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Antón R, Treviño MÁ, Pantoja-Uceda D, Félix S, Babu M, Cabrita EJ, Zweckstetter M, Tinnefeld P, Vera AM, Oroz J. Alternative low-populated conformations prompt phase transitions in polyalanine repeat expansions. Nat Commun 2024; 15:1925. [PMID: 38431667 PMCID: PMC10908835 DOI: 10.1038/s41467-024-46236-5] [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] [Received: 06/16/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Abnormal trinucleotide repeat expansions alter protein conformation causing malfunction and contribute to a significant number of incurable human diseases. Scarce structural insights available on disease-related homorepeat expansions hinder the design of effective therapeutics. Here, we present the dynamic structure of human PHOX2B C-terminal fragment, which contains the longest polyalanine segment known in mammals. The major α-helical conformation of the polyalanine tract is solely extended by polyalanine expansions in PHOX2B, which are responsible for most congenital central hypoventilation syndrome cases. However, polyalanine expansions in PHOX2B additionally promote nascent homorepeat conformations that trigger length-dependent phase transitions into solid condensates that capture wild-type PHOX2B. Remarkably, HSP70 and HSP90 chaperones specifically seize PHOX2B alternative conformations preventing phase transitions. The precise observation of emerging polymorphs in expanded PHOX2B postulates unbalanced phase transitions as distinct pathophysiological mechanisms in homorepeat expansion diseases, paving the way towards the search of therapeutics modulating biomolecular condensates in central hypoventilation syndrome.
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Affiliation(s)
- Rosa Antón
- Instituto de Química Física Blas Cabrera (IQF), CSIC, E-28006, Madrid, Spain
| | - Miguel Á Treviño
- Instituto de Química Física Blas Cabrera (IQF), CSIC, E-28006, Madrid, Spain
| | - David Pantoja-Uceda
- Instituto de Química Física Blas Cabrera (IQF), CSIC, E-28006, Madrid, Spain
| | - Sara Félix
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - María Babu
- German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - Eurico J Cabrita
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, München, 81377, Germany
| | - Andrés M Vera
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, München, 81377, Germany
| | - Javier Oroz
- Instituto de Química Física Blas Cabrera (IQF), CSIC, E-28006, Madrid, Spain.
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2
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Metamorphism in TDP-43 prion-like domain determines chaperone recognition. Nat Commun 2023; 14:466. [PMID: 36709343 PMCID: PMC9884275 DOI: 10.1038/s41467-023-36023-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/12/2023] [Indexed: 01/29/2023] Open
Abstract
The RNA binding protein TDP-43 forms cytoplasmic inclusions via its C-terminal prion-like domain in several neurodegenerative diseases. Aberrant TDP-43 aggregation arises upon phase de-mixing and transitions from liquid to solid states, following still unknown structural conversions which are primed by oxidative stress and chaperone inhibition. Despite the well-established protective roles for molecular chaperones against protein aggregation pathologies, knowledge on the determinants of chaperone recognition in disease-related prions is scarce. Here we show that chaperones and co-chaperones primarily recognize the structured elements in TDP-43´s prion-like domain. Significantly, while HSP70 and HSP90 chaperones promote TDP-43 phase separation, co-chaperones from the three classes of the large human HSP40 family (namely DNAJA2, DNAJB1, DNAJB4 and DNAJC7) show strikingly different effects on TDP-43 de-mixing. Dismantling of the second helical element in TDP-43 prion-like domain by methionine sulfoxidation impacts phase separation and amyloid formation, abrogates chaperone recognition and alters phosphorylation by casein kinase-1δ. Our results show that metamorphism in the post-translationally modified TDP-43 prion-like domain encodes determinants that command mechanisms with major relevance in disease.
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3
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Pantoja-Uceda D, Oroz J, Fernández C, de Alba E, Giraldo R, Laurents DV. Conformational Priming of RepA-WH1 for Functional Amyloid Conversion Detected by NMR Spectroscopy. Structure 2020; 28:336-347.e4. [PMID: 31918960 DOI: 10.1016/j.str.2019.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 10/03/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022]
Abstract
How proteins with a stable globular fold acquire the amyloid state is still largely unknown. RepA, a versatile plasmidic DNA binding protein from Pseudomonas savastanoi, is functional as a transcriptional repressor or as an initiator or inhibitor of DNA replication, the latter via assembly of an amyloidogenic oligomer. Its N-terminal domain (WH1) is responsible for discrimination between these functional abilities by undergoing insufficiently understood structural changes. RepA-WH1 is a stable dimer whose conformational dynamics had not been explored. Here, we have studied it through NMR {1H}-15N relaxation and H/D exchange kinetics measurements. The N- and the C-terminal α-helices, and the internal amyloidogenic loop, are partially unfolded in solution. S4-indigo, a small inhibitor of RepA-WH1 amyloidogenesis, binds to and tethers the N-terminal α-helix to a β-hairpin that is involved in dimerization, thus providing evidence for a priming role of fraying ends and dimerization switches in the amyloidogenesis of folded proteins.
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Affiliation(s)
- David Pantoja-Uceda
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, c/ Serrano 119, Madrid 28006, Spain
| | - Javier Oroz
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, c/ Serrano 119, Madrid 28006, Spain
| | - Cristina Fernández
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, c/ Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Eva de Alba
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, c/ Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Rafael Giraldo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, c/ Ramiro de Maeztu 9, Madrid 28040, Spain.
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, c/ Serrano 119, Madrid 28006, Spain.
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4
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Krichel C, Möckel C, Schillinger O, Huesgen PF, Sticht H, Strodel B, Weiergräber OH, Willbold D, Neudecker P. Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site. Sci Rep 2019; 9:14167. [PMID: 31578424 PMCID: PMC6775092 DOI: 10.1038/s41598-019-48155-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/26/2019] [Indexed: 11/09/2022] Open
Abstract
(Macro-)autophagy is a compartmental degradation pathway conserved from yeast to mammals. The yeast protein Atg8 mediates membrane tethering/hemifusion and cargo recruitment and is essential for autophagy. The human MAP1LC3/GABARAP family proteins show high sequence identity with Atg8, but MAP1LC3C is distinguished by a conspicuous amino-terminal extension with unknown functional significance. We have determined the high-resolution three-dimensional structure and measured the backbone dynamics of MAP1LC3C by NMR spectroscopy. From Ser18 to Ala120, MAP1LC3C forms an α-helix followed by the ubiquitin-like tertiary fold with two hydrophobic binding pockets used by MAP1LC3/GABARAP proteins to recognize targets presenting LC3-interacting regions (LIRs). Unlike other MAP1LC3/GABARAP proteins, the amino-terminal region of MAP1LC3C does not form a stable helix α1 but a "sticky arm" consisting of a polyproline II motif on a flexible linker. Ser18 at the interface between this linker and the structural core can be phosphorylated in vitro by protein kinase A, which causes additional conformational heterogeneity as monitored by NMR spectroscopy and molecular dynamics simulations, including changes in the LIR-binding interface. Based on these results we propose that the amino-terminal polyproline II motif mediates specific interactions with the microtubule cytoskeleton and that Ser18 phosphorylation modulates the interplay of MAP1LC3C with its various target proteins.
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Affiliation(s)
- Carsten Krichel
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Physikalische Biologie and BMFZ, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Christina Möckel
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Physikalische Biologie and BMFZ, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Oliver Schillinger
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Pitter F Huesgen
- ZEA-3 (Analytik), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Heinrich Sticht
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Birgit Strodel
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Oliver H Weiergräber
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Dieter Willbold
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany. .,Institut für Physikalische Biologie and BMFZ, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
| | - Philipp Neudecker
- ICS-6 (Strukturbiochemie) and JuStruct, Forschungszentrum Jülich, 52425, Jülich, Germany. .,Institut für Physikalische Biologie and BMFZ, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
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5
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Möckel C, Kubiak J, Schillinger O, Kühnemuth R, Della Corte D, Schröder GF, Willbold D, Strodel B, Seidel CAM, Neudecker P. Integrated NMR, Fluorescence, and Molecular Dynamics Benchmark Study of Protein Mechanics and Hydrodynamics. J Phys Chem B 2018; 123:1453-1480. [DOI: 10.1021/acs.jpcb.8b08903] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Christina Möckel
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jakub Kubiak
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Oliver Schillinger
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Ralf Kühnemuth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Dennis Della Corte
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gunnar F. Schröder
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
- Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Claus A. M. Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Philipp Neudecker
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
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6
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Ptak CP, Akif M, Hsieh C, Devarajan A, He P, Xu Y, Oswald RE, Chang Y. Comparative screening of recombinant antigen thermostability for improved leptospirosis vaccine design. Biotechnol Bioeng 2018; 116:260-271. [DOI: 10.1002/bit.26864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/29/2018] [Accepted: 11/07/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Christopher P. Ptak
- Department of Population Medicine and Diagnostic SciencesCollege of Veterinary Medicine, Cornell UniversityIthaca New York
- Department of Molecular MedicineCollege of Veterinary Medicine, Cornell UniversityIthaca New York
| | - Mohd. Akif
- Department of Population Medicine and Diagnostic SciencesCollege of Veterinary Medicine, Cornell UniversityIthaca New York
- Department of BiochemistryUniversity of HyderabadHyderabad India
| | - Ching‐Lin Hsieh
- Department of Population Medicine and Diagnostic SciencesCollege of Veterinary Medicine, Cornell UniversityIthaca New York
| | - Alex Devarajan
- Department of Molecular MedicineCollege of Veterinary Medicine, Cornell UniversityIthaca New York
| | - Ping He
- Department of Microbiology and ImmunologyInstitutes of Medical Science, Shanghai Jiao Tong University School of MedicineShanghai China
| | - Yinghua Xu
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug ControlBeijing China
| | - Robert E. Oswald
- Department of Molecular MedicineCollege of Veterinary Medicine, Cornell UniversityIthaca New York
| | - Yung‐Fu Chang
- Department of Population Medicine and Diagnostic SciencesCollege of Veterinary Medicine, Cornell UniversityIthaca New York
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7
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Abstract
Molecular recognition by proteins is fundamental to the molecular basis of biology. Dissection of the thermodynamic landscape governing protein-ligand interactions has proven difficult because determination of various entropic contributions is quite challenging. Nuclear magnetic resonance relaxation measurements, theory, and simulations suggest that conformational entropy can be accessed through a dynamical proxy. Here, we review the relationship between measures of fast side-chain motion and the underlying conformational entropy. The dynamical proxy reveals that the contribution of conformational entropy can range from highly favorable to highly unfavorable and demonstrates the potential of this key thermodynamic variable to modulate protein-ligand interactions. The dynamical so-called entropy meter also refines the role of solvent entropy and directly determines the loss in rotational-translational entropy that occurs upon formation of high-affinity complexes. The ability to quantify the roles of entropy through an entropy meter based on measurable dynamical properties promises to highlight its role in protein function.
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Affiliation(s)
- A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6059, USA; ,
| | - Kim A Sharp
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6059, USA; ,
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8
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Heller GT, Aprile FA, Vendruscolo M. Methods of probing the interactions between small molecules and disordered proteins. Cell Mol Life Sci 2017; 74:3225-3243. [PMID: 28631009 PMCID: PMC5533867 DOI: 10.1007/s00018-017-2563-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/15/2022]
Abstract
It is generally recognized that a large fraction of the human proteome is made up of proteins that remain disordered in their native states. Despite the fact that such proteins play key biological roles and are involved in many major human diseases, they still represent challenging targets for drug discovery. A major bottleneck for the identification of compounds capable of interacting with these proteins and modulating their disease-promoting behaviour is the development of effective techniques to probe such interactions. The difficulties in carrying out binding measurements have resulted in a poor understanding of the mechanisms underlying these interactions. In order to facilitate further methodological advances, here we review the most commonly used techniques to probe three types of interactions involving small molecules: (1) those that disrupt functional interactions between disordered proteins; (2) those that inhibit the aberrant aggregation of disordered proteins, and (3) those that lead to binding disordered proteins in their monomeric states. In discussing these techniques, we also point out directions for future developments.
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Affiliation(s)
- Gabriella T Heller
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
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9
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Mompeán M, Romano V, Pantoja-Uceda D, Stuani C, Baralle FE, Buratti E, Laurents DV. Point mutations in the N-terminal domain of transactive response DNA-binding protein 43 kDa (TDP-43) compromise its stability, dimerization, and functions. J Biol Chem 2017; 292:11992-12006. [PMID: 28566288 PMCID: PMC5512090 DOI: 10.1074/jbc.m117.775965] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/25/2017] [Indexed: 12/14/2022] Open
Abstract
Transactive response DNA-binding protein 43 (TDP-43) performs multiple tasks in mRNA processing, transport, and translational regulation, but it also forms aggregates implicated in amyotrophic lateral sclerosis. TDP-43's N-terminal domain (NTD) is important for these activities and dysfunctions; however, there is an open debate about whether or not it adopts a specifically folded, stable structure. Here, we studied NTD mutations designed to destabilize its structure utilizing NMR and fluorescence spectroscopies, analytical ultracentrifugation, splicing assays, and cell microscopy. The substitutions V31R and T32R abolished TDP-43 activity in splicing and aggregation processes, and even the rather mild L28A mutation severely destabilized the NTD, drastically reducing TDP-43's in vitro splicing activity and inducing aberrant localization and aggregation in cells. These findings strongly support the idea that a stably folded NTD is essential for correct TDP-43 function. The stably folded NTD also promotes dimerization, which is pertinent to the protein's activities and pathological aggregation, and we present an atomic-level structural model for the TDP-43 dimer based on NMR data. Leu-27 is evolutionarily well conserved even though it is exposed in the monomeric NTD. We found here that Leu-27 is buried in the dimer and that the L27A mutation promotes monomerization. In conclusion, our study sheds light on the structural and biological properties of the TDP-43 NTD, indicating that the NTD must be stably folded for TDP-43's physiological functions, and has implications for understanding the mechanisms promoting the pathological aggregation of this protein.
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Affiliation(s)
- Miguel Mompeán
- Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, E-28006 Madrid, Spain
| | - Valentina Romano
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, I-34149 Trieste, Italy
| | - David Pantoja-Uceda
- Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, E-28006 Madrid, Spain
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, I-34149 Trieste, Italy
| | - Francisco E Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, I-34149 Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, I-34149 Trieste, Italy.
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, E-28006 Madrid, Spain.
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10
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Mompeán M, Romano V, Pantoja-Uceda D, Stuani C, Baralle FE, Buratti E, Laurents DV. The TDP-43 N-terminal domain structure at high resolution. FEBS J 2016; 283:1242-60. [DOI: 10.1111/febs.13651] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/18/2015] [Accepted: 01/08/2016] [Indexed: 02/06/2023]
Affiliation(s)
| | - Valentina Romano
- International Centre for Genetic Engineering and Biotechnology; Trieste Italy
| | | | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology; Trieste Italy
| | | | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology; Trieste Italy
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11
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Tremblay ML, Xu L, Lefèvre T, Sarker M, Orrell KE, Leclerc J, Meng Q, Pézolet M, Auger M, Liu XQ, Rainey JK. Spider wrapping silk fibre architecture arising from its modular soluble protein precursor. Sci Rep 2015; 5:11502. [PMID: 26112753 PMCID: PMC4481645 DOI: 10.1038/srep11502] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/27/2015] [Indexed: 11/12/2022] Open
Abstract
Spiders store spidroins in their silk glands as high concentration aqueous solutions, spinning these dopes into fibres with outstanding mechanical properties. Aciniform (or wrapping) silk is the toughest spider silk and is devoid of the short amino acid sequence motifs characteristic of the other spidroins. Using solution-state NMR spectroscopy, we demonstrate that the 200 amino acid Argiope trifasciata AcSp1 repeat unit contrasts with previously characterized spidroins, adopting a globular 5-helix bundle flanked by intrinsically disordered N- and C-terminal tails. Split-intein-mediated segmental NMR-active isotope-enrichment allowed unambiguous demonstration of modular and malleable "beads-on-a-string" concatemeric behaviour. Concatemers form fibres upon manual drawing with silk-like morphology and mechanical properties, alongside secondary structuring and orientation consistent with native AcSp1 fibres. AcSp1 structural stability varies locally, with the fifth helix denaturing most readily. The structural transition of aciniform spidroin from a mostly α-helical dope to a mixed α-helix/β-sheet-containing fibre can be directly related to spidroin architecture and stability.
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Affiliation(s)
| | - Lingling Xu
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, P.R. China
| | - Thierry Lefèvre
- Département de Chimie, Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA) Université Laval, Québec, QC, Canada
| | - Muzaddid Sarker
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Kathleen E. Orrell
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Jérémie Leclerc
- Département de Chimie, Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA) Université Laval, Québec, QC, Canada
| | - Qing Meng
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, P.R. China
| | - Michel Pézolet
- Département de Chimie, Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA) Université Laval, Québec, QC, Canada
| | - Michèle Auger
- Département de Chimie, Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA) Université Laval, Québec, QC, Canada
| | - Xiang-Qin Liu
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada
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12
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Dunker AK, Oldfield CJ. Back to the Future: Nuclear Magnetic Resonance and Bioinformatics Studies on Intrinsically Disordered Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:1-34. [PMID: 26387098 DOI: 10.1007/978-3-319-20164-1_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
From the 1970s to the present, regions of missing electron density in protein structures determined by X-ray diffraction and the characterization of the functions of these regions have suggested that not all protein regions depend on prior 3D structure to carry out function. Motivated by these observations, in early 1996 we began to use bioinformatics approaches to study these intrinsically disordered proteins (IDPs) and IDP regions. At just about the same time, several laboratory groups began to study a collection of IDPs and IDP regions using nuclear magnetic resonance. The temporal overlap of the bioinformatics and NMR studies played a significant role in the development of our understanding of IDPs. Here the goal is to recount some of this history and to project from this experience possible directions for future work.
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Affiliation(s)
- A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202, Indianapolis, IN, USA.
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202, Indianapolis, IN, USA.
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13
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Contursi P, Farina B, Pirone L, Fusco S, Russo L, Bartolucci S, Fattorusso R, Pedone E. Structural and functional studies of Stf76 from the Sulfolobus islandicus plasmid-virus pSSVx: a novel peculiar member of the winged helix-turn-helix transcription factor family. Nucleic Acids Res 2014; 42:5993-6011. [PMID: 24682827 PMCID: PMC4027180 DOI: 10.1093/nar/gku215] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The hybrid plasmid–virus pSSVx from Sulfolobus islandicus presents an open reading frame encoding a 76 amino acid protein, namely Stf76, that does not show significant sequence homology with any protein with known 3D structure. The recombinant protein recognizes specifically two DNA-binding sites located in its own promoter, thus suggesting an auto-regulated role of its expression. Circular dichroism, spectrofluorimetric, light scattering and isothermal titration calorimetry experiments indicated a 2:1 molar ratio (protein:DNA) upon binding to the DNA target containing a single site. Furthermore, the solution structure of Stf76, determined by nuclear magnetic resonance (NMR) using chemical shift Rosetta software, has shown that the protein assumes a winged helix–turn–helix fold. NMR chemical shift perturbation analysis has been performed for the identification of the residues responsible for DNA interaction. In addition, a model of the Stf76–DNA complex has been built using as template a structurally related homolog.
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Affiliation(s)
- Patrizia Contursi
- Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Napoli 80126, Italy
| | - Biancamaria Farina
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | | | - Salvatore Fusco
- Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Napoli 80126, Italy
| | - Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta 81100, Italy
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Napoli 80126, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta 81100, Italy
| | - Emilia Pedone
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy Istituto di Biostrutture e Bioimmagini, C.N.R., Napoli 80134, Italy
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14
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Abstract
Formation of high-affinity complexes is critical for the majority of enzymatic reactions involving proteins. The creation of the family of Michaelis and other intermediate complexes during catalysis clearly involves a complicated manifold of interactions that are diverse and complex. Indeed, computing the energetics of interactions between proteins and small molecule ligands using molecular structure alone remains a great challenge. One of the most difficult contributions to the free energy of protein-ligand complexes to access experimentally is that due to changes in protein conformational entropy. Fortunately, recent advances in solution nuclear magnetic resonance (NMR) relaxation methods have enabled the use of measures-of-motion between conformational states of a protein as a proxy for conformational entropy. This review briefly summarizes the experimental approaches currently employed to characterize fast internal motion in proteins, how this information is used to gain insight into conformational entropy, what has been learned, and what the future may hold for this emerging view of protein function.
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15
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Ota M, Koike R, Amemiya T, Tenno T, Romero PR, Hiroaki H, Dunker AK, Fukuchi S. An assignment of intrinsically disordered regions of proteins based on NMR structures. J Struct Biol 2012; 181:29-36. [PMID: 23142703 DOI: 10.1016/j.jsb.2012.10.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 10/26/2012] [Accepted: 10/30/2012] [Indexed: 11/24/2022]
Abstract
Intrinsically disordered proteins (IDPs) do not adopt stable three-dimensional structures in physiological conditions, yet these proteins play crucial roles in biological phenomena. In most cases, intrinsic disorder manifests itself in segments or domains of an IDP, called intrinsically disordered regions (IDRs), but fully disordered IDPs also exist. Although IDRs can be detected as missing residues in protein structures determined by X-ray crystallography, no protocol has been developed to identify IDRs from structures obtained by Nuclear Magnetic Resonance (NMR). Here, we propose a computational method to assign IDRs based on NMR structures. We compared missing residues of X-ray structures with residue-wise deviations of NMR structures for identical proteins, and derived a threshold deviation that gives the best correlation of ordered and disordered regions of both structures. The obtained threshold of 3.2Å was applied to proteins whose structures were only determined by NMR, and the resulting IDRs were analyzed and compared to those of X-ray structures with no NMR counterpart in terms of sequence length, IDR fraction, protein function, cellular location, and amino acid composition, all of which suggest distinct characteristics. The structural knowledge of IDPs is still inadequate compared with that of structured proteins. Our method can collect and utilize IDRs from structures determined by NMR, potentially enhancing the understanding of IDPs.
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Affiliation(s)
- Motonori Ota
- Graduate School of Information Sciences, Nagoya University, Nagoya 464-8601, Japan.
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16
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Markwick PR, Nilges M. Computational approaches to the interpretation of NMR data for studying protein dynamics. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.11.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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17
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Sharma AK, Ye L, Alper SL, Rigby AC. Guanine nucleotides differentially modulate backbone dynamics of the STAS domain of the SulP/SLC26 transport protein Rv1739c of Mycobacterium tuberculosis. FEBS J 2011; 279:420-36. [PMID: 22118659 DOI: 10.1111/j.1742-4658.2011.08435.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymatic catalysis and protein signaling are dynamic processes that involve local and/or global conformational changes occurring across a broad range of time scales. (1) H-(15) N relaxation NMR provides a comprehensive understanding of protein backbone dynamics both in the apo (unliganded) and ligand-bound conformations, enabling both fast and slow internal motions of individual amino acid residues to be observed. We recently reported the structure and nucleotide binding properties of the sulfate transporter and anti-sigma factor antagonist (STAS) domain of Rv1739c, a SulP anion transporter protein of Mycobacterium tuberculosis. In the present study, we report (1) H-(15) N NMR backbone dynamics measurements [longitudinal (T(1) ), transverse (T(2) ) and steady-state ({(1) H}-(15) N) heteronuclear NOE] of the Rv1739c STAS domain, in the absence and presence of saturating concentrations of GTP and GDP. Analysis of measured relaxation data and estimated dynamic parameters indicated distinct features differentiating the binding of GTP and GDP to Rv1739c STAS. The 9.55 ns overall rotational correlation time of Rv1739c STAS increased to 10.48 ns in the presence of GTP, and to 13.25 ns in the presence of GDP, indicating significant nucleotide-induced conformational changes. These conformational changes were accompanied by slow time scale (μs to ms) motions in discrete regions of the protein, as reflected by guanine nucleotide-induced changes in relaxation parameters. The observed nucleotide-specific alterations in the relaxation properties of individual STAS residues reflect an increased molecular anisotropy and/or the emergence of conformational equilibria governing functional properties of the STAS domain.
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Affiliation(s)
- Alok K Sharma
- Division of Molecular and Vascular Medicine, Renal Division, and Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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18
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Morin S. A practical guide to protein dynamics from 15N spin relaxation in solution. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 59:245-62. [PMID: 21920220 DOI: 10.1016/j.pnmrs.2010.12.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 12/17/2010] [Indexed: 05/08/2023]
Affiliation(s)
- Sébastien Morin
- Department of Structural Biology, Biozentrum, University of Basel, Switzerland.
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19
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Carbajo RJ, Sanz L, Mosulén S, Pérez A, Marcinkiewicz C, Pineda-Lucena A, Calvete JJ. NMR structure and dynamics of recombinant wild type and mutated jerdostatin, a selective inhibitor of integrin α1
β1. Proteins 2011; 79:2530-42. [DOI: 10.1002/prot.23076] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 04/26/2011] [Accepted: 04/27/2011] [Indexed: 11/06/2022]
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20
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Tripet BP, Goel A, Copie V. Internal dynamics of the tryptophan repressor (TrpR) and two functionally distinct TrpR variants, L75F-TrpR and A77V-TrpR, in their l-Trp-bound forms. Biochemistry 2011; 50:5140-53. [PMID: 21553830 DOI: 10.1021/bi200389k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Backbone amide dynamics of the Escherichia coli tryptophan repressor protein (WT-TrpR) and two functionally distinct variants, L75F-TrpR and A77V-TrpR, in their holo (l-tryptophan corepressor-bound) form have been characterized using (15)N nuclear magnetic resonance (NMR) relaxation. The three proteins possess very similar structures, ruling out major conformational differences as the source of their functional differences, and suggest that changes in protein flexibility are at the origin of their distinct functional properties. Comparison of site specific (15)N-T(1), (15)N-T(2), (15)N-{(1)H} nuclear Overhauser effect, reduced spectral density, and generalized order (S(2)) parameters indicates that backbone dynamics in the three holo-repressors are overall very similar with a few notable and significant exceptions for backbone atoms residing within the proteins' DNA-binding domain. We find that flexibility is highly restricted for amides in core α-helices (i.e., helices A-C and F), and a comparable "stiffening" is observed for residues in the DNA recognition helix (helix E) of the helix D-turn-helix E (HTH) DNA-binding domain of the three holo-repressors. Unexpectedly, amides located in helix D and in adjacent turn regions remain flexible. These data support the concept that residual flexibility in TrpR is essential for repressor function, DNA binding, and molecular recognition of target operators. Comparison of the (15)N NMR relaxation parameters of the holo-TrpRs with those of the apo-TrpRs indicates that the single-point amino acid substitutions, L75F and A77V, perturb the flexibility of backbone amides of TrpR in very different ways and are most pronounced in the apo forms of the three repressors. Finally, we present these findings in the context of other DNA-binding proteins and the role of protein flexibility in molecular recognition.
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Affiliation(s)
- Brian P Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
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21
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Liang X, Arunima A, Zhao Y, Bhaskaran R, Shende A, Byrne TS, Fleeks J, Palmier MO, Van Doren SR. Apparent tradeoff of higher activity in MMP-12 for enhanced stability and flexibility in MMP-3. Biophys J 2010; 99:273-83. [PMID: 20655856 DOI: 10.1016/j.bpj.2010.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 03/15/2010] [Accepted: 04/01/2010] [Indexed: 12/17/2022] Open
Abstract
The greater activity of MMP-12 than MMP-3 toward substrates from protein fibrils has been quantified. Why is MMP-12 the more active protease? We looked for behaviors associated with the higher activity of MMP-12 than MMP-3, using nuclear magnetic resonance to monitor backbone dynamics and residue-specific stabilities of their catalytic domain. The proteolytic activities are likely to play important roles in inflammatory diseases of arteries, lungs, joints, and intestines. Nuclear magnetic resonance line broadening indicates that regions surrounding the active sites of both proteases sample conformational substates within milliseconds. The more extensive line broadening in MMP-3 suggests greater sampling of conformational substates, affecting the full length of helix B and beta-strand IV forming the active site, and more remote sites. This could suggest more excursions to functionally incompetent substates. MMP-3 also has enhanced subnanosecond fluctuations in helix A, in the beta-hairpin of strands IV and V, and before and including helix C. Hydrogen exchange protection in the EX2 regime suggests that MMP-3 possesses 2.8 kcal/mol higher folding stability than MMP-12(E219A). The beta-sheet of MMP-3 appears to be stabilized still more. The higher stability of MMP-3 relative to MMP-12 coincides with the former's considerably lower proteolytic activity. This relationship is consistent with the hypothesis that enzymes often trade stability for higher activity.
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Affiliation(s)
- Xiangyang Liang
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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22
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Goel A, Tripet BP, Tyler RC, Nebert LD, Copié V. Backbone amide dynamics studies of Apo-L75F-TrpR, a temperature-sensitive mutant of the tryptophan repressor protein (TrpR): comparison with the (15)N NMR relaxation profiles of wild-type and A77V mutant Apo-TrpR repressors. Biochemistry 2010; 49:8006-19. [PMID: 20718459 DOI: 10.1021/bi100508u] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Backbone amide dynamics studies were conducted on a temperature-sensitive mutant (L75F-TrpR) of the tryptophan repressor protein (TrpR) of Escherichia coli in its apo (i.e., no l-tryptophan corepressor-bound) form. The (15)N NMR relaxation profiles of apo-L75F-TrpR were analyzed and compared to those of wild-type (WT) and super-repressor mutant (A77V) TrpR proteins, also in their apo forms. The (15)N NMR relaxation data ((15)N-T(1), (15)N-T(2), and heteronuclear (15)N-{(1)H}-nOe) recorded on all three aporepressors at a magnetic field strength of 600 MHz ((1)H Larmor frequency) were analyzed to extract dynamics parameters, including diffusion tensor ratios (D(∥)/D(⊥)), correlation times (τ(m)) for overall reorientations of the proteins in solution, reduced spectral density terms [J(eff)(0), J(0.87ω(H)), J(ω(N))], and generalized order parameters (S(2)), which report on protein internal motions on the picosecond to nanosecond and slower microsecond to millisecond chemical exchange time scales. Our results indicate that all three aporepressors exhibit comparable D(∥)/D(⊥) ratios and characteristic time constants, τ(m), for overall global reorientation, indicating that in solution, all three apoproteins display very similar overall shape, structure, and rotational diffusion properties. Comparison of (15)N NMR relaxation data, reduced spectral density profiles, and generalized S(2) order parameters indicated that these parameters are quite uniform for backbone amides positioned within the four (A-C and F) core α-helices of all three aporepressors. In contrast, small but noticeable differences in internal dynamics were observed for backbone amides located within the helix D-turn-helix E DNA-binding domain of the apo-TrpR proteins. The significance of these dynamics differences in terms of the biophysical characteristics and ligand binding properties of the three apo-TrpR proteins is discussed.
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Affiliation(s)
- Anupam Goel
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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23
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Farina B, Pirone L, Russo L, Viparelli F, Doti N, Pedone C, Pedone EM, Fattorusso R. NMR backbone dynamics studies of human PED/PEA-15 outline protein functional sites. FEBS J 2010; 277:4229-40. [PMID: 20825483 DOI: 10.1111/j.1742-4658.2010.07812.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PED/PEA-15 (phosphoprotein enriched in diabetes/phosphoprotein enriched in astrocytes) is a ubiquitously expressed protein and a key regulator of cell growth and glucose metabolism. PED/PEA-15 mediates both homotypic and heterotypic interactions and is constituted by an N-terminal canonical death effector domain and a C-terminal tail. In the present study, the backbone dynamics of PED/PEA-15 via (15)N R(1) and R(2) and steady-state [(1)H]-(15)N NOE measurements is reported. The dynamic parameters were analyzed using both Lipari-Szabo model-free formalism and a reduced spectral density mapping approach. The results obtained define a polar and charged surface of the death effector domain characterized by internal motions in the micro- to millisecond timescale, which is crucial for the multiple heterotypic functional protein-protein interactions in which PED/PEA-15 is involved. The present study contributes to a better understanding of the molecular basis of the PED/PEA-15 functional interactions and provides a more detailed surface for the design and development of PED/PEA-15 binders.
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24
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Ho MR, Lou YC, Wei SY, Luo SC, Lin WC, Lyu PC, Chen C. Human RegIV protein adopts a typical C-type lectin fold but binds mannan with two calcium-independent sites. J Mol Biol 2010; 402:682-95. [PMID: 20692269 DOI: 10.1016/j.jmb.2010.07.061] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 07/30/2010] [Accepted: 07/31/2010] [Indexed: 10/19/2022]
Abstract
Human RegIV protein, which contains a sequence motif homologous to calcium-dependent (C-type) lectin-like domain, is highly expressed in mucosa cells of the gastrointestinal tract during pathogen infection and carcinogenesis and may be applied in both diagnosis and treatment of gastric and colon cancers. Here, we provide evidence that, unlike other C-type lectins, human RegIV binds to polysaccharides, mannan, and heparin in the absence of calcium. To elucidate the structural basis for carbohydrate recognition by NMR, we generated the mutant with Pro91 replaced by Ser (hRegIV-P91S) and showed that the structural property and carbohydrate binding ability of hRegIV-P91S are almost identical with those of wild-type protein. The solution structure of hRegIV-P91S was determined, showing that it adopts a typical fold of C-type lectin. Based on the chemical shift perturbations of amide resonances, two calcium-independent mannan-binding sites were proposed. One site is similar to the calcium-independent sugar-binding site on human RegIII and Langerin. Interestingly, the other site is adjacent to the conserved calcium-dependent site at position Ca-2 of typical C-type lectins. Moreover, model-free analysis of (15)N relaxation parameters and simplified Carr-Purcell-Meiboom-Gill relaxation dispersion experiments showed that a slow microsecond-to-millisecond time-scale backbone motion is involved in mannan binding by this site, suggesting a potential role for specific carbohydrate recognition. Our findings shed light on the sugar-binding mode of Reg family proteins, and we postulate that Reg family proteins evolved to bind sugar without calcium to keep the carbohydrate recognition activity under low-pH environments in the gastrointestinal tract.
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Affiliation(s)
- Meng-Ru Ho
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
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25
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Meirovitch E, Shapiro YE, Polimeno A, Freed JH. Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure approach. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 56:360-405. [PMID: 20625480 PMCID: PMC2899824 DOI: 10.1016/j.pnmrs.2010.03.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar–Ilan University, Ramat-Gan 52900 Israel
| | - Yury E. Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar–Ilan University, Ramat-Gan 52900 Israel
| | - Antonino Polimeno
- Department of Physical Chemistry, University of Padua, 35131 Padua, Italy
| | - Jack H. Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, U.S.A
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26
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Sgourakis NG, Patel MM, Garcia AE, Makhatadze GI, McCallum SA. Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain. J Mol Biol 2010; 396:1128-44. [PMID: 20053359 DOI: 10.1016/j.jmb.2009.12.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 12/03/2009] [Accepted: 12/24/2009] [Indexed: 12/11/2022]
Abstract
Ubiquitin-interacting motifs (UIMs) are an important class of protein domains that interact with ubiquitin or ubiquitin-like proteins. These approximately 20-residue-long domains are found in a variety of ubiquitin receptor proteins and serve as recognition modules towards intracellular targets, which may be individual ubiquitin subunits or polyubiquitin chains attached to a variety of proteins. Previous structural studies of interactions between UIMs and ubiquitin have shown that UIMs adopt an extended structure of a single alpha-helix, containing a hydrophobic surface with a conserved sequence pattern that interacts with key hydrophobic residues on ubiquitin. In light of this large body of structural studies, details regarding the presence and the roles of structural dynamics and plasticity are surprisingly lacking. In order to better understand the structural basis of ubiquitin-UIM recognition, we have characterized changes in the structure and dynamics of ubiquitin upon binding of a UIM domain from the yeast Vps27 protein. The solution structure of a ubiquitin-UIM fusion protein designed to study these interactions is reported here and found to consist of a well-defined ubiquitin core and a bipartite UIM helix. Moreover, we have studied the plasticity of the docking interface, as well as global changes in ubiquitin due to UIM binding at the picoseconds-to-nanoseconds and microseconds-to-milliseconds protein motions by nuclear magnetic resonance relaxation. Changes in generalized-order parameters of amide groups show a distinct trend towards increased structural rigidity at the UIM-ubiquitin interface relative to values determined in unbound ubiquitin. Analysis of (15)N Carr-Purcell-Meiboom-Gill relaxation dispersion measurements suggests the presence of two types of motions: one directly related to the UIM-binding interface and the other induced to distal parts of the protein. This study demonstrates a case where localized interactions among protein domains have global effects on protein motions at timescales ranging from picoseconds to milliseconds.
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Affiliation(s)
- Nikolaos G Sgourakis
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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27
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Zerbetto M, Polimeno A, Meirovitch E. General theoretical/computational tool for interpreting NMR spin relaxation in proteins. J Phys Chem B 2009; 113:13613-25. [PMID: 19775101 DOI: 10.1021/jp9046819] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We developed in recent years the slowly relaxing local structure (SRLS) approach for analyzing NMR spin relaxation in proteins. SRLS is a two-body coupled rotator model which accounts rigorously for mode-coupling between the global motion of the protein and the local motion of the spin-bearing probe and allows for general properties of the second rank tensors involved. We showed that a general tool of data analysis requires both capabilities. Several important functionalities were missing in our previous implementations of SRLS in data fitting schemes, and in some important cases, the calculations were tedious. Here we present a general implementation which allows for asymmetric local and global diffusion tensors, distinct local ordering and local diffusion frames, and features a rhombic local potential which includes Wigner matrix element terms of ranks 2 and 4. A recently developed hydrodynamics-based approach for calculating global diffusion tensors has been incorporated into the data-fitting scheme. The computational efficiency of the latter has been increased significantly through object-oriented programming within the scope of the C++ programming language, and code parallelization. A convenient graphical user interface is provided. Currently autocorrelated (15)N spin relaxation data can be analyzed effectively. Adaptation to any autocorrelated and cross-correlated relaxation analysis is straightforward. New physical insight is gleaned on largely preserved local structure in solution, even in chain segments which experience slow local motion. Prospects associated with improved dynamic models, and new applications made possible by the current implementation of SRLS, are delineated.
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Affiliation(s)
- Mirco Zerbetto
- Dipartimento di Scienze Chimiche, Università di Padova, Padova, Italy
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28
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Geng Y, Feng Y, Xie T, Shan L, Wang J. The Native-like Interactions between SNase121 and SNase(111−143) Fragments Induce the Recovery of Their Native-like Structures and the Ability to Degrade DNA. Biochemistry 2009; 48:8692-703. [DOI: 10.1021/bi901099s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yong Geng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Yingang Feng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Tao Xie
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Lu Shan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Jinfeng Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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29
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Shapiro YE, Kahana E, Meirovitch E. Domain Mobility in Proteins from NMR/SRLS. J Phys Chem B 2009; 113:12050-60. [DOI: 10.1021/jp901522c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Yury E. Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Edith Kahana
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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30
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Shapiro YE, Meirovitch E. Evidence for domain motion in proteins affecting global diffusion properties: a nuclear magnetic resonance study. J Phys Chem B 2009; 113:7003-11. [PMID: 19385637 DOI: 10.1021/jp9009806] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The rotational diffusion of proteins is an important hydrodynamic property. Compact protein structures were found previously to exhibit hydration layer viscosity, etaloc, higher than the viscosity of bulk water, eta. This implies an apparent activation energy for rotational diffusion higher than the activation energy of water viscosity, Eeta=15.4+/-0.3 kJ/mol. In this study we examine etaloc of internally mobile proteins using 15N spin relaxation methods. We also examine the activation enthalpy, DeltaH#, and activation entropy, DeltaS#, for rotational diffusion. Of particular relevance are internally mobile ligand-free forms and compact ligand-bound forms of multidomain proteins. Adenylate kinase (AKeco) and Ca2+-calmodulin (Ca2+-CaM) are typical examples. For AKeco (Ca2+-CaM) we find that DeltaH# is 14.5+/-0.5 (15.7+/-0.4) kJ/mol. For the complex of AKeco with the inhibitor AP5A (the complex of Ca2+-CaM with the peptide smMLCKp), we find that DeltaH# is 18.1+/-0.7 (18.2+/-0.5) kJ/mol. The internally mobile outer surface protein A has DeltaH#=12.6+/-0.8 kJ/mol, and the compact protein Staphylococcal nuclease has DeltaH#=18.8+/-0.6 kJ/mol. For the internally mobile and compact proteins studied, <|DeltaS(|> equals 62+/-7 J/(mol K) and 44+/-5 J/(mol K), respectively. The fact is that etaloc>eta (DeltaH#>Eeta) for compact proteins was ascribed previously to electrostatic interactions between surface sites and water rigidifying the hydration layer. We find herein that obliteration of these interactions by domain motion leads to etaloc approximately eta, DeltaH# approximately Eeta, and large activation entropy for internally mobile protein structures.
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Affiliation(s)
- Yury E Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
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Hall A, Parsonage D, Horita D, Karplus PA, Poole LB, Barbar E. Redox-dependent dynamics of a dual thioredoxin fold protein: evolution of specialized folds. Biochemistry 2009; 48:5984-93. [PMID: 19459661 DOI: 10.1021/bi900270w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An enzyme system protecting bacteria from oxidative stress includes the flavoprotein AhpF and the peroxiredoxin AhpC. The N-terminal domain of AhpF (NTD), with two fused thioredoxin (Trx) folds, belongs to the hyperthermophilic protein disulfide oxidoreductase family. The NTD is distinct in that it contains a redox active a fold with a CxxC sequence and a redox inactive b fold that has lost the CxxC motif. Here we characterize the stability, the (15)N backbone relaxation, and the hydrogen-deuterium exchange properties of reduced [NTD-(SH)(2)] and oxidized (NTD-S(2)) NTD from Salmonella typhimurium. While both NTD-(SH)(2) and NTD-S(2) exhibit similar equilibrium unfolding transitions and order parameters, R(ex) relaxation terms are quite distinct with considerably more intermediate time scale motions in NTD-S(2). Hydrogen exchange protection factors show that the slowly exchanging core corresponds to residues in the b fold in both NTD-(SH)(2) and NTD-S(2). Interestingly, folded-state dynamic fluctuations in the catalytic a fold are significantly increased for residues in NTD-S(2) compared to NTD-(SH)(2). Taken together, these data demonstrate that oxidation of the active site disulfide does not significantly increase stability but results in a dramatic increase in conformational heterogeneity in residues primarily in the redox active a fold. Differences in dynamics between the two folds of the NTD suggest that each evolved a specialized function which, in the a fold, couples redox state to internal motions which may enhance catalysis and specificity and, in the b fold, provides a redox insensitive stable core.
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Affiliation(s)
- Andrea Hall
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
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32
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Vugmeyster L, McKnight CJ. Phosphorylation-induced changes in backbone dynamics of the dematin headpiece C-terminal domain. JOURNAL OF BIOMOLECULAR NMR 2009; 43:39-50. [PMID: 19030997 PMCID: PMC2796552 DOI: 10.1007/s10858-008-9289-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 10/20/2008] [Indexed: 05/27/2023]
Abstract
Dematin is an actin-binding protein abundant in red blood cells and other tissues. It contains a villin-type 'headpiece' F-actin-binding domain at its extreme C-terminus. The isolated dematin headpiece domain (DHP) undergoes a significant conformational change upon phosphorylation. The mutation of Ser74 to Glu closely mimics the phosphorylation of DHP. We investigated motions in the backbone of DHP and its mutant DHPS74E using several complementary NMR relaxation techniques: laboratory frame (15)N NMR relaxation, which is sensitive primarily to the ps-ns time scale, cross-correlated chemical shift modulation NMR relaxation detecting correlated mus-ms time scale motions of neighboring (13)C' and (15)N nuclei, and cross-correlated relaxation of two (15)N-(1)H dipole-dipole interactions detecting slow motions of backbone NH vectors in successive amino acid residues. The results indicate a reduction in mobility upon the mutation in several regions of the protein. The additional salt bridge formed in DHPS74E that links the N- and C-terminal subdomains is likely to be responsible for these changes.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Alaska at Anchorage, 99508, USA.
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33
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Fang X, Cui Q, Tong Y, Feng Y, Shan L, Huang L, Wang J. A stabilizing alpha/beta-hydrophobic core greatly contributes to hyperthermostability of archaeal [P62A]Ssh10b. Biochemistry 2008; 47:11212-21. [PMID: 18821773 DOI: 10.1021/bi8007593] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hyperthermophilic Ssh10b from Sulfolobus shibatae is a member of the Sac10b family, which has been postulated to play a role in chromosomal organization in Archaea. Ssh10b is capable of significantly constraining negative DNA supercoils at elevated temperatures. In this study, the solution structure of the dimeric P62A mutant Ssh10b ([P62A]Ssh10b) was determined by multidimensional NMR spectroscopy. The backbone 15N dynamics, H/D exchange with and without the denaturant GdmSCN, and chemical and thermal denaturation experiments were performed to investigate the molecular basis of high thermostability of [P62A]Ssh10b. Data analysis has revealed an alpha/beta-hydrophobic core consisting of two alpha-helices and one beta-sheet which are stabilized by cooperative hydrophobic and hydrogen-bonding interactions. This stabilizing alpha/beta-hydrophobic core of [P62A]Ssh10b exhibiting highly restricted internal motions is composed of residues having highly protected amide protons which exchange with solvent mostly by means of a global unfolding process. The K40N mutation greatly destabilizes the mutant [P62A]Ssh10b because this mutation disturbs the packing of alpha-helix against the beta-sheet reducing the stability of the alpha/beta-hydrophobic core in the mutant protein. In comparison with homologous mesophilic and thermophilic proteins, it can be presumed that the stabilizing alpha/beta-hydrophobic core in the [P62A]Ssh10b structure greatly contributes to the high thermostability of the protein.
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Affiliation(s)
- Xianyang Fang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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34
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Dawson JE, Nicholson LK. Folding kinetics and thermodynamics of Pseudomonas syringae effector protein AvrPto provide insight into translocation via the type III secretion system. Protein Sci 2008; 17:1109-19. [PMID: 18577754 DOI: 10.1110/ps.034223.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In order to infect their hosts, many Gram-negative bacteria translocate agents of infection, called effector proteins, through the type III secretion system (TTSS) into the host cytoplasm. This process is thought to require at least partial unfolding of these agents, raising the question of how an effector protein might unfold to enable its translocation and then refold once it reaches the host cytoplasm. AvrPto is a well-studied effector protein of Pseudomonas syringae pv tomato. The presence of a readily observed unfolded population of AvrPto in aqueous solution and the lack of a known secretion chaperone make it ideal for studying the kinetic and thermodynamic characteristics that facilitate translocation. Application of Nzz exchange spectroscopy revealed a global, two-state folding equilibrium with 16% unfolded population, a folding rate of 1.8 s(-1), and an unfolding rate of 0.33 s(-1) at pH 6.1. TrAvrPto stability increases with increasing pH, with only 2% unfolded population observed at pH 7.0. The R(1) relaxation of TrAvrPto, which is sensitive to both the global anisotropy of folded TrAvrPto and slow exchange between folded and unfolded conformations, provided independent verification of the global kinetic rate constants. Given the acidic apoplast in which the pathogen resides and the more basic host cytoplasm, these results offer an intriguing mechanism by which the pH dependence of stability and slow folding kinetics of AvrPto would allow efficient translocation of the unfolded form through the TTSS and refolding into its functional folded form once inside the host.
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Affiliation(s)
- Jennifer E Dawson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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35
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Pantoja-Uceda D, Arolas JL, García P, López-Hernández E, Padró D, Aviles FX, Blanco FJ. The NMR Structure and Dynamics of the Two-Domain Tick Carboxypeptidase Inhibitor Reveal Flexibility in Its Free Form and Stiffness upon Binding to Human Carboxypeptidase B. Biochemistry 2008; 47:7066-78. [DOI: 10.1021/bi800403m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David Pantoja-Uceda
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Joan L. Arolas
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Pascal García
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Eva López-Hernández
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Daniel Padró
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Francesc X. Aviles
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
| | - Francisco J. Blanco
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain, NMR Group, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Melchor Fernández Almagro 3, 28029 Madrid, Spain, Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
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36
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Palacios A, Muñoz IG, Pantoja-Uceda D, Marcaida MJ, Torres D, Martín-García JM, Luque I, Montoya G, Blanco FJ. Molecular basis of histone H3K4me3 recognition by ING4. J Biol Chem 2008; 283:15956-64. [PMID: 18381289 DOI: 10.1074/jbc.m710020200] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The inhibitors of growth (ING) family of tumor suppressors consists of five homologous proteins involved in chromatin remodeling. They form part of different acetylation and deacetylation complexes and are thought to direct them to specific regions of the chromatin, through the recognition of H3K4me3 (trimethylated K4 in the histone 3 tail) by their conserved plant homeodomain (PHD). We have determined the crystal structure of ING4-PHD bound to H3K4me3, which reveals a tight complex stabilized by numerous interactions. NMR shows that there is a reduction in the backbone mobility on the regions of the PHD that participate in the peptide binding, and binding affinities differ depending on histone tail lengths Thermodynamic analysis reveals that the discrimination in favor of methylated lysine is entropy-driven, contrary to what has been described for chromodomains. The molecular basis of H3K4me3 recognition by ING4 differs from that of ING2, which is consistent with their different affinities for methylated histone tails. These differences suggest a distinct role in transcriptional regulation for these two ING family members because of the antagonistic effect of the complexes that they recruit onto chromatin. Our results illustrate the versatility of PHD fingers as readers of the histone code.
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Affiliation(s)
- Alicia Palacios
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain
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37
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Bhattacharya N, Yi M, Zhou HX, Logan TM. Backbone dynamics in an intramolecular prolylpeptide-SH3 complex from the diphtheria toxin repressor, DtxR. J Mol Biol 2007; 374:977-92. [PMID: 17976643 DOI: 10.1016/j.jmb.2007.09.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 09/09/2007] [Accepted: 09/21/2007] [Indexed: 10/22/2022]
Abstract
The diphtheria toxin repressor contains an SH3-like domain that forms an intramolecular complex with a proline-rich (Pr) peptide segment and stabilizes the inactive state of the repressor. Upon activation of diphtheria toxin repressor (DtxR) by transition metals, this intramolecular complex must dissociate as the SH3 domain and Pr segment form different interactions in the active repressor. Here we investigate the dynamics of this intramolecular complex using backbone amide nuclear spin relaxation rates determined using NMR spectroscopy and molecular dynamics trajectories. The SH3 domain in the unbound and bound states showed typical dynamics in that the secondary structures were fairly ordered with high generalized order parameters and low effective correlation times, while residues in the loops connecting beta-strands exhibited reduced generalized order parameters and required additional motional terms to adequately model the relaxation rates. Residues forming the Pr segment exhibited low-order parameters with internal rotational correlation times on the order of 0.6 ns-1 ns. Further analysis showed that the SH3 domain was rich in millisecond time scale motions while the Pr segment exhibited motions on the 100 mus time scale. Molecular dynamics simulations indicated structural rearrangements that may contribute to the observed relaxation rates and, together with the observed relaxation rate data, suggested that the Pr segment exhibits a binding<-->unbinding equilibrium. The results here provide new insights into the nature of the intramolecular complex and provide a better understanding of the biological role of the SH3 domain in regulating DtxR activity.
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Affiliation(s)
- Nilakshee Bhattacharya
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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38
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Meirovitch E, Shapiro YE, Polimeno A, Freed JH. Protein dynamics from NMR: the slowly relaxing local structure analysis compared with model-free analysis. J Phys Chem A 2007; 110:8366-96. [PMID: 16821820 PMCID: PMC2758167 DOI: 10.1021/jp056975t] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(15)N-(1)H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N-H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multifield data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the slowly relaxing local structure (SRLS) approach, which accounts rigorously for mode mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulas are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF analysis force-fits the experimental data because mode mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multifield multitemperature data analyzed with the MF approach may lead to the detection of incorrect phenomena, and conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS spectral densities comply with this requirement.
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Affiliation(s)
- Eva Meirovitch
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
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39
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Chang SL, Hinck AP, Ishima R. Model-free analysis for large proteins at high magnetic field strengths. JOURNAL OF BIOMOLECULAR NMR 2007; 38:315-24. [PMID: 17593525 DOI: 10.1007/s10858-007-9171-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Accepted: 05/21/2007] [Indexed: 05/16/2023]
Abstract
Protein backbone dynamics is often characterized using model-free analysis of three sets of (15)N relaxation data: longitudinal relaxation rate (R1), transverse relaxation rate (R2), and (15)N-{H} NOE values. Since the experimental data is limited, a simplified model-free spectral density function is often used that contains one Lorentzian describing overall rotational correlation but not one describing internal motion. The simplified spectral density function may be also used in estimating the overall rotational correlation time, by making the R2/R1 largely insensitive to internal motions, as well as used as one of the choices in the model selection protocol. However, such approximation may not be valid for analysis of relaxation data of large proteins recorded at high magnetic field strengths since the contribution to longitudinal relaxation from the Lorentzian describing the overall rotational diffusion of the molecule is comparably small relative to that describing internal motion. Here, we quantitatively estimate the errors introduced by the use of the simplified spectral density in model-free analysis for large proteins at high magnetic field strength.
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Affiliation(s)
- Shou-Lin Chang
- Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University, HsinChu 30055, Taiwan
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40
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Siggers K, Soto C, Palmer AG. Conformational dynamics in loop swap mutants of homologous fibronectin type III domains. Biophys J 2007; 93:2447-56. [PMID: 17526562 PMCID: PMC1965443 DOI: 10.1529/biophysj.106.100578] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fibronectin type III (FN-III) domains are autonomously folded modules found in a variety of multidomain proteins. The 10th FN-III domain from fibronectin (fnFN10) and the 3rd FN-III domain from tenascin-C (tnFN3) have 27% sequence identity and the same overall fold; however, the CC' loop has a different pattern of backbone hydrogen bonds and the FG loop is longer in fnFN10 compared to tnFN3. To examine the influence of length, sequence, and context in determining dynamical properties of loops, CC' and FG loops were swapped between fnFN10 and tnFN3 to generate four mutant proteins and backbone conformational dynamics on ps-ns and mus-ms timescales were characterized by solution (15)N-NMR spin relaxation spectroscopy. The grafted loops do not strongly perturb the properties of the protein scaffold; however, specific effects of the mutations are observed for amino acids that are proximal in space to the sites of mutation. The amino acid sequence primarily dictates conformational dynamics when the wild-type and grafted loop have the same length, but both sequence and context contribute to conformational dynamics when the loop lengths differ. The results suggest that changes in conformational dynamics of mutant proteins must be considered in both theoretical studies and protein design efforts.
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Affiliation(s)
- Keri Siggers
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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41
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Doucet N, Savard PY, Pelletier JN, Gagné SM. NMR investigation of Tyr105 mutants in TEM-1 beta-lactamase: dynamics are correlated with function. J Biol Chem 2007; 282:21448-59. [PMID: 17426035 DOI: 10.1074/jbc.m609777200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The existence of coupled residue motions on various time scales in enzymes is now well accepted, and their detailed characterization has become an essential element in understanding the role of dynamics in catalysis. To this day, a handful of enzyme systems has been shown to rely on essential residue motions for catalysis, but the generality of such phenomena remains to be elucidated. Using NMR spectroscopy, we investigated the electronic and dynamic effects of several mutations at position 105 in TEM-1 beta-lactamase, an enzyme responsible for antibiotic resistance. Even in absence of substrate, our results show that the number and magnitude of short and long range effects on (1)H-(15)N chemical shifts are correlated with the catalytic efficiencies of the various Y105X mutants investigated. In addition, (15)N relaxation experiments on mutant Y105D show that several active-site residues of TEM-1 display significantly altered motions on both picosecond-nanosecond and microsecond-millisecond time scales despite many being far away from the site of mutation. The altered motions among various active-site residues in mutant Y105D may account for the observed decrease in catalytic efficiency, therefore suggesting that short and long range residue motions could play an important catalytic role in TEM-1 beta-lactamase. These results support previous observations suggesting that internal motions play a role in promoting protein function.
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Affiliation(s)
- Nicolas Doucet
- Département de Biochimie, Université de Montréal, Montréal, Québec H3C 3J7
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42
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d'Auvergne EJ, Gooley PR. Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. MOLECULAR BIOSYSTEMS 2007; 3:483-94. [PMID: 17579774 DOI: 10.1039/b702202f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Model-free analysis of NMR relaxation data, which describes the motion of individual atoms, is a problem intricately linked to the Brownian rotational diffusion of the macromolecule. The diffusion tensor parameters strongly influence the optimisation of the various model-free models and the subsequent model selection between them. Finding the optimal model of the dynamics of the system among the numerous diffusion and model-free models is hence quite complex. Using set theory, the entirety of this global problem has been encapsulated by the universal set Ll, and its resolution mathematically formulated as the universal solution Ll. Ever since the original Lipari and Szabo papers the model-free dynamics of a molecule has most often been solved by initially estimating the diffusion tensor. The model-free models which depend on the diffusion parameter values are then optimised and the best model is chosen to represent the dynamics of the residue. Finally, the global model of all diffusion and model-free parameters is optimised. These steps are repeated until convergence. For simplicity this approach to Ll will be labelled the diffusion seeded model-free paradigm. Although this technique suffers from a number of problems many have been solved. All aspects of the diffusion seeded paradigm and its consequences, together with a few alternatives to the paradigm, will be reviewed through the use of set notation.
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Affiliation(s)
- Edward J d'Auvergne
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Biotechnology and Molecular Science, University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
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43
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Yao S, Liu MS, Masters SL, Zhang JG, Babon JJ, Nicola NA, Nicholson SE, Norton RS. Dynamics of the SPRY domain-containing SOCS box protein 2: flexibility of key functional loops. Protein Sci 2006; 15:2761-72. [PMID: 17088318 PMCID: PMC2242441 DOI: 10.1110/ps.062477806] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The SPRY domain was identified originally as a sequence repeat in the dual-specificity kinase splA and ryanodine receptors and subsequently found in many other distinct proteins, including more than 70 encoded in the human genome. It is a subdomain of the B30.2/SPRY domain and is believed to function as a protein-protein interaction module. Three-dimensional structures of several B30.2/SPRY domain-containing proteins have been reported recently: murine SSB-2 in solution by NMR spectroscopy, a Drosophila SSB (GUSTAVUS), and human PRYSPRY protein by X-ray crystallography. The three structures share a core of two antiparallel beta-sheets for the B30.2/SPRY domain but show differences located mainly at one end of the beta-sandwich. Analysis of SSB-2 residues required for interactions with its intracellular ligands has provided insights into B30.2/SPRY binding specificity and identified loop residues critical for the function of this domain. We have investigated the backbone dynamics of SSB-2 by means of Modelfree analysis of its backbone (15)N relaxation parameters and carried out coarse-grained dynamics simulation of B30.2/SPRY domain-containing proteins using normal mode analysis. Translational self-diffusion coefficients of SSB-2 measured using pulsed field gradient NMR were used to confirm the monomeric state of SSB-2 in solution. These results, together with previously reported amide exchange data, highlight the underlying flexibility of the loop regions of B30.2/SPRY domain-containing proteins that have been shown to be important for protein-protein interactions. The underlying flexibility of certain regions of the B30.2/SPRY domain-containing proteins may also contribute to some apparent structural differences observed between GUSTAVUS or PRYSPRY and SSB-2.
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Affiliation(s)
- Shenggen Yao
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3050, Victoria, Australia.
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Sauvé S, Naud JF, Lavigne P. The mechanism of discrimination between cognate and non-specific DNA by dimeric b/HLH/LZ transcription factors. J Mol Biol 2006; 365:1163-75. [PMID: 17109882 DOI: 10.1016/j.jmb.2006.10.044] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Revised: 09/21/2006] [Indexed: 12/27/2022]
Abstract
The Myc/Max/Mad proteins are basic region-helix-loop-helix-leucine zipper (b/HLH/LZ) transcription factors that regulate the transcription of numerous genes involved in cell growth and proliferation. The Max protein is the obligate heterodimeric partner of the Myc and Mad proteins. Heterodimerization and DNA binding to target gene promoters are mediated by the b/HLH/LZ domains. Max can also form a homodimeric b/HLH/LZ. The enhanced expression of Myc and binding to promoters of target genes contribute to almost every aspect of tumor biology. However, the detailed mechanism by which dimeric and heterodimeric b/HLH/LZs discriminate cognate DNA (E-Box: CACGTG) from non-specific sequences in the target gene promoters is still unknown. Here, we use the Max b/HLH/LZ homodimer as a model for this class of transcription factors in the characterization and understanding of the mechanism of discrimination between the E-Box and non-specific DNA sequences. We report the characterization of a cognate and a non-specific Max b/HLH/LZ/DNA complex by EMSA, CD and NMR. Our results support a detailed mechanism by which dimeric b/HLH/LZ transcription factors can discriminate E-Box sequences from non-specific DNA. The mechanism proceeds via the conformational selection of fitting b/HLH/LZ homodimers with the basic region only partially helical. Next, the basic region undergoes a DNA-assisted folding or induced-fit. It is this step that provides the discrimination by stabilizing and destabilizing the alpha-helical conformation of the basic region in the cognate and non-specific complexes, respectively. This leads to a low affinity complex with a higher probability of being dissociated and hence to discrimination. A description of the side-chains and nucleotides proposed to be involved in the discrimination process is provided.
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Affiliation(s)
- Simon Sauvé
- Département de Pharmacologie, Faculté de médecine, Université de Sherbrooke, Sherbrooke, Qc, Canada J1H 5N4
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45
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Meirovitch E, Polimeno A, Freed JH. Methyl Dynamics in Proteins from NMR Slowly Relaxing Local Structure Spin Relaxation Analysis: A New Perspective. J Phys Chem B 2006; 110:20615-28. [PMID: 17034251 DOI: 10.1021/jp061403+] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NMR spin relaxation of (2)H nuclei in (13)CH(2)D groups is a powerful method for studying side-chain motion in proteins. The analysis is typically carried out with the original model-free (MF) approach adapted to methyl dynamics. The latter is described in terms of axial local motions around, and of, the methyl averaging axis, mutually decoupled and independent of the global motion of the protein. Methyl motion is characterized primarily by the axial squared order parameter, S(axis)2, associated with fluctuations of the methyl averaging axis. This view is shown to be oversimplified by applying to typical experimental data the slowly relaxing local structure (SRLS) approach of Polimeno and Freed (Adv. Chem. Phys. 1993, 83, 89) which can be considered the generalization of the MF approach. Neglecting mode coupling and the asymmetry of the local ordering and treating approximately features of local geometry imply inaccurate values of S(axis)2, hence of the residual configurational entropy derived from it. S(axis)2, interpreted as amplitude of motion, was found to range from near disorder to almost complete order. Contrary to this picture, we find with the SRLS approach a moderate distribution in the magnitude of asymmetric local ordering and significant variation in its symmetry. The latter important property can be associated implicitly with the contribution of side-chain rotamer jumps. This is consistent with experimental residual dipolar coupling studies and theoretical work based on molecular dynamics simulations and molecular mechanics considerations. Configurational entropy is obtained in the SRLS approach directly from experimentally determined asymmetric potentials. Inconsistency between order parameters from 2H relaxation and from eta(HC-HH) cross-correlation and increase in order parameters with increasing temperature were observed with the MF approach. These discrepancies are reconciled, and physically tenable temperature dependence is obtained with the SRLS approach.
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Affiliation(s)
- Eva Meirovitch
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
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46
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Savard PY, Gagné SM. Backbone Dynamics of TEM-1 Determined by NMR: Evidence for a Highly Ordered Protein†. Biochemistry 2006; 45:11414-24. [PMID: 16981701 DOI: 10.1021/bi060414q] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Backbone dynamics of TEM-1 beta-lactamase (263 amino acids, 28.9 kDa) were studied by 15N nuclear magnetic resonance relaxation at 11.7, 14.1, and 18.8 T. The high quality of the spectra allowed us to measure the longitudinal relaxation rate (R1), the transverse relaxation rate (R2), and the {1H}-15N NOE for up to 227 of the 250 potentially observable backbone amide groups. The model-free formalism was used to determine internal motional parameters using an axially anisotropic model. TEM-1 exhibits a small prolate axial anisotropy (D(parallel)/D(perpendicular) = 1.23 +/- 0.01) and a global correlation time (tau(m)) of 12.41 +/- 0.01 ns. The unusually high average generalized order parameter (S2) of 0.90 +/- 0.02 indicates that TEM-1 is one of the most ordered proteins studied by liquid-state NMR to date. Although the omega-loop has a high degree of order in the picosecond-to-nanosecond time scale (mean S2 value of 0.90 +/- 0.02), we observed the presence of microsecond-to-millisecond time scale motions for this loop, as for the vicinity of the active site. These motions could be relevant for the catalytic function of TEM-1. Amide exchange experiments were also performed, and several amide groups were not exchanged after 12 days, an indication that global motions in TEM-1 are also very limited. Although detailed dynamics characterization by NMR cannot be readily applied to TEM-1 in the presence of relevant substrates, the unusual picosecond-to-nanosecond dynamics behavior of TEM-1 presented here will be essential to the validation and improvement of future molecular dynamics simulations of TEM-1 in the presence of functionally relevant substrates.
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Affiliation(s)
- Pierre-Yves Savard
- Département de Biochimie et de Microbiologie and CREFSIP, Université Laval, Québec, Canada G1K 7P4
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47
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Prasch S, Schwarz S, Eisenmann A, Wöhrl BM, Schweimer K, Rösch P. Interaction of the intrinsically unstructured phage lambda N Protein with Escherichia coli NusA. Biochemistry 2006; 45:4542-9. [PMID: 16584189 DOI: 10.1021/bi0523411] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N protein of the Escherichia coli phage lambda (lambdaN) is involved in antitermination, a transcription regulatory process that is essential for the expression of delayed early genes during phage lytic development. lambdaN is an intrinsically unstructured protein that possesses three distinct binding sites interacting with the carboxy terminus of the E. coli host factor protein NusA, the viral nutBoxB-RNA, and RNA polymerase, respectively. Heteronuclear NMR experiments with lambdaN(1-53) in complex with NusA(339-495) revealed that upon complex formation the lambdaN-binding interface, lambdaN(34-47), adopts a rigid structure. NMR data also indicate the induction of a weak helical structure in the nutboxB RNA-binding region lambdaN(1-22) upon binding to NusA(339-495) even in the absence of RNA. Titration experiments of the lambdaN(1-53)-nutBoxB RNA complex with NusA(339-495) revealed that the ternary complex can be described in terms of two structurally independent binary interactions. Furthermore, chemical-shift perturbation experiments with different NusA constructs and different lambdaN peptides showed that only NusA(353-416) is involved in lambdaN binding. We found that only one molecule of NusA(339-426) binds to one molecule of lambdaN(1-53). We also clarified the role of the lambdaN-binding region and could show that N41-R47 also binds to NusA(339-495). Furthermore, we observe that lambdaN(1-22) adopts a helical fold upon binding to NusA(339-495), in agreement with one of the theoretical models of lambdaN action.
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Affiliation(s)
- Stefan Prasch
- Lehrstuhl Biopolymere, Universität Bayreuth, Universitaetsstrasse 30, 95440 Bayreuth, Germany
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48
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Shapiro YE, Meirovitch E. Activation Energy of Catalysis-Related Domain Motion in E. coli Adenylate Kinase. J Phys Chem B 2006; 110:11519-24. [PMID: 16771428 DOI: 10.1021/jp060282a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adenylate kinase from E. coli (AKeco), folded into domains CORE, AMPbd, and LID, catalyzes the reaction AMP + ATP <--> 2ADP. Previous X-ray crystallography and optical solution methods showed that the domains AMPbd and LID, and the conserved P-loop, execute large-amplitude catalysis-related motions. We used (15)N NMR spin relaxation methods to find that the simplified model-free (MF) analysis does not, whereas our general Slowly Relaxing Local Structure analysis does, detect catalytic domain motion. SRLS set for the first time the correlation time for domain motion at tau(L)perpendicular = 8.2 ns, to be compared with tau(m) = 15.1 ns for global tumbling. These results were obtained at 303 K. Herein we conduct a temperature-dependent investigation of tau(L)perpendicular and tau(m) in the range of 288-310 K. We found that the activation energy for global tumbling is Ea = 16.9 +/- 0.5 kJ/mol, the hydrodynamic volume of hydrated AKeco is 65.6 +/- 2.1 nm3, its radius is 2.50 +/- 0.03 nm, and the number of hydration layers is 1.77. The average tau(L)perpendicular value decreases from 11 ns at 288 K to 4 ns at 310 K, with activation energies of 29.7 +/- 3.3, 32.1 +/- 4.3, and 30.4 +/- 4.3 kJ/mol for the domains AMPbd and LID, and the catalytic P-loop, respectively. These values are two-to-three times smaller than typical activation energies of enzymatic reactions. Hence kinase catalysis appears not to be controlled by domain motion in the ligand-free enzyme. However, the latter process clearly facilitates important mechanical aspects such as steric recognition and capturing of the AMP and ATP substrates, their proper positioning for phosphorylation, and the release of the ADP product.
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Affiliation(s)
- Yury E Shapiro
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
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Ragona L, Catalano M, Luppi M, Cicero D, Eliseo T, Foote J, Fogolari F, Zetta L, Molinari H. NMR dynamic studies suggest that allosteric activation regulates ligand binding in chicken liver bile acid-binding protein. J Biol Chem 2006; 281:9697-709. [PMID: 16439356 DOI: 10.1074/jbc.m513003200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apo chicken liver bile acid-binding protein has been structurally characterized by NMR. The dynamic behavior of the protein in its apo- and holo-forms, complexed with chenodeoxycholate, has been determined via (15)N relaxation and steady state heteronuclear (15)N((1)H) nuclear Overhauser effect measurements. The dynamic parameters were obtained at two pH values (5.6 and 7.0) for the apoprotein and at pH 7.0 for the holoprotein, using the model free approach. Relaxation studies, performed at three different magnetic fields, revealed a substantial conformational flexibility on the microsecond to millisecond time scales, mainly localized in the C-terminal face of the beta-barrel. The observed dynamics are primarily caused by the protonation/deprotonation of a buried histidine residue, His(98), located on this flexible face. A network of polar buried side chains, defining a spine going from the E to J strand, is likely to provide the long range connectivity needed to communicate motion from His(98) to the EF loop region. NMR data are accompanied by molecular dynamics simulations, suggesting that His(98) protonation equilibrium is the triggering event for the modulation of a functionally important motion, i.e. the opening/closing at the protein open end, whereas ligand binding stabilizes one of the preexisting conformations (the open form). The results presented here, complemented with an analysis of proteins belonging to the intracellular lipid-binding protein family, are consistent with a model of allosteric activation governing the binding mechanism. The functional role of this mechanism is thoroughly discussed within the framework of the mechanism for the enterohepatic circulation of bile acids.
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Affiliation(s)
- Laura Ragona
- Laboratorio NMR, ISMAC, Consiglio Nazionale delle Ricerche, via Bassini 15, 20133 Milano, Italy
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50
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Ding Z, Lee GI, Liang X, Gallazzi F, Arunima A, Van Doren SR. PhosphoThr peptide binding globally rigidifies much of the FHA domain from Arabidopsis receptor kinase-associated protein phosphatase. Biochemistry 2005; 44:10119-34. [PMID: 16042389 PMCID: PMC2813517 DOI: 10.1021/bi050414a] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A net increase in the backbone rigidity of the kinase-interacting FHA domain (KI-FHA) from the Arabidopsis receptor kinase-associated protein phosphatase (KAPP) accompanies the binding of a phosphoThr peptide from its CLV1 receptor-like kinase partner, according to (15)N NMR relaxation at 11.7 and 14.1 T. All of the loops of free KI-FHA display evidence of nanosecond-scale motions. Many of these same residues have residual dipolar couplings that deviate from structural predictions. Binding of the CLV1 pT868 peptide seems to reduce nanosecond-scale fluctuations of all loops, including half of the residues of recognition loops. Residues important for affinity are found to be rigid, i.e., conserved residues and residues of the subsite for the key pT+3 peptide position. This behavior parallels SH2 and PTB domain recognition of pTyr peptides. PhosphoThr peptide binding increases KI-FHA backbone rigidity (S(2)) of three recognition loops, a loop nearby, seven strands from the beta-sandwich, and a distal loop. Compensating the trend of increased rigidity, binding enhances fast mobility at a few sites in four loops on the periphery of the recognition surface and in two loops on the far side of the beta-sandwich. Line broadening evidence of microsecond- to millisecond-scale fluctuations occurs across the six-stranded beta-sheet and nearby edges of the beta-sandwich; this forms a network connected by packing of interior side chains and H-bonding. A patch of the slowly fluctuating residues coincides with the site of segment-swapped dimerization in crystals of the FHA domain of human Chfr. Phosphopeptide binding introduces microsecond- to millisecond-scale fluctuations to more residues of the long 8/9 recognition loop of KI-FHA. The rigidity of this FHA domain appears to couple as a whole to pThr peptide binding.
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Affiliation(s)
| | | | - Xiangyang Liang
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri, 65211
| | - Fabio Gallazzi
- Molecular Biology Program, 125 Chemistry, 601 S. College Ave., University of Missouri, Columbia, Missouri, 65211 USA
| | - A. Arunima
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri, 65211
| | - Steven R. Van Doren
- To whom correspondence should be addressed, E-mail: , Phone: 1 (573) 882-5113, FAX: 1 (573) 884-4812
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