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Jaramillo-Martinez V, Dominguez MJ, Bell GM, Souness ME, Carhart AH, Cuibus MA, Masoumzadeh E, Lantz BJ, Adkins AJ, Latham MP, Ball KA, Stollar EJ. How a highly acidic SH3 domain folds in the absence of its charged peptide target. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.532811. [PMID: 36993259 PMCID: PMC10055188 DOI: 10.1101/2023.03.21.532811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Charged residues on the surface of proteins are critical for both protein stability and interactions. However, many proteins contain binding regions with a high net-charge that may destabilize the protein but are useful for binding to oppositely charged targets. We hypothesized that these domains would be marginally stable, as electrostatic repulsion would compete with favorable hydrophobic collapse during folding. Furthermore, by increasing the salt concentration we predict that these protein folds would be stabilized by mimicking some of the favorable electrostatic interactions that take place during target binding. We varied the salt and urea concentrations to probe the contributions of electrostatic and hydrophobic interactions for the folding of the 60-residue yeast SH3 domain found in Abp1p. The SH3 domain was significantly stabilized with increased salt concentrations according to the Debye-Huckel limiting law. Molecular dynamics and NMR show that sodium ions interact with all 15 acidic residues but do little to change backbone dynamics or overall structure. Folding kinetics experiments show that the addition of urea or salt primarily affects the folding rate, indicating that almost all the hydrophobic collapse and electrostatic repulsion occurs in the transition state. After the transition state formation, modest yet favorable short-range salt-bridges are formed along with hydrogen bonds, as the native state fully folds. Thus, hydrophobic collapse offsets electrostatic repulsion to ensure this highly charged binding domain can still fold and be ready to bind to its charged peptide targets, a property that is likely evolutionarily conserved over one billion years. Statement for broader audience Some protein domains are highly charged because they are adapted to bind oppositely charged proteins and nucleic acids. However, it is unknown how these highly charged domains fold as during folding there will be significant repulsion between like-charges. We investigate how one of these highly charged domains folds in the presence of salt, which can screen the charge repulsion and make folding easier, allowing us to understand how folding occurs despite the protein’s high charge. Supplementary material Supplementary material document containing additional details on protein expression methods, thermodynamics and kinetics equations, and the effect of urea on electrostatic interactions, as well as 4 supplemental figures and 4 supplemental data tables. ( Supplementary_Material.docx ), 15 pages Supplemental excel file containing covariation data across AbpSH3 orthologs ( FileS1.xlsx ).
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2
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McCord JJ, Engavale M, Masoumzadeh E, Villarreal J, Mapp B, Latham MP, Keyel PA, Sutton RB. Structural features of Dnase1L3 responsible for serum antigen clearance. Commun Biol 2022; 5:825. [PMID: 35974043 PMCID: PMC9381713 DOI: 10.1038/s42003-022-03755-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/22/2022] [Indexed: 11/09/2022] Open
Abstract
Autoimmunity develops when extracellular DNA released from dying cells is not cleared from serum. While serum DNA is primarily digested by Dnase1 and Dnase1L3, Dnase1 cannot rescue autoimmunity arising from Dnase1L3 deficiencies. Dnase1L3 uniquely degrades antigenic forms of cell-free DNA, including DNA complexed with lipids and proteins. The distinct activity of Dnase1L3 relies on its unique C-terminal Domain (CTD), but the mechanism is unknown. We used multiple biophysical techniques and functional assays to study the interplay between the core catalytic domain and the CTD. While the core domain resembles Dnase1, there are key structural differences between the two enzymes. First, Dnase1L3 is not inhibited by actin due to multiple differences in the actin recognition site. Second, the CTD augments the ability of the core to bind DNA, thereby facilitating the degradation of complexed DNA. Together, these structural insights will inform the development of Dnase1L3-based therapies for autoimmunity.
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Affiliation(s)
- Jon J McCord
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA
| | - Minal Engavale
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - Elahe Masoumzadeh
- Texas Tech University, Dept. of Chemistry & Biochemistry, Lubbock, TX, USA
| | - Johanna Villarreal
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA
| | - Britney Mapp
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - Michael P Latham
- Texas Tech University, Dept. of Chemistry & Biochemistry, Lubbock, TX, USA
| | - Peter A Keyel
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - R Bryan Sutton
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA.
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3
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Gerlach GJ, Carrock R, Stix R, Stollar EJ, Ball KA. A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway. PLoS Comput Biol 2020; 16:e1007815. [PMID: 32925900 PMCID: PMC7514057 DOI: 10.1371/journal.pcbi.1007815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 09/24/2020] [Accepted: 08/15/2020] [Indexed: 12/20/2022] Open
Abstract
Protein-protein interactions are involved in a wide range of cellular processes. These interactions often involve intrinsically disordered proteins (IDPs) and protein binding domains. However, the details of IDP binding pathways are hard to characterize using experimental approaches, which can rarely capture intermediate states present at low populations. SH3 domains are common protein interaction domains that typically bind proline-rich disordered segments and are involved in cell signaling, regulation, and assembly. We hypothesized, given the flexibility of SH3 binding peptides, that their binding pathways include multiple steps important for function. Molecular dynamics simulations were used to characterize the steps of binding between the yeast Abp1p SH3 domain (AbpSH3) and a proline-rich IDP, ArkA. Before binding, the N-terminal segment 1 of ArkA is pre-structured and adopts a polyproline II helix, while segment 2 of ArkA (C-terminal) adopts a 310 helix, but is far less structured than segment 1. As segment 2 interacts with AbpSH3, it becomes more structured, but retains flexibility even in the fully engaged state. Binding simulations reveal that ArkA enters a flexible encounter complex before forming the fully engaged bound complex. In the encounter complex, transient nonspecific hydrophobic and long-range electrostatic contacts form between ArkA and the binding surface of SH3. The encounter complex ensemble includes conformations with segment 1 in both the forward and reverse orientation, suggesting that segment 2 may play a role in stabilizing the correct binding orientation. While the encounter complex forms quickly, the slow step of binding is the transition from the disordered encounter ensemble to the fully engaged state. In this transition, ArkA makes specific contacts with AbpSH3 and buries more hydrophobic surface. Simulating the binding between ApbSH3 and ArkA provides insight into the role of encounter complex intermediates and nonnative hydrophobic interactions for other SH3 domains and IDPs in general.
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Affiliation(s)
- Gabriella J. Gerlach
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
| | - Rachel Carrock
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
| | - Robyn Stix
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
| | - Elliott J. Stollar
- School of Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - K. Aurelia Ball
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
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4
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Dujardin M, Madan V, Gandhi NS, Cantrelle FX, Launay H, Huvent I, Bartenschlager R, Lippens G, Hanoulle X. Cyclophilin A allows the allosteric regulation of a structural motif in the disordered domain 2 of NS5A and thereby fine-tunes HCV RNA replication. J Biol Chem 2019; 294:13171-13185. [PMID: 31315928 DOI: 10.1074/jbc.ra119.009537] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/28/2019] [Indexed: 12/13/2022] Open
Abstract
Implicated in numerous human diseases, intrinsically disordered proteins (IDPs) are dynamic ensembles of interconverting conformers that often contain many proline residues. Whether and how proline conformation regulates the functional aspects of IDPs remains an open question, however. Here, we studied the disordered domain 2 of nonstructural protein 5A (NS5A-D2) of hepatitis C virus (HCV). NS5A-D2 comprises a short structural motif (PW-turn) embedded in a proline-rich sequence, whose interaction with the human prolyl isomerase cyclophilin A (CypA) is essential for viral RNA replication. Using NMR, we show here that the PW-turn motif exists in a conformational equilibrium between folded and disordered states. We found that the fraction of conformers in the NS5A-D2 ensemble that adopt the structured motif is allosterically modulated both by the cis/trans isomerization of the surrounding prolines that are CypA substrates and by substitutions conferring resistance to cyclophilin inhibitor. Moreover, we noted that this fraction is directly correlated with HCV RNA replication efficiency. We conclude that CypA can fine-tune the dynamic ensemble of the disordered NS5A-D2, thereby regulating viral RNA replication efficiency.
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Affiliation(s)
- Marie Dujardin
- University of Lille, CNRS, UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Vanesa Madan
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Neha S Gandhi
- School of Mathematical Sciences and Institute for Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - François-Xavier Cantrelle
- University of Lille, CNRS, UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Hélène Launay
- University of Lille, CNRS, UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Isabelle Huvent
- University of Lille, CNRS, UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Guy Lippens
- University of Lille, CNRS, UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Xavier Hanoulle
- University of Lille, CNRS, UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France.
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5
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Shen Q, Shi J, Zeng D, Zhao B, Li P, Hwang W, Cho JH. Molecular Mechanisms of Tight Binding through Fuzzy Interactions. Biophys J 2019; 114:1313-1320. [PMID: 29590589 DOI: 10.1016/j.bpj.2018.01.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/18/2018] [Accepted: 01/29/2018] [Indexed: 12/19/2022] Open
Abstract
Many intrinsically disordered proteins (IDPs) form fuzzy complexes upon binding to their targets. Although many IDPs are weakly bound in fuzzy complexes, some IDPs form high-affinity complexes. One example is the nonstructural protein 1 (NS1) of the 1918 Spanish influenza A virus, which hijacks cellular CRKII through the strong binding affinity (Kd ∼10 nM) of its proline-rich motif (PRMNS1) to the N-terminal Src-homology 3 domain of CRKII. However, its molecular mechanism remains elusive. Here, we examine the interplay between structural disorder of a bound PRMNS1 and its long-range electrostatic interactions. Using x-ray crystallography and NMR spectroscopy, we found that PRMNS1 retains substantial conformational flexibility in the bound state. Moreover, molecular dynamics simulations showed that structural disorder of the bound PRMNS1 increases the number of electrostatic interactions and decreases the mean distances between the positively charged residues in PRMNS1 and the acidic residues in the N-terminal Src-homology 3 domain. These results are analyzed using a polyelectrostatic model. Our results provide an insight into the molecular recognition mechanism for a high-affinity fuzzy complex.
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Affiliation(s)
- Qingliang Shen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Jie Shi
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas
| | - Danyun Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Baoyu Zhao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas; Department of Materials Science and Engineering, Texas A&M University, College Station, Texas; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea.
| | - Jae-Hyun Cho
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
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6
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Ramos S, Horness RE, Collins JA, Haak D, Thielges MC. Site-specific 2D IR spectroscopy: a general approach for the characterization of protein dynamics with high spatial and temporal resolution. Phys Chem Chem Phys 2019; 21:780-788. [PMID: 30548035 PMCID: PMC6360950 DOI: 10.1039/c8cp06146g] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The conformational heterogeneity and dynamics of protein side chains contribute to function, but investigating exactly how is hindered by experimental challenges arising from the fast timescales involved and the spatial heterogeneity of protein structures. The potential of two-dimensional infrared (2D IR) spectroscopy for measuring conformational heterogeneity and dynamics with unprecedented spatial and temporal resolution has motivated extensive effort to develop amino acids with functional groups that have frequency-resolved absorptions to serve as probes of their protein microenvironments. We demonstrate the full advantage of the approach by selective incorporation of the probe p-cyanophenylalanine at six distinct sites in a Src homology 3 domain and the application of 2D IR spectroscopy to site-specifically characterize heterogeneity and dynamics and their contribution to cognate ligand binding. The approach revealed a wide range of microenvironments and distinct responses to ligand binding, including at the three adjacent, conserved aromatic residues that form the recognition surface of the protein. Molecular dynamics simulations performed for all the labeled proteins provide insight into the underlying heterogeneity and dynamics. Similar application of 2D IR spectroscopy and site-selective probe incorporation will allow for the characterization of heterogeneity and dynamics of other proteins, how heterogeneity and dynamics are affected by solvation and local structure, and how they might contribute to biological function.
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Affiliation(s)
- Sashary Ramos
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rachel E. Horness
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jessica A. Collins
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - David Haak
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
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7
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Bukowski GS, Thielges MC. Residue-Specific Conformational Heterogeneity of Proline-Rich Sequences Uncovered via Infrared Spectroscopy. Anal Chem 2018; 90:14355-14362. [PMID: 30462480 DOI: 10.1021/acs.analchem.8b03813] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational heterogeneity is critical to understanding protein function but challenging to quantify. Experimental approaches that can provide sufficient temporal and spatial resolution to measure even rapidly interconverting states at specific locations in proteins are needed to fully elucidate the contribution of conformational heterogeneity and dynamics to function. Infrared spectroscopy in combination with the introduction of carbon deuterium bonds, which provide frequency-resolved probes of their environments, can uncover rapidly interconverting states with residue-specific detail. Using this approach, we quantify conformational heterogeneity of proline-rich peptides associated with different proline backbone conformations, as well as reveal their dependence on the sequence context.
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Affiliation(s)
- Gregory S Bukowski
- Department of Chemistry , Indiana University , 800 East Kirkwood , Bloomington , Indiana 47405 , United States
| | - Megan C Thielges
- Department of Chemistry , Indiana University , 800 East Kirkwood , Bloomington , Indiana 47405 , United States
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8
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Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores. J Mol Biol 2018; 431:336-350. [PMID: 30471255 DOI: 10.1016/j.jmb.2018.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/04/2018] [Accepted: 11/14/2018] [Indexed: 11/21/2022]
Abstract
Hydrophobic cores are often viewed as tightly packed and rigid, but they do show some plasticity and could thus be attractive targets for protein design. Here we explored the role of different functional pressures on the core packing and ligand recognition of the SH3 domain from human Fyn tyrosine kinase. We randomized the hydrophobic core and used phage display to select variants that bound to each of three distinct ligands. The three evolved groups showed remarkable differences in core composition, illustrating the effect of different selective pressures on the core. Changes in the core did not significantly alter protein stability, but were linked closely to changes in binding affinity and specificity. Structural analysis and molecular dynamics simulations revealed the structural basis for altered specificity. The evolved domains had significantly reduced core volumes, which in turn induced increased backbone flexibility. These motions were propagated from the core to the binding surface and induced significant conformational changes. These results show that alternative core packing and consequent allosteric modulation of binding interfaces could be used to engineer proteins with novel functions.
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9
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A multi-column plate adapter provides an economical and versatile high-throughput protein purification system. Protein Expr Purif 2018; 152:84-91. [PMID: 30041031 DOI: 10.1016/j.pep.2018.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/20/2018] [Accepted: 07/20/2018] [Indexed: 11/21/2022]
Abstract
Protein purification is essential in the study of protein structure and function, and the development of novel therapeutics. Many studies require purifying multiple proteins at once, increasing the demand for improved purification methods. We hypothesized that multiple chromatography columns could be interfaced with a multi-well collection plate for rapid and convenient protein purification without the need of expensive instrumentation. As such, we developed a multi-column plate adapter (MCPA), which provides an economical yet versatile and time efficient, high-throughput protein purification system. The MCPA system simultaneously purified milligrams of different proteins under gravity or under vacuum for faster purification. The MCPA handles up to twenty-four 12 mL columns and multiple MCPA's in sequence allow milligram-scale purification of 96 different samples with relative ease. We also used the MCPA system for large scale affinity purification of four proteins, providing sufficient yields and purity for protein crystallization and biophysical characterization. The MCPA system is ideal for optimizing resin type and volume or any other purification parameter by customizing individual columns during the same purification. The high-throughput and versatile nature of this system should prove to be useful in obtaining adequate amounts of protein for subsequent analyses in any laboratory setting.
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10
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Brown T, Brown N, Stollar EJ. Most yeast SH3 domains bind peptide targets with high intrinsic specificity. PLoS One 2018; 13:e0193128. [PMID: 29470497 PMCID: PMC5823434 DOI: 10.1371/journal.pone.0193128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/04/2018] [Indexed: 01/07/2023] Open
Abstract
A need exists to develop bioinformatics for predicting differences in protein function, especially for members of a domain family who share a common fold, yet are found in a diverse array of proteins. Many domain families have been conserved over large evolutionary spans and representative genomic data during these periods are now available. This allows a simple method for grouping domain sequences to reveal common and unique/specific binding residues. As such, we hypothesize that sequence alignment analysis of the yeast SH3 domain family across ancestral species in the fungal kingdom can determine whether each member encodes specific information to bind unique peptide targets. With this approach, we identify important specific residues for a given domain as those that show little conservation within an alignment of yeast domain family members (paralogs) but are conserved in an alignment of its direct relatives (orthologs). We find most of the yeast SH3 domain family members have maintained unique amino acid conservation patterns that suggest they bind peptide targets with high intrinsic specificity through varying degrees of non-canonical recognition. For a minority of domains, we predict a less diverse binding surface, likely requiring additional factors to bind targets specifically. We observe that our predictions are consistent with high throughput binding data, which suggests our approach can probe intrinsic binding specificity in any other interaction domain family that is maintained during evolution.
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Affiliation(s)
- Tom Brown
- Math and Computer Science Department, Eastern New Mexico University, Portales, NM, United States of America
| | - Nick Brown
- Portales High School, Portales, NM, United States of America
| | - Elliott J. Stollar
- Physical Sciences Department, Eastern New Mexico University, Portales, NM, United States of America
- * E-mail:
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11
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Sanz-Hernández M, De Simone A. The PROSECCO server for chemical shift predictions in ordered and disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 69:147-156. [PMID: 29119515 PMCID: PMC5711976 DOI: 10.1007/s10858-017-0145-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/12/2017] [Indexed: 06/07/2023]
Abstract
The chemical shifts measured in solution-state and solid-state nuclear magnetic resonance (NMR) are powerful probes of the structure and dynamics of protein molecules. The exploitation of chemical shifts requires methods to correlate these data with the protein structures and sequences. We present here an approach to calculate accurate chemical shifts in both ordered and disordered proteins using exclusively the information contained in their sequences. Our sequence-based approach, protein sequences and chemical shift correlations (PROSECCO), achieves the accuracy of the most advanced structure-based methods in the characterization of chemical shifts of folded proteins and improves the state of the art in the study of disordered proteins. Our analyses revealed fundamental insights on the structural information carried by NMR chemical shifts of structured and unstructured protein states.
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Affiliation(s)
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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12
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Plucinsky SM, Glover KJ. Secondary Structure Analysis of a Functional Construct of Caveolin-1 Reveals a Long C-Terminal Helix. Biophys J 2016; 109:1686-8. [PMID: 26488659 DOI: 10.1016/j.bpj.2015.08.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 08/06/2015] [Accepted: 08/10/2015] [Indexed: 01/11/2023] Open
Abstract
Caveolin-1 is an integral membrane protein that is the primary component of cell membrane invaginations called caveolae. While caveolin-1 is known to participate in a myriad of vital cellular processes, structural data on caveolin-1 of any kind is severely limited. In order to rectify this dearth, secondary structure analysis of a functional construct of caveolin-1, containing the intact C-terminal domain, was performed using NMR spectroscopy in lyso-myristoylphosphatidylglycerol micelles. Complete backbone assignments of caveolin-1 (residues 62-178) were made, and it was determined that residues 62-79 were dynamic; residues 89-107, 111-128, and 132-175 were helical; and residues 80-88, 108-110, and 129-131 represent unstructured breaks between the helices.
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13
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Boulton S, Melacini G. Advances in NMR Methods To Map Allosteric Sites: From Models to Translation. Chem Rev 2016; 116:6267-304. [PMID: 27111288 DOI: 10.1021/acs.chemrev.5b00718] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The last five years have witnessed major developments in the understanding of the allosteric phenomenon, broadly defined as coupling between remote molecular sites. Such advances have been driven not only by new theoretical models and pharmacological applications of allostery, but also by progress in the experimental approaches designed to map allosteric sites and transitions. Among these techniques, NMR spectroscopy has played a major role given its unique near-atomic resolution and sensitivity to the dynamics that underlie allosteric couplings. Here, we highlight recent progress in the NMR methods tailored to investigate allostery with the goal of offering an overview of which NMR approaches are best suited for which allosterically relevant questions. The picture of the allosteric "NMR toolbox" is provided starting from one of the simplest models of allostery (i.e., the four-state thermodynamic cycle) and continuing to more complex multistate mechanisms. We also review how such an "NMR toolbox" has assisted the elucidation of the allosteric molecular basis for disease-related mutations and the discovery of novel leads for allosteric drugs. From this overview, it is clear that NMR plays a central role not only in experimentally validating transformative theories of allostery, but also in tapping the full translational potential of allosteric systems.
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Affiliation(s)
- Stephen Boulton
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
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14
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Horness RE, Basom EJ, Mayer JP, Thielges MC. Resolution of Site-Specific Conformational Heterogeneity in Proline-Rich Molecular Recognition by Src Homology 3 Domains. J Am Chem Soc 2016; 138:1130-3. [PMID: 26784847 DOI: 10.1021/jacs.5b11999] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational heterogeneity and dynamics are increasingly evoked in models of protein molecular recognition but are challenging to experimentally characterize. Here we combine the inherent temporal resolution of infrared (IR) spectroscopy with the spatial resolution afforded by selective incorporation of carbon-deuterium (C-D) bonds, which provide frequency-resolved absorptions within a protein IR spectrum, to characterize the molecular recognition of the Src homology 3 (SH3) domain of the yeast protein Sho1 with its cognate proline-rich (PR) sequence of Pbs2. The IR absorptions of C-D bonds introduced at residues along a peptide of the Pbs2 PR sequence report on the changes in the local environments upon binding to the SH3 domain. Interestingly, upon forming the complex the IR spectra of the peptides labeled with C-D bonds at either of the two conserved prolines of the PXXP consensus recognition sequence show more absorptions than there are C-D bonds, providing evidence for the population of multiple states. In contrast, the NMR spectra of the peptides labeled with (13)C at the same residues show only single resonances, indicating rapid interconversion on the NMR time scale. Thus, the data suggest that the SH3 domain recognizes its cognate peptide with a component of induced fit molecular recognition involving the adoption of multiples states, which have previously gone undetected due to interconversion between the populated states that is too fast to resolve using conventional methods.
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Affiliation(s)
- Rachel E Horness
- Department of Chemistry, Indiana University , 800 East Kirkwood, Bloomington, Indiana 47405, United States
| | - Edward J Basom
- Department of Chemistry, Indiana University , 800 East Kirkwood, Bloomington, Indiana 47405, United States
| | - John P Mayer
- Department of Chemistry, Indiana University , 800 East Kirkwood, Bloomington, Indiana 47405, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University , 800 East Kirkwood, Bloomington, Indiana 47405, United States
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15
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Wang Q, Waterhouse N, Feyijinmi O, Dominguez MJ, Martinez LM, Sharp Z, Service R, Bothe JR, Stollar EJ. Development and Application of a High Throughput Protein Unfolding Kinetic Assay. PLoS One 2016; 11:e0146232. [PMID: 26745729 PMCID: PMC4706425 DOI: 10.1371/journal.pone.0146232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 12/15/2015] [Indexed: 11/18/2022] Open
Abstract
The kinetics of folding and unfolding underlie protein stability and quantification of these rates provides important insights into the folding process. Here, we present a simple high throughput protein unfolding kinetic assay using a plate reader that is applicable to the studies of the majority of 2-state folding proteins. We validate the assay by measuring kinetic unfolding data for the SH3 (Src Homology 3) domain from Actin Binding Protein 1 (AbpSH3) and its stabilized mutants. The results of our approach are in excellent agreement with published values. We further combine our kinetic assay with a plate reader equilibrium assay, to obtain indirect estimates of folding rates and use these approaches to characterize an AbpSH3-peptide hybrid. Our high throughput protein unfolding kinetic assays allow accurate screening of libraries of mutants by providing both kinetic and equilibrium measurements and provide a means for in-depth ϕ-value analyses.
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Affiliation(s)
- Qiang Wang
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Nicklas Waterhouse
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Olusegun Feyijinmi
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Matthew J. Dominguez
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Lisa M. Martinez
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Zoey Sharp
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Rachel Service
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Jameson R. Bothe
- NMRFAM, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Elliott J. Stollar
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
- * E-mail:
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16
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Tomaselli S, Pagano K, Boulton S, Zanzoni S, Melacini G, Molinari H, Ragona L. Lipid binding protein response to a bile acid library: a combined NMR and statistical approach. FEBS J 2015; 282:4094-113. [PMID: 26260520 DOI: 10.1111/febs.13405] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/20/2015] [Accepted: 08/06/2015] [Indexed: 01/23/2023]
Abstract
Primary bile acids, differing in hydroxylation pattern, are synthesized from cholesterol in the liver and, once formed, can undergo extensive enzyme-catalysed glycine/taurine conjugation, giving rise to a complex mixture, the bile acid pool. Composition and concentration of the bile acid pool may be altered in diseases, posing a general question on the response of the carrier (bile acid binding protein) to the binding of ligands with different hydrophobic and steric profiles. A collection of NMR experiments (H/D exchange, HET-SOFAST, ePHOGSY NOESY/ROESY and (15) N relaxation measurements) was thus performed on apo and five different holo proteins, to monitor the binding pocket accessibility and dynamics. The ensemble of obtained data could be rationalized by a statistical approach, based on chemical shift covariance analysis, in terms of residue-specific correlations and collective protein response to ligand binding. The results indicate that the same residues are influenced by diverse chemical stresses: ligand binding always induces silencing of motions at the protein portal with a concomitant conformational rearrangement of a network of residues, located at the protein anti-portal region. This network of amino acids, which do not belong to the binding site, forms a contiguous surface, sensing the presence of the bound lipids, with a signalling role in switching protein-membrane interactions on and off.
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Affiliation(s)
- Simona Tomaselli
- NMR Laboratory, Istituto per lo Studio delle Macromolecole (ISMAC), Milano, Italy
| | - Katiuscia Pagano
- NMR Laboratory, Istituto per lo Studio delle Macromolecole (ISMAC), Milano, Italy
| | - Stephen Boulton
- Departments of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | | | - Giuseppe Melacini
- Departments of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Henriette Molinari
- NMR Laboratory, Istituto per lo Studio delle Macromolecole (ISMAC), Milano, Italy
| | - Laura Ragona
- NMR Laboratory, Istituto per lo Studio delle Macromolecole (ISMAC), Milano, Italy
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17
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Rouka E, Simister PC, Janning M, Kumbrink J, Konstantinou T, Muniz JRC, Joshi D, O'Reilly N, Volkmer R, Ritter B, Knapp S, von Delft F, Kirsch KH, Feller SM. Differential Recognition Preferences of the Three Src Homology 3 (SH3) Domains from the Adaptor CD2-associated Protein (CD2AP) and Direct Association with Ras and Rab Interactor 3 (RIN3). J Biol Chem 2015; 290:25275-92. [PMID: 26296892 DOI: 10.1074/jbc.m115.637207] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Indexed: 11/06/2022] Open
Abstract
CD2AP is an adaptor protein involved in membrane trafficking, with essential roles in maintaining podocyte function within the kidney glomerulus. CD2AP contains three Src homology 3 (SH3) domains that mediate multiple protein-protein interactions. However, a detailed comparison of the molecular binding preferences of each SH3 remained unexplored, as well as the discovery of novel interactors. Thus, we studied the binding properties of each SH3 domain to the known interactor Casitas B-lineage lymphoma protein (c-CBL), conducted a peptide array screen based on the recognition motif PxPxPR and identified 40 known or novel candidate binding proteins, such as RIN3, a RAB5-activating guanine nucleotide exchange factor. CD2AP SH3 domains 1 and 2 generally bound with similar characteristics and specificities, whereas the SH3-3 domain bound more weakly to most peptide ligands tested yet recognized an unusually extended sequence in ALG-2-interacting protein X (ALIX). RIN3 peptide scanning arrays revealed two CD2AP binding sites, recognized by all three SH3 domains, but SH3-3 appeared non-functional in precipitation experiments. RIN3 recruited CD2AP to RAB5a-positive early endosomes via these interaction sites. Permutation arrays and isothermal titration calorimetry data showed that the preferred binding motif is Px(P/A)xPR. Two high-resolution crystal structures (1.65 and 1.11 Å) of CD2AP SH3-1 and SH3-2 solved in complex with RIN3 epitopes 1 and 2, respectively, indicated that another extended motif is relevant in epitope 2. In conclusion, we have discovered novel interaction candidates for CD2AP and characterized subtle yet significant differences in the recognition preferences of its three SH3 domains for c-CBL, ALIX, and RIN3.
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Affiliation(s)
- Evgenia Rouka
- From the Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Philip C Simister
- From the Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, Oxford OX3 9DS, United Kingdom,
| | - Melanie Janning
- From the Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Joerg Kumbrink
- the Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Tassos Konstantinou
- From the Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - João R C Muniz
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Dhira Joshi
- the Peptide Chemistry Laboratory, London Research Institute Cancer Research UK, London WC2A 3LY, United Kingdom
| | - Nicola O'Reilly
- the Peptide Chemistry Laboratory, London Research Institute Cancer Research UK, London WC2A 3LY, United Kingdom
| | - Rudolf Volkmer
- the Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, 10115 Berlin, Germany
| | - Brigitte Ritter
- the Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Stefan Knapp
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Frank von Delft
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, the Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom, and the Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Kathrin H Kirsch
- the Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Stephan M Feller
- From the Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, Oxford OX3 9DS, United Kingdom, the Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany,
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18
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Landrieu I, Verger A, Baert JL, Rucktooa P, Cantrelle FX, Dewitte F, Ferreira E, Lens Z, Villeret V, Monté D. Characterization of ERM transactivation domain binding to the ACID/PTOV domain of the Mediator subunit MED25. Nucleic Acids Res 2015; 43:7110-21. [PMID: 26130716 PMCID: PMC4538835 DOI: 10.1093/nar/gkv650] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 05/28/2015] [Indexed: 01/12/2023] Open
Abstract
The N-terminal acidic transactivation domain (TAD) of ERM/ETV5 (ERM38–68), a PEA3 group member of Ets-related transcription factors, directly interacts with the ACID/PTOV domain of the Mediator complex subunit MED25. Molecular details of this interaction were investigated using nuclear magnetic resonance (NMR) spectroscopy. The TAD is disordered in solution but has a propensity to adopt local transient secondary structure. We show that it folds upon binding to MED25 and that the resulting ERM–MED25 complex displays characteristics of a fuzzy complex. Mutational analysis further reveals that two aromatic residues in the ERM TAD (F47 and W57) are involved in the binding to MED25 and participate in the ability of ERM TAD to activate transcription. Mutation of a key residue Q451 in the VP16 H1 binding pocket of MED25 affects the binding of ERM. Furthermore, competition experiments show that ERM and VP16 H1 share a common binding interface on MED25. NMR data confirms the occupancy of this binding pocket by ERM TAD. Based on these experimental data, a structural model of a functional interaction is proposed. This study provides mechanistic insights into the Mediator–transactivator interactions.
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Affiliation(s)
- Isabelle Landrieu
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Alexis Verger
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Jean-Luc Baert
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Prakash Rucktooa
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - François-Xavier Cantrelle
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Frédérique Dewitte
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Elisabeth Ferreira
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Zoé Lens
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Vincent Villeret
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Didier Monté
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
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19
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Favretto F, Santambrogio C, D'Onofrio M, Molinari H, Grandori R, Assfalg M. Bile salt recognition by human liver fatty acid binding protein. FEBS J 2015; 282:1271-88. [PMID: 25639618 DOI: 10.1111/febs.13218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/22/2014] [Accepted: 01/26/2015] [Indexed: 12/24/2022]
Abstract
Fatty acid binding proteins (FABPs) act as intracellular carriers of lipid molecules, and play a role in global metabolism regulation. Liver FABP (L-FABP) is prominent among FABPs for its wide ligand repertoire, which includes long-chain fatty acids as well as bile acids (BAs). In this work, we performed a detailed molecular- and atomic-level analysis of the interactions established by human L-FABP with nine BAs to understand the binding specificity for this important class of cholesterol-derived metabolites. Protein-ligand complex formation was monitored using heteronuclear NMR, steady-state fluorescence spectroscopy, and mass spectrometry. BAs were found to interact with L-FABP with dissociation constants in the narrow range of 0.6-7 μm; however, the diverse substitution patterns of the sterol nucleus and the presence of side-chain conjugation resulted in complexes endowed with various degrees of conformational heterogeneity. Trihydroxylated BAs formed monomeric complexes in which single ligand molecules occupied similar internal binding sites, based on chemical-shift perturbation data. Analysis of NMR line shapes upon progressive addition of taurocholate indicated that the binding mechanism departed from a simple binary association equilibrium, and instead involved intermediates along the binding path. The co-linear chemical shift behavior observed for L-FABP complexes with cholate derivatives added insight into conformational dynamics in the presence of ligands. The observed spectroscopic features of L-FABP/BA complexes, discussed in relation to ligand chemistry, suggest possible molecular determinants of recognition, with implications regarding intracellular BA transport. Our findings suggest that human L-FABP is a poorly selective, universal BA binder.
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20
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Horness RE, Basom EJ, Thielges MC. Site-selective Characterization of Src Homology 3 Domain Molecular Recognition with Cyanophenylalanine Infrared Probes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2015; 7:7234-7241. [PMID: 26491469 PMCID: PMC4609639 DOI: 10.1039/c5ay00523j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Local heterogeneity of microenvironments in proteins is important in biological function, but difficult to characterize experimentally. One approach is the combination of infrared (IR) spectroscopy and site-selective incorporation of probe moieties with spectrally resolved IR absorptions that enable characterization within inherently congested protein IR spectra. We employed this method to study molecular recognition of a Src homology 3 (SH3) domain from the yeast protein Sho1 for a peptide containing the proline-rich recognition sequence of its physiological binding partner Pbs2. Nitrile IR probes were introduced at four distinct sites in the protein by selective incorporation of p-cyanophenylalanine via the amber codon suppressor method and characterized by IR spectroscopy. Variation among the IR absorption bands reports on heterogeneity in local residue environments dictated by the protein structure, as well as on residue-dependent changes upon peptide binding. The study informs on the molecular recognition of SH3 Sho1 and illustrates the speed and simplicity of this approach for characterization of select microenvironments within proteins.
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Affiliation(s)
| | - Edward J. Basom
- Department of Chemistry, Indiana University, Bloomington, USA
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, Bloomington, USA
- Corresponding authors,
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21
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A tool set to map allosteric networks through the NMR chemical shift covariance analysis. Sci Rep 2014; 4:7306. [PMID: 25482377 PMCID: PMC4258684 DOI: 10.1038/srep07306] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 11/07/2014] [Indexed: 11/30/2022] Open
Abstract
Allostery is an essential regulatory mechanism of biological function. Allosteric sites are also pharmacologically relevant as they are often targeted with higher selectivity than orthosteric sites. However, a comprehensive map of allosteric sites poses experimental challenges because allostery is driven not only by structural changes, but also by modulations in dynamics that typically remain elusive to classical structure determination methods. An avenue to overcome these challenges is provided by the NMR chemical shift covariance analysis (CHESCA), as chemical shifts are exquisitely sensitive to redistributions in dynamic conformational ensembles. Here, we propose a set of complementary CHESCA algorithms designed to reliably detect allosteric networks with minimal occurrences of false positives or negatives. The proposed CHESCA toolset was tested for two allosteric proteins (PKA and EPAC) and is expected to complement traditional comparative structural analyses in the comprehensive identification of functionally relevant allosteric sites, including those in otherwise elusive partially unstructured regions.
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22
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Cembran A, Kim J, Gao J, Veglia G. NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding. Phys Chem Chem Phys 2014; 16:6508-18. [PMID: 24604024 PMCID: PMC4117682 DOI: 10.1039/c4cp00110a] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proteins exist as an ensemble of conformers that are distributed on free energy landscapes resembling folding funnels. While the most stable conformers populate low energy basins, protein function is often carried out through low-populated conformational states that occupy high energy basins. Ligand binding shifts the populations of these states, changing the distribution of these conformers. Understanding how the equilibrium among the states is altered upon ligand binding, interaction with other binding partners, and/or mutations and post-translational modifications is of critical importance for explaining allosteric signaling in proteins. Here, we propose a statistical analysis of the linear trajectories of NMR chemical shifts (CONCISE, COordiNated ChemIcal Shifts bEhavior) for the interpretation of protein conformational equilibria. CONCISE enables one to quantitatively measure the population shifts associated with ligand titrations and estimate the degree of collectiveness of the protein residues' response to ligand binding, giving a concise view of the structural transitions. The combination of CONCISE with thermocalorimetric and kinetic data allows one to depict a protein's approximate conformational energy landscape. We tested this method with the catalytic subunit of cAMP-dependent protein kinase A, a ubiquitous enzyme that undergoes conformational transitions upon both nucleotide and pseudo-substrate binding. When complemented with chemical shift covariance analysis (CHESCA), this new method offers both collective response and residue-specific correlations for ligand binding to proteins.
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Affiliation(s)
- Alessandro Cembran
- Department of Biochemistry, Biophysics & Molecular Biology, University of Minnesota, 6-155 Jackson Hall, MN 55455, USA.
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23
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McGraw J, Tatipelli VK, Feyijinmi O, Traore MC, Eangoor P, Lane S, Stollar EJ. A semi-automated method for purification of milligram quantities of proteins on the QIAcube. Protein Expr Purif 2014; 96:48-53. [PMID: 24508590 DOI: 10.1016/j.pep.2014.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/16/2014] [Accepted: 01/27/2014] [Indexed: 11/17/2022]
Abstract
A growing number of studies require the purification of multiple proteins simultaneously and the development of simple economical high-throughput purification methods is essential. We have tested the purification of two related proteins in a variety of conditions to benchmark the semi-automated affinity chromatography method for the QIAcube that we have developed. We find that this new QIAcube method can successfully purify milligram quantities of proteins with minimal user involvement and performs as well as methods based on gravity. The method could easily be adapted to other chromatography resins and should prove to be a versatile method for optimizing protein expression or purification conditions for multiple proteins while obtaining sufficient amounts for subsequent biochemical analyses.
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Affiliation(s)
- J McGraw
- Eastern New Mexico University, Department of Physical Sciences, Station #33, Portales, NM 88130, United States
| | - V K Tatipelli
- Eastern New Mexico University, Department of Physical Sciences, Station #33, Portales, NM 88130, United States
| | - O Feyijinmi
- Eastern New Mexico University, Department of Physical Sciences, Station #33, Portales, NM 88130, United States
| | - M C Traore
- Eastern New Mexico University, Department of Physical Sciences, Station #33, Portales, NM 88130, United States
| | - P Eangoor
- Eastern New Mexico University, Department of Physical Sciences, Station #33, Portales, NM 88130, United States
| | - S Lane
- Eastern New Mexico University, Department of Physical Sciences, Station #33, Portales, NM 88130, United States
| | - E J Stollar
- Eastern New Mexico University, Department of Physical Sciences, Station #33, Portales, NM 88130, United States.
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24
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Lukhele S, Bah A, Lin H, Sonenberg N, Forman-Kay JD. Interaction of the eukaryotic initiation factor 4E with 4E-BP2 at a dynamic bipartite interface. Structure 2013; 21:2186-96. [PMID: 24207126 DOI: 10.1016/j.str.2013.08.030] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/29/2013] [Accepted: 08/13/2013] [Indexed: 10/26/2022]
Abstract
Cap-dependent translation initiation is regulated by the interaction of eukaryotic initiation factor 4E (eIF4E) with eIF4E binding proteins (4E-BPs). Whereas the binding of 4E-BP peptides containing the eIF4E-binding ⁵⁴YXXXXLΦ⁶⁰ motif has been studied, atomic-level characterization of the interaction of eIF4E with full-length 4E-BPs has been lacking. Here, we use isothermal titration calorimetry and nuclear magnetic resonance spectroscopy to characterize the dynamic, structural and binding properties of 4E-BP2. Although disordered, 4E-BP2 contains significant fluctuating secondary structure and binds eIF4E at an extensive bipartite interface including the canonical ⁵⁴YXXXXLΦ⁶⁰ and ⁷⁸IPGVT⁸² sites. Each of the two binding elements individually has submicromolar affinity and exchange on and off of the eIF4E surface within the context of the overall nanomolar complex. This dynamic interaction facilitates exposure of regulatory phosphorylation sites within the complex. The 4E-BP2 interface on eIF4E overlaps yet is more extensive than the eIF4G:eIF4E interface, suggesting that these key interactions may be differentially targeted for therapeutics.
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Affiliation(s)
- Sabelo Lukhele
- Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
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25
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Nourse A, Mittag T. The cytoplasmic domain of the T-cell receptor zeta subunit does not form disordered dimers. J Mol Biol 2013; 426:62-70. [PMID: 24120941 DOI: 10.1016/j.jmb.2013.09.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/11/2013] [Accepted: 09/25/2013] [Indexed: 01/14/2023]
Abstract
Intrinsically disordered regions in proteins play active roles in recognition, signaling and molecular sorting. They often undergo coupled folding and binding giving rise to largely ordered interfaces with their binding partners. The cytoplasmic region of the T-cell receptor zeta subunit (ζcyt) has been previously proposed to specifically dimerize in the absence of a disorder-to-order transition, suggesting an intriguing dimerization mechanism that may involve multiple transient interfaces. We show here using analytical ultracentrifugation, NMR, size-exclusion chromatography (SEC) and multi-angle light scattering that neither ζcyt nor the cytoplasmic region of CD3ε significantly populates a dimeric state but that they are mostly monomers in solution up to millimolar concentrations. They experience a salt- and concentration-dependent shift of their elution volume in SEC previously interpreted as dimerization. Our data show that ζcyt does not form a highly disordered protein complex and leaves open the question as to whether completely disordered dimers (or other oligomers) exist in nature.
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Affiliation(s)
- Amanda Nourse
- Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 311, Memphis, TN 38105, USA.
| | - Tanja Mittag
- Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 311, Memphis, TN 38105, USA.
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26
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Dawson JE, Farber PJ, Forman-Kay JD. Allosteric coupling between the intracellular coupling helix 4 and regulatory sites of the first nucleotide-binding domain of CFTR. PLoS One 2013; 8:e74347. [PMID: 24058550 PMCID: PMC3776845 DOI: 10.1371/journal.pone.0074347] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 08/01/2013] [Indexed: 12/25/2022] Open
Abstract
Cystic fibrosis is caused by mutations in CFTR (cystic fibrosis transmembrane conductance regulator), leading to folding and processing defects and to chloride channel gating misfunction. CFTR is regulated by ATP binding to its cytoplasmic nucleotide-binding domains, NBD1 and NBD2, and by phosphorylation of the NBD1 regulatory insert (RI) and the regulatory extension (RE)/R region. These regulatory effects are transmitted to the rest of the channel via NBD interactions with intracellular domain coupling helices (CL), particularly CL4. Using a sensitive method for detecting inter-residue correlations between chemical shift changes in NMR spectra, an allosteric network was revealed within NBD1, with a construct lacking RI. The CL4-binding site couples to the RI-deletion site and the C-terminal residues of NBD1 that precede the R region in full-length CFTR. Titration of CL4 peptide into NBD1 perturbs the conformational ensemble in these sites with similar titration patterns observed in F508del, the major CF-causing mutant, and in suppressor mutants F494N, V510D and Q637R NBD1, as well as in a CL4-NBD1 fusion construct. Reciprocally, the C-terminal mutation, Q637R, perturbs dynamics in these three sites. This allosteric network suggests a mechanism synthesizing diverse regulatory NBD1 interactions and provides biophysical evidence for the allosteric coupling required for CFTR function.
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Affiliation(s)
- Jennifer E. Dawson
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Patrick J. Farber
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Julie D. Forman-Kay
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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