and super resolution imaging of endogenous proteins in situ. These approaches can be used to study interactions among proteins that form clusters. We will illustrate this approach by using the urea cycle enzymes that localize in the mitochondrial matrix, and form clusters at the inner mitochondrial membrane.
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Affiliation(s)
- Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA.
| | | | - Jyoti Jaiswal
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
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Li ZL, Buck M. Beyond history and "on a roll": The list of the most well-studied human protein structures and overall trends in the protein data bank. Protein Sci 2021; 30:745-760. [PMID: 33550681 DOI: 10.1002/pro.4038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/17/2022]
Abstract
Of the roughly 20,000 canonical human protein sequences, as of January 20, 2021, 7,077 proteins have had their full or partial, medium- to high-resolution structures determined by x-ray crystallography or other methods. Which of these proteins dominate the protein data bank (the PDB) and why? In this paper, we list the 273 top human protein structures based on the number of their PDB entries. This set of proteins accounts for more than 40% of all available human PDB entries and represent past trends as well as current status for protein structural biology. We briefly discuss the relationship which some of the prominent protein structures have with protein research as a whole and mention their relevance to human diseases. The top-10 soluble and membrane proteins are all well-known (most of their first structures being deposited more than 30 years ago). Overall, there is no dramatic change in recent trends in the PDB. Remarkably, the number of structure depositions has grown nearly exponentially over the last 10 or more years (with a doubling time of 7 years for proteins, obtained from any organism). Growth in human protein structures is slightly faster (at 5.9 years). The information in this paper may be informative to senior scientists but also inspire researchers who are new to protein science, providing the year 2021 snap-shot for the state of protein structural biology.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA.,Department of Pharmacology; Department of Neurosciences and Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA
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8
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Bagheri Y, Ali AA, You M. Current Methods for Detecting Cell Membrane Transient Interactions. Front Chem 2020; 8:603259. [PMID: 33365301 PMCID: PMC7750205 DOI: 10.3389/fchem.2020.603259] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/16/2020] [Indexed: 12/28/2022] Open
Abstract
Short-lived cell membrane complexes play a key role in regulating cell signaling and communication. Many of these complexes are formed based on low-affinity and transient interactions among various lipids and proteins. New techniques have emerged to study these previously overlooked membrane transient interactions. Exciting functions of these transient interactions have been discovered in cellular events such as immune signaling, host-pathogen interactions, and diseases such as cancer. In this review, we have summarized current experimental methods that allow us to detect and analyze short-lived cell membrane protein-protein, lipid-protein, and lipid-lipid interactions. These methods can provide useful information about the strengths, kinetics, and/or spatial patterns of membrane transient interactions. However, each method also has its own limitations. We hope this review can be used as a guideline to help the audience to choose proper approaches for studying membrane transient interactions in different membrane trafficking and cell signaling events.
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Affiliation(s)
| | | | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
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Ille AM, Kishel E, Bodea R, Ille A, Lamont H, Amico-Ruvio S. Protein LY6E as a candidate for mediating transport of adeno-associated virus across the human blood-brain barrier. J Neurovirol 2020; 26:769-778. [PMID: 32839948 DOI: 10.1007/s13365-020-00890-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 07/14/2020] [Accepted: 08/04/2020] [Indexed: 01/06/2023]
Abstract
The blood-brain barrier (BBB) is a major obstacle for the treatment of central nervous system (CNS) disorders. Significant progress has been made in developing adeno-associated virus (AAV) variants with increased ability to cross the BBB in mice. However, these variants are not efficacious in non-human primates. Herein, we employed various bioinformatic techniques to identify lymphocyte antigen-6E (LY6E) as a candidate for mediating transport of AAV across the human BBB based on the previously determined mechanism of transport in mice. Our results provide insight into future discovery and optimization of AAV variants for CNS gene delivery in humans.
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Affiliation(s)
- Alexander M Ille
- Graduate School of Biomedical Sciences, Rutgers University, Newark, NJ, 07103, USA.,STEM Biomedical, Kitchener, ON, N2M 3B9, Canada
| | - Eric Kishel
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | - Raoul Bodea
- STEM Biomedical, Kitchener, ON, N2M 3B9, Canada
| | - Anetta Ille
- STEM Biomedical, Kitchener, ON, N2M 3B9, Canada
| | - Hannah Lamont
- Graduate School of Biomedical Sciences, Rutgers University, Newark, NJ, 07103, USA
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Dhusia K, Su Z, Wu Y. Understanding the Impacts of Conformational Dynamics on the Regulation of Protein-Protein Association by a Multiscale Simulation Method. J Chem Theory Comput 2020; 16:5323-5333. [PMID: 32667783 PMCID: PMC10829009 DOI: 10.1021/acs.jctc.0c00439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Complexes formed among diverse proteins carry out versatile functions in nearly all physiological processes. Association rates which measure how fast proteins form various complexes are of fundamental importance to characterize their functions. The association rates are not only determined by the energetic features at binding interfaces of a protein complex but also influenced by the intrinsic conformational dynamics of each protein in the complex. Unfortunately, how this conformational effect regulates protein association has never been calibrated on a systematic level. To tackle this problem, we developed a multiscale strategy to incorporate the information on protein conformational variations from Langevin dynamic simulations into a kinetic Monte Carlo algorithm of protein-protein association. By systematically testing this approach against a large-scale benchmark set, we found the association of a protein complex with a relatively rigid structure tends to be reduced by its conformational fluctuations. With specific examples, we further show that higher degrees of structural flexibility in various protein complexes can facilitate the searching and formation of intermolecular interactions and thereby accelerate their associations. In general, the integration of conformational dynamics can improve the correlation between experimentally measured association rates and computationally derived association probabilities. Finally, we analyzed the statistical distributions of different secondary structural types on protein-protein binding interfaces and their preference to the change of association rates. Our study, to the best of our knowledge, is the first computational method that systematically estimates the impacts of protein conformational dynamics on protein-protein association. It throws lights on the molecular mechanisms of how protein-protein recognition is kinetically modulated.
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Affiliation(s)
- Kalyani Dhusia
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
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11
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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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12
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Hoop CL, Zhu J, Bhattacharya S, Tobita CA, Radford SE, Baum J. Collagen I Weakly Interacts with the β-Sheets of β 2-Microglobulin and Enhances Conformational Exchange To Induce Amyloid Formation. J Am Chem Soc 2020; 142:1321-1331. [PMID: 31875390 PMCID: PMC7135851 DOI: 10.1021/jacs.9b10421] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Amyloidogenesis is
significant in both protein function and pathology.
Amyloid formation of folded, globular proteins is commonly initiated
by partial or complete unfolding. However, how this unfolding event
is triggered for proteins that are otherwise stable in their native
environments is not well understood. The accumulation of the immunoglobulin
protein β2-microglobulin (β2m) into
amyloid plaques in the joints of long-term hemodialysis patients is
the hallmark of dialysis-related amyloidosis (DRA). While β2m does not form amyloid unassisted near neutral pH in vitro, the localization of β2m deposits
to joint spaces suggests a role for the local extracellular matrix
(ECM) proteins, specifically collagens, in promoting amyloid formation.
Indeed, collagen and other ECM components have been observed to facilitate
β2m amyloid formation, but the large size and anisotropy
of the complex, combined with the low affinity of these interactions,
have limited atomic-level elucidation of the amyloid-promoting mechanism(s)
by these molecules. Using solution NMR approaches that uniquely probe
weak interactions in large molecular weight complexes, we are able
to map the binding interfaces on β2m for collagen
I and detect collagen I-induced μs–ms time-scale dynamics
in the β2m backbone. By combining solution NMR relaxation
methods and 15N-dark-state exchange saturation transfer
experiments, we propose a model in which weak, multimodal collagen
I−β2m interactions promote exchange with a
minor population of amyloid-competent species to induce fibrillogenesis.
The results portray the intimate role of the environment in switching
an innocuous protein into an amyloid-competent state, rationalizing
the localization of amyloid deposits in DRA.
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Affiliation(s)
- Cody L Hoop
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Jie Zhu
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | | | - Caitlyn A Tobita
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
| | - Jean Baum
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
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13
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Ding Z, Kihara D. Computational identification of protein-protein interactions in model plant proteomes. Sci Rep 2019; 9:8740. [PMID: 31217453 PMCID: PMC6584649 DOI: 10.1038/s41598-019-45072-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/30/2019] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) play essential roles in many biological processes. A PPI network provides crucial information on how biological pathways are structured and coordinated from individual protein functions. In the past two decades, large-scale PPI networks of a handful of organisms were determined by experimental techniques. However, these experimental methods are time-consuming, expensive, and are not easy to perform on new target organisms. Large-scale PPI data is particularly sparse in plant organisms. Here, we developed a computational approach for detecting PPIs trained and tested on known PPIs of Arabidopsis thaliana and applied to three plants, Arabidopsis thaliana, Glycine max (soybean), and Zea mays (maize) to discover new PPIs on a genome-scale. Our method considers a variety of features including protein sequences, gene co-expression, functional association, and phylogenetic profiles. This is the first work where a PPI prediction method was developed for is the first PPI prediction method applied on benchmark datasets of Arabidopsis. The method showed a high prediction accuracy of over 90% and very high precision of close to 1.0. We predicted 50,220 PPIs in Arabidopsis thaliana, 13,175,414 PPIs in corn, and 13,527,834 PPIs in soybean. Newly predicted PPIs were classified into three confidence levels according to the availability of existing supporting evidence and discussed. Predicted PPIs in the three plant genomes are made available for future reference.
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Affiliation(s)
- Ziyun Ding
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, 45229, USA.
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14
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Ortega-Roldan JL, Blackledge M, Jensen MR. Characterizing Protein-Protein Interactions Using Solution NMR Spectroscopy. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 1764:73-85. [PMID: 29605909 DOI: 10.1007/978-1-4939-7759-8_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this chapter, we describe how NMR chemical shift titrations can be used to study the interaction between two proteins with emphasis on mapping the interface of the complex and determining the binding affinity from a quantitative analysis of the experimental data. In particular, we discuss the appearance of NMR spectra in different chemical exchange regimes (fast, intermediate, and slow) and how these regimes affect NMR data analysis.
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15
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Cao S, Chung S, Kim S, Li Z, Manor D, Buck M. K-Ras G-domain binding with signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2): membrane association, protein orientation, and function. J Biol Chem 2019; 294:7068-7084. [PMID: 30792310 DOI: 10.1074/jbc.ra118.004021] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/12/2018] [Indexed: 12/14/2022] Open
Abstract
Ras genes potently drive human cancers, with mutated proto-oncogene GTPase KRAS4B (K-Ras4B) being the most abundant isoform. Targeted inhibition of oncogenic gene products is considered the "holy grail" of present-day cancer therapy, and recent discoveries of small-molecule KRas4B inhibitors were made thanks to a deeper understanding of the structure and dynamics of this GTPase. Because interactions with biological membranes are key for Ras function, Ras-lipid interactions have become a major focus, especially because such interactions evidently involve both the Ras C terminus for lipid anchoring and its G-protein domain. Here, using NMR spectroscopy and molecular dynamics simulations complemented by biophysical- and cell-biology assays, we investigated the interaction between K-Ras4B with the signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2). We discovered that the β2 and β3 strands as well as helices 4 and 5 of the GTPase G-domain bind to PIP2 and identified the specific residues in these structural elements employed in these interactions, likely occurring in two K-Ras4B orientation states relative to the membrane. Importantly, we found that some of these residues known to be oncogenic when mutated (D47K, D92N, K104M, and D126N) are critical for K-Ras-mediated transformation of fibroblast cells, but do not substantially affect basal and assisted nucleotide hydrolysis and exchange. Moreover, the K104M substitution abolished localization of K-Ras to the plasma membrane. The findings suggest that specific G-domain residues can critically regulate Ras function by mediating interactions with membrane-associated PIP2 lipids; these insights that may inform the future design of therapeutic reagents targeting Ras activity.
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Affiliation(s)
- Shufen Cao
- From the Departments of Physiology and Biophysics
| | | | | | - Zhenlu Li
- From the Departments of Physiology and Biophysics
| | - Danny Manor
- Nutrition, .,Pharmacology, and.,the Case Comprehensive Cancer Center and
| | - Matthias Buck
- From the Departments of Physiology and Biophysics, .,the Case Comprehensive Cancer Center and.,Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106 and.,Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
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16
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Chasapis CT. Building Bridges Between Structural and Network-Based Systems Biology. Mol Biotechnol 2019; 61:221-229. [DOI: 10.1007/s12033-018-0146-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Sarkar A, Mehra M, Dasgupta D, Negi L, Saxena A. Evidence of Cooperativity among van der Waals Interactions in Segmented Polysiloxane. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01636] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alok Sarkar
- Corporate R&D Center, Momentive Performance Materials Inc., Survey No. 09, Hosur Road, Electronic City (West), Bangalore 560100, India
| | - Meenal Mehra
- Corporate R&D Center, Momentive Performance Materials Inc., Survey No. 09, Hosur Road, Electronic City (West), Bangalore 560100, India
| | - Debarshi Dasgupta
- Corporate R&D Center, Momentive Performance Materials Inc., Survey No. 09, Hosur Road, Electronic City (West), Bangalore 560100, India
| | - Lalit Negi
- Momentive Performance
Materials Inc., B-3, Sipcot, Oragadam, Kancheepuram Dist., Sriperumpudur 602105, India
| | - Anubhav Saxena
- Corporate R&D Center, Momentive Performance Materials Inc., Survey No. 09, Hosur Road, Electronic City (West), Bangalore 560100, India
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18
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Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
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Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
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19
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Ding Z, Kihara D. Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2018; 93:e62. [PMID: 29927082 PMCID: PMC6097941 DOI: 10.1002/cpps.62] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding protein-protein interactions (PPIs) in a cell is essential for learning protein functions, pathways, and mechanism of diseases. PPIs are also important targets for developing drugs. Experimental methods, both small-scale and large-scale, have identified PPIs in several model organisms. However, results cover only a part of PPIs of organisms; moreover, there are many organisms whose PPIs have not yet been investigated. To complement experimental methods, many computational methods have been developed that predict PPIs from various characteristics of proteins. Here we provide an overview of literature reports to classify computational PPI prediction methods that consider different features of proteins, including protein sequence, genomes, protein structure, function, PPI network topology, and those which integrate multiple methods. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ziyun Ding
- Department of Biological Science, Purdue University, West Lafayette, IN, 47907 USA
| | - Daisuke Kihara
- Department of Biological Science, Purdue University, West Lafayette, IN, 47907 USA
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907 USA
- Corresponding author: DK; , Phone: 1-765-496-2284 (DK)
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20
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Nguyen K, Li J, Puthenveetil R, Lin X, Poe MM, Hsiao CHC, Vinogradova O, Wiemer AJ. The butyrophilin 3A1 intracellular domain undergoes a conformational change involving the juxtamembrane region. FASEB J 2017; 31:4697-4706. [PMID: 28705810 DOI: 10.1096/fj.201601370rr] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/27/2017] [Indexed: 12/23/2022]
Abstract
Small isoprenoid diphosphates, such as (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP), are ligands of the internal domain of BTN3A1. Ligand binding in target cells promotes activation of Vγ9Vδ2 T cells. We demonstrate by small-angle X-ray scattering (SAXS) that HMBPP binding to the internal domain of BTN3A1 induces a conformational change in the position of the B30.2 domain relative to the juxtamembrane (JM) region. To better understand the molecular details of this conformational rearrangement, NMR spectroscopy was used to discover that the JM region interacts with HMBPP, specifically at the diphosphate. The spectral location of the affected amide peaks, partial NMR assignments, and JM mutants (ST296AA or T304A) investigated, confirm that the backbone amide of at least one Thr (Thr304), adjacent to conserved Ser, comes close to the HMBPP diphosphate, whereas double mutation of nonconserved residues (Ser/Thr296/297) may perturb the local fold. Cellular mutation of either of the identified Thr residues reduces the activation of Vγ9Vδ2 T cells by HMBPP, zoledronate, and POM2-C-HMBP, but not by a partial agonist BTN3 antibody. Taken together, our results show that ligand binding to BTN3A1 induces a conformational change within the intracellular domain that involves the JM region and is required for full activation.-Nguyen, K., Li, J., Puthenveetil, R., Lin, X., Poe, M. M., Hsiao, C.-H. C., Vinogradova, O., Wiemer, A. J. The butyrophilin 3A1 intracellular domain undergoes a conformational change involving the juxtamembrane region.
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Affiliation(s)
- Khiem Nguyen
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, USA
| | - Jin Li
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, USA
| | - Robbins Puthenveetil
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Xiaochen Lin
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, USA
| | - Michael M Poe
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, USA
| | | | - Olga Vinogradova
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, USA
| | - Andrew J Wiemer
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, USA; .,Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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21
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Karki I, Christen MT, Spiriti J, Slack RL, Oda M, Kanaori K, Zuckerman DM, Ishima R. Entire-Dataset Analysis of NMR Fast-Exchange Titration Spectra: A Mg 2+ Titration Analysis for HIV-1 Ribonuclease H Domain. J Phys Chem B 2016; 120:12420-12431. [PMID: 27973819 DOI: 10.1021/acs.jpcb.6b08323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This article communicates our study to elucidate the molecular determinants of weak Mg2+ interaction with the ribonuclease H (RNH) domain of HIV-1 reverse transcriptase in solution. As the interaction is weak (a ligand-dissociation constant >1 mM), nonspecific Mg2+ interaction with the protein or interaction of the protein with other solutes that are present in the buffer solution can confound the observed Mg2+-titration data. To investigate these indirect effects, we monitored changes in the chemical shifts of backbone amides of RNH by recording NMR 1H-15N heteronuclear single-quantum coherence spectra upon titration of Mg2+ into an RNH solution. We performed the titration under three different conditions: (1) in the absence of NaCl, (2) in the presence of 50 mM NaCl, and (3) at a constant 160 mM Cl- concentration. Careful analysis of these three sets of titration data, along with molecular dynamics simulation data of RNH with Na+ and Cl- ions, demonstrates two characteristic phenomena distinct from the specific Mg2+ interaction with the active site: (1) weak interaction of Mg2+, as a salt, with the substrate-handle region of the protein and (2) overall apparent lower Mg2+ affinity in the absence of NaCl compared to that in the presence of 50 mM NaCl. A possible explanation may be that the titrated MgCl2 is consumed as a salt and interacts with RNH in the absence of NaCl. In addition, our data suggest that Na+ increases the kinetic rate of the specific Mg2+ interaction at the active site of RNH. Taken together, our study provides biophysical insight into the mechanism of weak metal interaction on a protein.
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Affiliation(s)
- Ichhuk Karki
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Martin T Christen
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Justin Spiriti
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Ryan L Slack
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Masayuki Oda
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Kenji Kanaori
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Daniel M Zuckerman
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Rieko Ishima
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
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22
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Zhao L, Ehrt C, Koch O, Wu YW. One-Pot N2C/C2C/N2N Ligation To Trap Weak Protein-Protein Interactions. Angew Chem Int Ed Engl 2016; 55:8129-33. [PMID: 27213482 DOI: 10.1002/anie.201601299] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/13/2016] [Indexed: 01/19/2023]
Abstract
Weak transient protein-protein interactions (PPIs) play an essential role in cellular dynamics. However, it is challenging to obtain weak protein complexes owing to their short lifetime. Herein we present a general and facile method for trapping weak PPIs in an unbiased manner using proximity-induced ligations. To expand the chemical ligation spectrum, we developed novel N2N (N-terminus to N-terminus) and C2C (C-terminus to C-terminus) ligation approaches. By using N2C (N-terminus to C-terminus), N2N, and C2C ligations in one pot, the interacting proteins were linked. The weak Ypt1:GDI interaction drove C2C ligation with t1/2 of 4.8 min and near quantitative conversion. The Ypt1-GDI conjugate revealed that binding of Ypt1 G-domain causes opening of the lipid-binding site of GDI, which can accommodate one prenyl group, giving insights into Rab membrane recycling. Moreover, we used this strategy to trap the KRas homodimer, which plays an important role in Ras signaling.
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Affiliation(s)
- Lei Zhao
- Chemical Genomics Center of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany
| | - Christiane Ehrt
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Oliver Koch
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Yao-Wen Wu
- Chemical Genomics Center of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany.
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23
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Zhao L, Ehrt C, Koch O, Wu YW. Eintopf-N2C/C2C/N2N-Proteinligationsstrategien zur Analyse schwacher Protein-Protein-Wechselwirkungen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lei Zhao
- Chemical Genomics Center der Max-Planck-Gesellschaft; Otto-Hahn-Straße 15 44227 Dortmund Deutschland
| | - Christiane Ehrt
- Technische Universität Dortmund; Fakultät für Chemie und Chemische Biologie; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Oliver Koch
- Technische Universität Dortmund; Fakultät für Chemie und Chemische Biologie; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Yao-Wen Wu
- Chemical Genomics Center der Max-Planck-Gesellschaft; Otto-Hahn-Straße 15 44227 Dortmund Deutschland
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24
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Visualizing the Ensemble Structures of Protein Complexes Using Chemical Cross-Linking Coupled with Mass Spectrometry. BIOPHYSICS REPORTS 2015; 1:127-138. [PMID: 27340691 PMCID: PMC4871902 DOI: 10.1007/s41048-015-0015-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/11/2015] [Indexed: 11/30/2022] Open
Abstract
Graphical Abstract ![]()
Abstract Chemical cross-linking coupled with mass spectrometry (CXMS) identifies protein residues that are close in space, and has been increasingly used for modeling the structures of protein complexes. Here we show that a single structure is usually sufficient to account for the intermolecular cross-links identified for a stable complex with sub-µmol/L binding affinity. In contrast, we show that the distance between two cross-linked residues in the different subunits of a transient or fleeting complex may exceed the maximum length of the cross-linker used, and the cross-links cannot be fully accounted for with a unique complex structure. We further show that the seemingly incompatible cross-links identified with high confidence arise from alternative modes of protein-protein interactions. By converting the intermolecular cross-links to ambiguous distance restraints, we established a rigid-body simulated annealing refinement protocol to seek the minimum set of conformers collectively satisfying the CXMS data. Hence we demonstrate that CXMS allows the depiction of the ensemble structures of protein complexes and elucidates the interaction dynamics for transient and fleeting complexes. Electronic supplementary material The online version of this article (doi:10.1007/s41048-015-0015-y) contains supplementary material, which is available to authorized users.
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Ma KY, Liu ZQ, Lin JY, Li JL, Qiu GF. Molecular characterization of a novel ovary-specific gene fem-1 homolog from the oriental river prawn, Macrobrachium nipponense. Gene 2015; 575:244-52. [PMID: 26367327 DOI: 10.1016/j.gene.2015.08.070] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/16/2015] [Accepted: 08/31/2015] [Indexed: 01/23/2023]
Abstract
The feminization-1 (fem-1) gene is characterized by one of the most common protein-protein interaction motifs, ankyrin repeat motifs, displays many expression patterns in vertebrates and invertebrates, and plays an essential role in the sex-determination/differentiation pathway in Caenorhabditis elegans. In this study, a fem-1 homolog, designated as Mnfem-1, was first cloned from the oriental river prawn Macrobrachium nipponense. The prawn Mnfem-1 gene consists of six exons and five introns. The full-length cDNA (2603bp) of Mnfem-1 contains an open reading frame (ORF) encoding a protein of 622 amino acids. The Mnfem-1 RNA and protein are exclusively expressed in the ovary in adult prawns as revealed by RT-PCR and immunofluorescence analysis, respectively. In situ hybridization results showed that strong positive signals were concentrated at the edge of the previtellogenic and vitellogenic oocyte. During embryogenesis, Mnfem-1 is highly expressed in both unfertilized eggs and embryos at cleavage stage and thereafter dropped to a low level from blastula to zoea, indicating that the Mnfem-1 in early embryos is maternal. After hatching, the Mnfem-1 expression significantly increased in the larvae at length of 2cm, an important stage of sex differentiation. Yeast two hybridization results showed that the Mnfem-1 protein can be potentially interactive with cathepsin L and proteins containing the domains of insulinase, ankyrin or ubiquitin. Our results suggested that Mnfem-1 could have roles in prawn ovarian development and sex determination/differentiation.
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Affiliation(s)
- Ke-Yi Ma
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, PR China
| | - Zhi-Qiang Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jing-Yun Lin
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jia-Le Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, PR China; E-Institute of Shanghai Universities, Shanghai Ocean University, Shanghai 201306, PR China.
| | - Gao-Feng Qiu
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, PR China; E-Institute of Shanghai Universities, Shanghai Ocean University, Shanghai 201306, PR China.
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26
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Rees JS, Li XW, Perrett S, Lilley KS, Jackson AP. Protein Neighbors and Proximity Proteomics. Mol Cell Proteomics 2015; 14:2848-56. [PMID: 26355100 PMCID: PMC4638030 DOI: 10.1074/mcp.r115.052902] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Indexed: 12/31/2022] Open
Abstract
Within cells, proteins can co-assemble into functionally integrated and spatially restricted multicomponent complexes. Often, the affinities between individual proteins are relatively weak, and proteins within such clusters may interact only indirectly with many of their other protein neighbors. This makes proteomic characterization difficult using methods such as immunoprecipitation or cross-linking. Recently, several groups have described the use of enzyme-catalyzed proximity labeling reagents that covalently tag the neighbors of a targeted protein with a small molecule such as fluorescein or biotin. The modified proteins can then be isolated by standard pulldown methods and identified by mass spectrometry. Here we will describe the techniques as well as their similarities and differences. We discuss their applications both to study protein assemblies and to provide a new way for characterizing organelle proteomes. We stress the importance of proteomic quantitation and independent target validation in such experiments. Furthermore, we suggest that there are biophysical and cell-biological principles that dictate the appropriateness of enzyme-catalyzed proximity labeling methods to address particular biological questions of interest.
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Affiliation(s)
- Johanna S Rees
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW, the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Xue-Wen Li
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Sarah Perrett
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Kathryn S Lilley
- the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Antony P Jackson
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW,
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Brahmkhatri VP, Chandra K, Dubey A, Atreya HS. An ultrastable conjugate of silver nanoparticles and protein formed through weak interactions. NANOSCALE 2015; 7:12921-12931. [PMID: 26166696 DOI: 10.1039/c5nr03047a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In recent years, silver nanoparticles (AgNPs) have attracted significant attention owing to their unique physicochemical, optical, conductive and antimicrobial properties. One of the properties of AgNPs which is crucial for all applications is their stability. In the present study we unravel a mechanism through which silver nanoparticles are rendered ultrastable in an aqueous solution in complex with the protein ubiquitin (Ubq). This involves a dynamic and reversible association and dissociation of ubiquitin from the surface of AgNP. The exchange occurs at a rate much greater than 25 s(-1) implying a residence time of <40 ms for the protein. The AgNP-Ubq complex remains stable for months due to steric stabilization over a wide pH range compared to unconjugated AgNPs. NMR studies reveal that the protein molecules bind reversibly to AgNP with an approximate dissociation constant of 55 μM and undergo fast exchange. At pH > 4 the positively charged surface of the protein comes in contact with the citrate capped AgNP surface. Further, NMR relaxation-based experiments suggest that in addition to the dynamic exchange, a conformational rearrangement of the protein takes place upon binding to AgNP. The ultrastability of the AgNP-Ubq complex was found to be useful for its anti-microbial activity, which allowed the recycling of this complex multiple times without the loss of stability. Altogether, the study provides new insights into the mechanism of protein-silver nanoparticle interactions and opens up new avenues for its application in a wide range of systems.
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28
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Cui W, Zhang H, Blankenship RE, Gross ML. Electron-capture dissociation and ion mobility mass spectrometry for characterization of the hemoglobin protein assembly. Protein Sci 2015; 24:1325-32. [PMID: 26032343 DOI: 10.1002/pro.2712] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/19/2015] [Indexed: 12/12/2022]
Abstract
Native spray has the potential to probe biophysical properties of protein assemblies. Here we report an investigation using both ECD top-down sequencing with an FTICR mass spectrometer and ion mobility (IM) measurements on a Q-TOF to investigate the collisionally induced unfolding of a native-like heterogeneous tetrameric assembly, human hemoglobin (hHb), in the gas phase. To our knowledge, this is the first report combining ECD and ion-mobility data on the same target protein assembly to delineate the effects of collisional activation on both assembly size and the extent and location of fragmentation. Although the collision-induced unfolding of the hemoglobin assembly is clearly seen by both IMMS and ECD, the latter delineates the regions that increasingly unfold as the collision energy is increased. The results are consistent with previous outcomes for homogeneous protein assemblies and reinforce our interpretation that activation opens the structure of the protein assembly from the flexible regions to make available ECD fragmentation, without dissociating the component proteins.
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Affiliation(s)
- Weidong Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130.,Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
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29
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The low-affinity complex of cytochrome c and its peroxidase. Nat Commun 2015; 6:7073. [PMID: 25944250 PMCID: PMC4432590 DOI: 10.1038/ncomms8073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/30/2015] [Indexed: 01/07/2023] Open
Abstract
The complex of yeast cytochrome c peroxidase and cytochrome c is a paradigm of the biological electron transfer (ET). Building on seven decades of research, two different models have been proposed to explain its functional redox activity. One postulates that the intermolecular ET occurs only in the dominant, high-affinity protein–protein orientation, while the other posits formation of an additional, low-affinity complex, which is much more active than the dominant one. Unlike the high-affinity interaction—extensively studied by X-ray crystallography and NMR spectroscopy—until now the binding of cytochrome c to the low-affinity site has not been observed directly, but inferred mainly from kinetics experiments. Here we report the structure of this elusive, weak protein complex and show that it consists of a dominant, inactive bound species and an ensemble of minor, ET-competent protein–protein orientations, which summarily account for the experimentally determined value of the ET rate constant. The redox activity of cytochrome c in complex with its peroxidase has been rationalized by two possible models; a readily observable high-affinity complex and a more elusive but potentially more active low-affinity complex. Here, the authors provide an NMR-based structural mapping of this low-affinity complex.
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30
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Liu Z, Gong Z, Dong X, Tang C. Transient protein-protein interactions visualized by solution NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:115-22. [PMID: 25896389 DOI: 10.1016/j.bbapap.2015.04.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 01/18/2023]
Abstract
Proteins interact with each other to establish their identities in cell. The affinities for the interactions span more than ten orders of magnitude, and KD values in μM-mM regimen are considered transient and are important in cell signaling. Solution NMR including diamagnetic and paramagnetic techniques has enabled atomic-resolution depictions of transient protein-protein interactions. Diamagnetic NMR allows characterization of protein complexes with KD values up to several mM, whereas ultraweak and fleeting complexes can be modeled with the use of paramagnetic NMR especially paramagnetic relaxation enhancement (PRE). When tackling ever-larger protein complexes, PRE can be particularly useful in providing long-range intermolecular distance restraints. As NMR measurements are averaged over the ensemble of complex structures, structural information for dynamic protein-protein interactions besides the stereospecific one can often be extracted. Herein the protein interaction dynamics are exemplified by encounter complexes, alternative binding modes, and coupled binding/folding of intrinsically disordered proteins. Further integration of NMR with other biophysical techniques should allow better visualization of transient protein-protein interactions. In particular, single-molecule data may facilitate the interpretation of ensemble-averaged NMR data. Though same structures of proteins and protein complexes were found in cell as in diluted solution, we anticipate that the dynamics of transient protein protein-protein interactions be different, which awaits awaits exploration by NMR. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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Affiliation(s)
- Zhu Liu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310028, China; Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310028, China
| | - Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Xu Dong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China.
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31
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Abstract
Solution-state NMR has been widely applied to determine the three-dimensional structure, dynamics, and molecular interactions of proteins. The designs of experiments used in protein NMR differ from those used for small-molecule NMR, primarily because the information available prior to an experiment, such as molecular mass and knowledge of the primary structure, is unique for proteins compared to small molecules. In this review article, protein NMR for structural biology is introduced with comparisons to small-molecule NMR, such as descriptions of labeling strategies and the effects of molecular dynamics on relaxation. Next, applications for protein NMR are reviewed, especially practical aspects for protein-observed ligand-protein interaction studies. Overall, the following topics are described: (1) characteristics of protein NMR, (2) methods to detect protein-ligand interactions by NMR, and (3) practical aspects of carrying out protein-observed inhibitor-protein interaction studies.
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Affiliation(s)
- Rieko Ishima
- Address correspondence to Rieko Ishima: Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Tel: 412-648-9056; Fax: 412-648-9008;
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Lin X, Vinogradova O. Phospho-Tyrosine(s) vs. Phosphatidylinositol Binding in Shc Mediated Integrin Signaling. ACTA ACUST UNITED AC 2015; 5:17-31. [PMID: 25893141 PMCID: PMC4397963 DOI: 10.4236/ajmb.2015.52003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Shc adaptor protein, particularly its p52 isoform, has been identified as a primary signaling partner for the tyrosine(s)-phosphorylated cytoplasmic tails of activated β3 integrins. Inspired by our recent structure of the Shc PTB domain in complex with a bi-phosphorylated peptide derived from β3 cytoplasmic tail, we have initiated the investigation of Shc interaction with phospholipids of the membrane. We are particularly focused on PtdIns and their effects on Shc mediated integrin signaling in vitro. Here we present thermodynamic profiles and molecular details of the interactions between Shc, integrin, and PtdIns, all of which have been studied by ITC and solution NMR methods. A model of p52 Shc interaction with phosphorylated β3 integrin cytoplasmic tail at the cytosolic face of the plasma membrane is proposed based on these data.
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Affiliation(s)
- Xiaochen Lin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut at Storrs, Storrs, USA
| | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut at Storrs, Storrs, USA
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33
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Thompson PM, Beck MR, Campbell SL. Protein-protein interaction analysis by nuclear magnetic resonance spectroscopy. Methods Mol Biol 2015; 1278:267-279. [PMID: 25859955 DOI: 10.1007/978-1-4939-2425-7_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Nuclear magnetic resonance (NMR) has continued to evolve as a powerful method, with an increase in the number of pulse sequences and techniques available to study protein-protein interactions. In this chapter, a straightforward method to map a protein-protein interface and design a structural model is described, using chemical shift perturbation, paramagnetic relaxation enhancement, and data-driven docking.
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Affiliation(s)
- Peter M Thompson
- Department of Biochemistry and Biophysics, University of North Carolina, 120 Mason Farm Road, CB # 7260, 3100A-C Genetic Medicine, Chapel Hill, NC, 27599, USA
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34
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Xing Q, Huang P, Yang J, Sun JQ, Gong Z, Dong X, Guo DC, Chen SM, Yang YH, Wang Y, Yang MH, Yi M, Ding YM, Liu ML, Zhang WP, Tang C. Visualizing an Ultra-Weak Protein-Protein Interaction in Phosphorylation Signaling. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Kamnesky G, Hirschhorn O, Shaked H, Chen J, Yao L, Chill JH. Molecular determinants of tetramerization in the KcsA cytoplasmic domain. Protein Sci 2014; 23:1403-16. [PMID: 25042120 DOI: 10.1002/pro.2525] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 11/11/2022]
Abstract
The cytoplasmic C-terminal domain (CTD) of KcsA, a bacterial homotetrameric potassium channel, is an amphiphilic domain that forms a helical bundle with four-fold symmetry mediated by hydrophobic and electrostatic interactions. Previously we have established that a CTD-derived 34-residue peptide associates into a tetramer in a pH-dependent manner (Kamnesky et al., JMB 2012;418:237-247). Here we further investigate the molecular determinants of tetramer formation in the CTD by characterizing the kinetics of monomer-tetramer equilibrium for 10 alanine mutants using NMR, sedimentation equilibrium (SE) and molecular dynamics simulation. NMR and SE concur in finding single-residue contributions to tetramer stability to be in the 0.5 to 3.5 kcal/mol range. Hydrophobic interactions between residues lining the tetramer core generally contributed more to formation of tetramer than electrostatic interactions between residues R147, D149 and E152. In particular, alanine replacement of residue R147, a key contributor to inter-subunit salt bridges, resulted in only a minor effect on tetramer dissociation. Mutations outside of the inter-subunit interface also influenced tetramer stability by affecting the tetramerization on-rate, possibly by changing the inherent helical propensity of the peptide. These findings are interpreted in the context of established paradigms of protein-protein interactions and protein folding, and lay the groundwork for further studies of the CTD in full-length KcsA channels.
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Affiliation(s)
- Guy Kamnesky
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
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36
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Visualizing an Ultra-Weak Protein-Protein Interaction in Phosphorylation Signaling. Angew Chem Int Ed Engl 2014; 53:11501-5. [DOI: 10.1002/anie.201405976] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Indexed: 11/07/2022]
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37
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Kubrycht J, Sigler K, Souček P, Hudeček J. Structures composing protein domains. Biochimie 2013; 95:1511-24. [DOI: 10.1016/j.biochi.2013.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 04/02/2013] [Indexed: 12/21/2022]
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38
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Lian LY. NMR studies of weak protein-protein interactions. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:59-72. [PMID: 23611315 DOI: 10.1016/j.pnmrs.2012.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Accepted: 11/22/2012] [Indexed: 06/02/2023]
Affiliation(s)
- Lu-Yun Lian
- NMR Centre for Structural Biology, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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39
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Yang Y, Ramelot TA, Ni S, McCarrick RM, Kennedy MA. Measurement of rate constants for homodimer subunit exchange using double electron-electron resonance and paramagnetic relaxation enhancements. JOURNAL OF BIOMOLECULAR NMR 2013; 55:47-58. [PMID: 23180051 PMCID: PMC3697061 DOI: 10.1007/s10858-012-9685-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 11/04/2012] [Indexed: 06/05/2023]
Abstract
Here, we report novel methods to measure rate constants for homodimer subunit exchange using double electron-electron resonance (DEER) electron paramagnetic resonance spectroscopy measurements and nuclear magnetic resonance spectroscopy based paramagnetic relaxation enhancement (PRE) measurements. The techniques were demonstrated using the homodimeric protein Dsy0195 from the strictly anaerobic bacterium Desulfitobacterium hafniense Y51. At specific times following mixing site-specific MTSL-labeled Dsy0195 with uniformly (15)N-labeled Dsy0195, the extent of exchange was determined either by monitoring the decrease of MTSL-labeled homodimer from the decay of the DEER modulation depth or by quantifying the increase of MTSL-labeled/(15)N-labeled heterodimer using PREs. Repeated measurements at several time points following mixing enabled determination of the homodimer subunit dissociation rate constant, k (-1), which was 0.037 ± 0.005 min(-1) derived from DEER experiments with a corresponding half-life time of 18.7 min. These numbers agreed with independent measurements obtained from PRE experiments. These methods can be broadly applied to protein-protein and protein-DNA complex studies.
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Affiliation(s)
- Yunhuang Yang
- Department of Chemistry and Biochemistry, and Northeast Structural Genomics Consortium (NESG), Miami University, Oxford, Ohio 45056
| | - Theresa A. Ramelot
- Department of Chemistry and Biochemistry, and Northeast Structural Genomics Consortium (NESG), Miami University, Oxford, Ohio 45056
| | - Shuisong Ni
- Department of Chemistry and Biochemistry, and Northeast Structural Genomics Consortium (NESG), Miami University, Oxford, Ohio 45056
| | - Robert M. McCarrick
- Department of Chemistry and Biochemistry, and Northeast Structural Genomics Consortium (NESG), Miami University, Oxford, Ohio 45056
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, and Northeast Structural Genomics Consortium (NESG), Miami University, Oxford, Ohio 45056
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40
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Bledzka K, Liu J, Xu Z, Perera HD, Yadav SP, Bialkowska K, Qin J, Ma YQ, Plow EF. Spatial coordination of kindlin-2 with talin head domain in interaction with integrin β cytoplasmic tails. J Biol Chem 2012; 287:24585-94. [PMID: 22648415 PMCID: PMC3397883 DOI: 10.1074/jbc.m111.336743] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 05/29/2012] [Indexed: 12/20/2022] Open
Abstract
Both talin head domain and kindlin-2 interact with integrin β cytoplasmic tails, and they function in concert to induce integrin activation. Binding of talin head domain to β cytoplasmic tails has been characterized extensively, but information on the interaction of kindin-2 with this integrin segment is limited. In this study, we systematically examine the interactions of kindlin-2 with integrin β tails. Kindlin-2 interacted well with β(1) and β(3) tails but poorly with the β(2) cytoplasmic tail. This binding selectivity was determined by the non-conserved residues, primarily the three amino acids at the extreme C terminus of the β(3) tail, and the sequence in β(2) was non-permissive. The region at the C termini of integrin β(1) and β(3) tails recognized by kindlin-2 was a binding core of 12 amino acids. Kindlin-2 and talin head do not interact with one another but can bind simultaneously to the integrin β(3) tail without enhancing or inhibiting the interaction of the other binding partner. Kindlin-2 itself failed to directly unclasp integrin α/β tail complex, indicating that kindlin-2 must cooperate with talin to support the integrin activation mechanism.
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Affiliation(s)
- Kamila Bledzka
- From the Department of Molecular Cardiology, Joseph J. Jacobs Center for Thrombosis and Vascular Biology/NB-50 and
| | - Jianmin Liu
- From the Department of Molecular Cardiology, Joseph J. Jacobs Center for Thrombosis and Vascular Biology/NB-50 and
| | - Zhen Xu
- Blood Research Institute, Blood Center of Wisconsin, Milwaukee, Wisconsin 53226
| | - H. Dhanuja Perera
- From the Department of Molecular Cardiology, Joseph J. Jacobs Center for Thrombosis and Vascular Biology/NB-50 and
| | - Satya P. Yadav
- Research Core Services, Department of Molecular Biotechnology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195 and
| | - Katarzyna Bialkowska
- From the Department of Molecular Cardiology, Joseph J. Jacobs Center for Thrombosis and Vascular Biology/NB-50 and
| | - Jun Qin
- From the Department of Molecular Cardiology, Joseph J. Jacobs Center for Thrombosis and Vascular Biology/NB-50 and
| | - Yan-Qing Ma
- Blood Research Institute, Blood Center of Wisconsin, Milwaukee, Wisconsin 53226
| | - Edward F. Plow
- From the Department of Molecular Cardiology, Joseph J. Jacobs Center for Thrombosis and Vascular Biology/NB-50 and
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41
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Xia W, Li H, Yang X, Wong KB, Sun H. Metallo-GTPase HypB from Helicobacter pylori and its interaction with nickel chaperone protein HypA. J Biol Chem 2011; 287:6753-63. [PMID: 22179820 DOI: 10.1074/jbc.m111.287581] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The maturation of [NiFe]-hydrogenase is highly dependent on a battery of chaperone proteins. Among these, HypA and HypB were proposed to exert nickel delivery functions in the metallocenter assembly process, although the detailed mechanism remains unclear. Herein, we have overexpressed and purified wild-type HypB as well as two mutants, K168A and M186L/F190V, from Helicobacter pylori. We demonstrated that all proteins bind Ni(2+) at a stoichiometry of one Ni(2+) per monomer of the proteins with dissociation constants at micromolar levels. Ni(2+) elevated GTPase activity of WT HypB, which is attributable to a lower affinity of the protein toward GDP as well as Ni(2+)-induced dimerization. The disruption of GTP-dependent dimerization has led to GTPase activities of both mutants in apo-forms almost completely abolished, compared with the wild-type protein. The GTPase activity is partially restored for HypB(M186L/F190V) mutant but not for HypB(K168A) mutant upon Ni(2+) binding. HypB forms a complex with its partner protein HypA with a low affinity (K(d) of 52.2 ± 8.8 μM). Such interactions were also observed in vivo both in the absence and presence of nickel using a GFP-fragment reassembly technique. The putative protein-protein interfaces on H. pylori HypA and HypB proteins were identified by NMR chemical shift perturbation and mutagenesis studies, respectively. Intriguingly, the unique N terminus of H. pylori HypB was identified to participate in the interaction with H. pylori HypA. These structural and functional studies provide insight into the molecular mechanism of Ni(2+) delivery during maturation of [NiFe]-hydrogenase.
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Affiliation(s)
- Wei Xia
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong, China
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