1
|
Vaz DC, Rodrigues JR, Loureiro-Ferreira N, Müller TD, Sebald W, Redfield C, Brito RMM. Lessons on protein structure from interleukin-4: All disulfides are not created equal. Proteins 2024; 92:219-235. [PMID: 37814578 DOI: 10.1002/prot.26611] [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: 03/01/2023] [Revised: 09/09/2023] [Accepted: 09/25/2023] [Indexed: 10/11/2023]
Abstract
Interleukin-4 (IL-4) is a hematopoietic cytokine composed by a four-helix bundle stabilized by an antiparallel beta-sheet and three disulfide bonds: Cys3-Cys127, Cys24-Cys65, and Cys46-Cys99. IL-4 is involved in several immune responses associated to infection, allergy, autoimmunity, and cancer. Besides its physiological relevance, IL-4 is often used as a "model" for protein design and engineering. Hence, to understand the role of each disulfide in the structure and dynamics of IL-4, we carried out several spectroscopic analyses (circular dichroism [CD], fluorescence, nuclear magnetic resonance [NMR]), and molecular dynamics (MD) simulations on wild-type IL-4 and four IL-4 disulfide mutants. All disulfide mutants showed loss of structure, altered interhelical angles, and looser core packings, showing that all disulfides are relevant for maintaining the overall fold and stability of the four-helix bundle motif, even at very low pH. In the absence of the disulfide connecting both protein termini Cys3-Cys127, C3T-IL4 showed a less packed protein core, loss of secondary structure (~9%) and fast motions on the sub-nanosecond time scale (lower S2 order parameters and larger τc correlation time), especially at the two protein termini, loops, beginning of helix A and end of helix D. In the absence of Cys24-Cys65, C24T-IL4 presented shorter alpha-helices (14% loss in helical content), altered interhelical angles, less propensity to form the small anti-parallel beta-sheet and increased dynamics. Simultaneously deprived of two disulfides (Cys3-Cys127 and Cys24-Cys65), IL-4 formed a partially folded "molten globule" with high 8-anilino-1-naphtalenesulphonic acid-binding affinity and considerable loss of secondary structure (~50%decrease), as shown by the far UV-CD, NMR, and MD data.
Collapse
Affiliation(s)
- Daniela C Vaz
- School of Health Sciences, Polytechnic of Leiria, Leiria, Portugal
- Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, Coimbra Chemistry Centre, Institute of Molecular Sciences, Coimbra, Portugal
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), School of Technology and Management, Polytechnic of Leiria, Leiria, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), University of Porto, Porto, Portugal
| | - J Rui Rodrigues
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), School of Technology and Management, Polytechnic of Leiria, Leiria, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), University of Porto, Porto, Portugal
| | | | - Thomas D Müller
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, University of Würzburg, Würzburg, Germany
| | - Walter Sebald
- Department of Physiological Chemistry II, Theodor-Boveri-Institute (Biocentre), University of Würzburg, Würzburg, Germany
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Rui M M Brito
- Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, Coimbra Chemistry Centre, Institute of Molecular Sciences, Coimbra, Portugal
| |
Collapse
|
2
|
Shen Y, Bax A. Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:040901. [PMID: 37448874 PMCID: PMC10338066 DOI: 10.1063/4.0000192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
The important role of structural dynamics in protein function is widely recognized. Thermal or B-factors and their anisotropy, seen in x-ray analysis of protein structures, report on the presence of atomic coordinate heterogeneity that can be attributed to motion. However, their quantitative evaluation in terms of protein dynamics by x-ray ensemble refinement remains challenging. NMR spectroscopy provides quantitative information on the amplitudes and time scales of motional processes. Unfortunately, with a few exceptions, the NMR data do not provide direct insights into the atomic details of dynamic trajectories. Residual dipolar couplings, measured by solution NMR, are very precise parameters reporting on the time-averaged bond-vector orientations and may offer the opportunity to derive correctly weighted dynamic ensembles of structures for cases where multiple high-resolution x-ray structures are available. Applications to the SARS-CoV-2 main protease, Mpro, and ubiquitin highlight this complementarity of NMR and crystallography for quantitative assessment of internal motions.
Collapse
Affiliation(s)
| | - Ad Bax
- Author to whom correspondence should be addressed:
| |
Collapse
|
3
|
Shen Y, Robertson AJ, Bax A. Validation of X-ray Crystal Structure Ensemble Representations of SARS-CoV-2 Main Protease by Solution NMR Residual Dipolar Couplings. J Mol Biol 2023; 435:168067. [PMID: 37330294 PMCID: PMC10270724 DOI: 10.1016/j.jmb.2023.168067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
Considerable debate has focused on whether sampling of molecular dynamics trajectories restrained by crystallographic data can be used to develop realistic ensemble models for proteins in their natural, solution state. For the SARS-CoV-2 main protease, Mpro, we evaluated agreement between solution residual dipolar couplings (RDCs) and various recently reported multi-conformer and dynamic-ensemble crystallographic models. Although Phenix-derived ensemble models showed only small improvements in crystallographic Rfree, substantially improved RDC agreement over fits to a conventionally refined 1.2-Å X-ray structure was observed, in particular for residues with above average disorder in the ensemble. For a set of six lower resolution (1.55-2.19 Å) Mpro X-ray ensembles, obtained at temperatures ranging from 100 to 310 K, no significant improvement over conventional two-conformer representations was found. At the residue level, large differences in motions were observed among these ensembles, suggesting high uncertainties in the X-ray derived dynamics. Indeed, combining the six ensembles from the temperature series with the two 1.2-Å X-ray ensembles into a single 381-member "super ensemble" averaged these uncertainties and substantially improved agreement with RDCs. However, all ensembles showed excursions that were too large for the most dynamic fraction of residues. Our results suggest that further improvements to X-ray ensemble refinement are feasible, and that RDCs provide a sensitive benchmark in such endeavors. Remarkably, a weighted ensemble of 350 PDB Mpro X-ray structures provided slightly better cross-validated agreement with RDCs than any individual ensemble refinement, implying that differences in lattice confinement also limit the fit of RDCs to X-ray coordinates.
Collapse
Affiliation(s)
- Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Angus J Robertson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. https://twitter.com/angusjrobertson
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
4
|
Gallo M, Luti S, Baroni F, Baccelli I, Cilli EM, Cicchi C, Leri M, Spisni A, Pertinhez TA, Pazzagli L. Plant Defense Elicitation by the Hydrophobin Cerato-Ulmin and Correlation with Its Structural Features. Int J Mol Sci 2023; 24:2251. [PMID: 36768573 PMCID: PMC9916430 DOI: 10.3390/ijms24032251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023] Open
Abstract
Cerato-ulmin (CU) is a 75-amino-acid-long protein that belongs to the hydrophobin family. It self-assembles at hydrophobic-hydrophilic interfaces, forming films that reverse the wettability properties of the bound surface: a capability that may confer selective advantages to the fungus in colonizing and infecting elm trees. Here, we show for the first time that CU can elicit a defense reaction (induction of phytoalexin synthesis and ROS production) in non-host plants (Arabidopsis) and exerts its eliciting capacity more efficiently when in its soluble monomeric form. We identified two hydrophobic clusters on the protein's loops endowed with dynamical and physical properties compatible with the possibility of reversibly interconverting between a disordered conformation and a β-strand-rich conformation when interacting with hydrophilic or hydrophobic surfaces. We propose that the plasticity of those loops may be part of the molecular mechanism that governs the protein defense elicitation capability.
Collapse
Affiliation(s)
- Mariana Gallo
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy
| | - Simone Luti
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, 50121 Firenze, Italy
| | - Fabio Baroni
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy
| | - Ivan Baccelli
- Institute for Sustainable Plant Protection, National Research Council of Italy, Sesto Fiorentino, 50019 Florence, Italy
| | - Eduardo Maffud Cilli
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara 14800-901, Brazil
| | - Costanza Cicchi
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, 50121 Firenze, Italy
| | - Manuela Leri
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, 50121 Firenze, Italy
| | - Alberto Spisni
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy
| | | | - Luigia Pazzagli
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, 50121 Firenze, Italy
| |
Collapse
|
5
|
Krishnarjuna B, Ravula T, Faison EM, Tonelli M, Zhang Q, Ramamoorthy A. Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids. Biomolecules 2022; 12:1628. [PMID: 36358983 PMCID: PMC9687133 DOI: 10.3390/biom12111628] [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: 09/29/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Residual dipolar couplings (RDCs) are increasingly used for high-throughput NMR-based structural studies and to provide long-range angular constraints to validate and refine structures of various molecules determined by X-ray crystallography and NMR spectroscopy. RDCs of a given molecule can be measured in an anisotropic environment that aligns in an external magnetic field. Here, we demonstrate the first application of polymer-based nanodiscs for the measurement of RDCs from nucleic acids. Polymer-based nanodiscs prepared using negatively charged SMA-EA polymer and zwitterionic DMPC lipids were characterized by size-exclusion chromatography, 1H NMR, dynamic light-scattering, and 2H NMR. The magnetically aligned polymer-nanodiscs were used as an alignment medium to measure RDCs from a 13C/15N-labeled fluoride riboswitch aptamer using 2D ARTSY-HSQC NMR experiments. The results showed that the alignment of nanodiscs is stable for nucleic acids and nanodisc-induced RDCs fit well with the previously determined solution structure of the riboswitch. These results demonstrate that SMA-EA-based lipid-nanodiscs can be used as a stable alignment medium for high-resolution structural and dynamical studies of nucleic acids, and they can also be applicable to study various other biomolecules and small molecules in general.
Collapse
Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Edgar M. Faison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
6
|
Chiliveri SC, Robertson AJ, Shen Y, Torchia DA, Bax A. Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems. Chem Rev 2021; 122:9307-9330. [PMID: 34766756 DOI: 10.1021/acs.chemrev.1c00730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The measurement and application of residual dipolar couplings (RDCs) in solution NMR studies of biological macromolecules has become well established over the past quarter of a century. Numerous methods for generating the requisite anisotropic orientational molecular distribution have been demonstrated, each with its specific strengths and weaknesses. In parallel, an enormous number of pulse schemes have been introduced to measure the many different types of RDCs, ranging from the most widely measured backbone amide 15N-1H RDCs, to 1H-1H RDCs and couplings between low-γ nuclei. Applications of RDCs range from structure validation and refinement to the determination of relative domain orientations, the measurement of backbone and domain motions, and de novo structure determination. Nevertheless, it appears that the power of the RDC methodology remains underutilized. This review aims to highlight the practical aspects of sample preparation and RDC measurement while describing some of the most straightforward applications that take advantage of the exceptionally precise information contained in such data. Some emphasis will be placed on more recent developments that enable the accurate measurement of RDCs in larger systems, which is key to the ongoing shift in focus of biological NMR spectroscopy from structure determination toward gaining improved understanding of how molecular flexibility drives protein function.
Collapse
Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Angus J Robertson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dennis A Torchia
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| |
Collapse
|
7
|
Ibáñez de Opakua A, Zweckstetter M. Extending the applicability of P3D for structure determination of small molecules. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:105-116. [PMID: 37904779 PMCID: PMC10539764 DOI: 10.5194/mr-2-105-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/15/2021] [Indexed: 11/01/2023]
Abstract
The application of anisotropic nuclear magnetic resonance (NMR) parameters for the correct structural assignment of small molecules requires the use of partially ordered media. Previously we demonstrated that the use of P3D simulations using poly(γ -benzyl-L-glutamate) (PBLG) as an alignment medium allows for the determination of the correct diastereomer from extremely sparse NMR data. Through the analysis of the structural characteristics of small molecules in different alignment media, here we show that when steric or electrostatic factors dominate the alignment, P3D-PBLG retains its diastereomer discrimination power. We also demonstrate that P3D simulations can define the different conformations of a flexible small molecule from sparse NMR data.
Collapse
Affiliation(s)
- Alain Ibáñez de Opakua
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| |
Collapse
|
8
|
Wang Y, An L, Yang Y, Yao L. Generating Five Independent Molecular Alignments for Simultaneous Protein Structure and Dynamics Determination Using Nuclear Magnetic Resonance Spectroscopy. Anal Chem 2020; 92:15263-15269. [PMID: 33166130 DOI: 10.1021/acs.analchem.0c02882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) are commonly used in NMR for protein structure and dynamics studies, but it is challenging to generate five independent RDC data sets (required for simultaneous structure and dynamics determination) for most protein molecules in the magnetic field. In this work, a reporter protein with a lanthanide tag is introduced to create five independent alignments. This reporter protein is then attached to target proteins where five independent sets of RDCs are also obtained for the target proteins. The fitting of RDCs provides important information about the structure and dynamics of the target proteins. The method is simple and effective and, in principle, can be used to generate complete sets of RDCs for different protein molecules.
Collapse
Affiliation(s)
| | - Liaoyuan An
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | | |
Collapse
|
9
|
Giassa IC, Vavrinská A, Zelinka J, Šebera J, Sychrovský V, Boelens R, Fiala R, Trantírek L. HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids. Chempluschem 2020; 85:2177-2185. [PMID: 32986260 DOI: 10.1002/cplu.202000505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Indexed: 11/06/2022]
Abstract
Field-Induced Residual Dipolar Couplings (fiRDC) are a valuable source of long-range information on structure of nucleic acids (NA) in solution. A web application (HERMES) was developed for structure-based prediction and analysis of the (fiRDCs) in NA. fiRDC prediction is based on input 3D model structure(s) of NA and a built-in library of nucleobase-specific magnetic susceptibility tensors and reference geometries. HERMES allows three basic applications: (i) the prediction of fiRDCs for a given structural model of NAs, (ii) the validation of experimental or modeled NA structures using experimentally derived fiRDCs, and (iii) assessment of the oligomeric state of the NA fragment and/or the identification of a molecular NA model that is consistent with experimentally derived fiRDC data. Additionally, the program's built-in routine for rigid body modeling allows the evaluation of relative orientation of domains within NA that is in agreement with experimental fiRDCs.
Collapse
Affiliation(s)
| | - Andrea Vavrinská
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Jiří Zelinka
- Department of Mathematics and Statistics, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, 166 10, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, 166 10, Czech Republic
| | - Rolf Boelens
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Brno
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Brno
| |
Collapse
|
10
|
Tolkatchev D, Smith GE, Schultz LE, Colpan M, Helms GL, Cort JR, Gregorio CC, Kostyukova AS. Leiomodin creates a leaky cap at the pointed end of actin-thin filaments. PLoS Biol 2020; 18:e3000848. [PMID: 32898131 PMCID: PMC7500696 DOI: 10.1371/journal.pbio.3000848] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 09/18/2020] [Accepted: 08/17/2020] [Indexed: 01/26/2023] Open
Abstract
Improper lengths of actin-thin filaments are associated with altered contractile activity and lethal myopathies. Leiomodin, a member of the tropomodulin family of proteins, is critical in thin filament assembly and maintenance; however, its role is under dispute. Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. Our structural data indicate that the leiomodin/tropomyosin complex only forms at the pointed end of thin filaments, where the tropomyosin N-terminus is not blocked by an adjacent tropomyosin protomer. This discovery provides evidence supporting the debated mechanism where leiomodin and tropomodulin regulate thin filament lengths by competing for thin filament binding. Data from experiments performed in cardiomyocytes provide additional support for the competition model; specifically, expression of a leiomodin mutant that is unable to interact with tropomyosin fails to displace tropomodulin at thin filament pointed ends and fails to elongate thin filaments. Together with previous structural and biochemical data, we now propose a molecular mechanism of actin polymerization at the pointed end in the presence of bound leiomodin. In the proposed model, the N-terminal actin-binding site of leiomodin can act as a "swinging gate" allowing limited actin polymerization, thus making leiomodin a leaky pointed-end cap. Results presented in this work answer long-standing questions about the role of leiomodin in thin filament length regulation and maintenance.
Collapse
Affiliation(s)
- Dmitri Tolkatchev
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States of America
| | - Garry E. Smith
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States of America
| | - Lauren E. Schultz
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, Arizona, United States of America
| | - Mert Colpan
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, Arizona, United States of America
| | - Gregory L. Helms
- The Center for NMR Spectroscopy, Washington State University, Pullman, Washington, United States of America
| | - John R. Cort
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Carol C. Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, Arizona, United States of America
| | - Alla S. Kostyukova
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States of America
| |
Collapse
|
11
|
Nardelli F, Borsacchi S, Calucci L, Carignani E, Martini F, Geppi M. Anisotropy and NMR spectroscopy. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2020. [DOI: 10.1007/s12210-020-00945-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abstract
In this paper, different aspects concerning anisotropy in Nuclear Magnetic Resonance (NMR) spectroscopy have been reviewed. In particular, the relevant theory has been presented, showing how anisotropy stems from the dependence of internal nuclear spin interactions on the molecular orientation with respect to the external magnetic field direction. The consequences of anisotropy in the use of NMR spectroscopy have been critically discussed: on one side, the availability of very detailed structural and dynamic information, and on the other side, the loss of spectral resolution. The experiments used to measure the anisotropic properties in solid and soft materials, where, in contrast to liquids, such properties are not averaged out by the molecular tumbling, have been described. Such experiments can be based either on static low-resolution techniques or on one- and two-dimensional pulse sequences exploiting Magic Angle Spinning (MAS). Examples of applications of NMR spectroscopy have been shown, which exploit anisotropy to obtain important physico-chemical information on several categories of systems, including pharmaceuticals, inorganic materials, polymers, liquid crystals, and self-assembling amphiphiles in water. Solid-state NMR spectroscopy can be considered, nowadays, one of the most powerful characterization techniques for all kinds of solid, either amorphous or crystalline, and semi-solid systems for the obtainment of both structural and dynamic properties on a molecular and supra-molecular scale.
Graphic abstract
Collapse
|
12
|
Danmaliki GI, Hwang PM. Solution NMR spectroscopy of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183356. [PMID: 32416193 DOI: 10.1016/j.bbamem.2020.183356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 02/06/2023]
Abstract
Integral membrane proteins (IMPs) perform unique and indispensable functions in the cell, making them attractive targets for fundamental research and drug discovery. Developments in protein production, isotope labeling, sample preparation, and pulse sequences have extended the utility of solution NMR spectroscopy for studying IMPs with multiple transmembrane segments. Here we review some recent applications of solution NMR for studying structure, dynamics, and interactions of polytopic IMPs, emphasizing strategies used to overcome common technical challenges.
Collapse
Affiliation(s)
- Gaddafi I Danmaliki
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Peter M Hwang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
| |
Collapse
|
13
|
Shine A, Shenoy J, Jayan P, Jiji AC, Vijayan V. Residual Dipolar‐Coupling‐Based Conformational Comparison of Noncovalent Ubiquitin Homodimer with Covalently Linked Diubiquitin. Chemphyschem 2020; 21:888-894. [DOI: 10.1002/cphc.201901100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/06/2020] [Indexed: 11/08/2022]
Affiliation(s)
- A. Shine
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| | - J. Shenoy
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| | - Parvathy Jayan
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| | - A. C. Jiji
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| | - Vinesh Vijayan
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| |
Collapse
|
14
|
Ibáñez de Opakua A, Klama F, Ndukwe IE, Martin GE, Williamson RT, Zweckstetter M. Determination of Complex Small-Molecule Structures Using Molecular Alignment Simulation. Angew Chem Int Ed Engl 2020; 59:6172-6176. [PMID: 31971323 PMCID: PMC7187346 DOI: 10.1002/anie.202000311] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/23/2020] [Indexed: 11/12/2022]
Abstract
Correct structural assignment of small molecules and natural products is critical for drug discovery and organic chemistry. Anisotropy-based NMR spectroscopy is a powerful tool for the structural assignment of organic molecules, but it relies on the utilization of a medium that disrupts the isotropic motion of molecules in organic solvents. Here, we establish a quantitative correlation between the atomic structure of the alignment medium, the molecular structure of the small molecule, and molecule-specific anisotropic NMR parameters. The quantitative correlation uses an accurate three-dimensional molecular alignment model that predicts residual dipolar couplings of small molecules aligned by poly(γ-benzyl-l-glutamate). The technique facilitates reliable determination of the correct stereoisomer and enables unequivocal, rapid determination of complex molecular structures from extremely sparse NMR data.
Collapse
Affiliation(s)
- Alain Ibáñez de Opakua
- Structural Biology in DementiaGerman Center for Neurodegenerative Diseases (DZNE)Von-Siebold-Strasse 3a37075GöttingenGermany
| | - Frederik Klama
- Department for NMR-based Structural BiologyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Ikenna E. Ndukwe
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Complex Carbohydrate Research CenterUniversity of GeorgiaAthensGA30602USA
| | - Gary E. Martin
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Department of Chemistry and BiochemistrySeton Hall UniversitySouth OrangeNJ07079USA
| | - R. Thomas Williamson
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Department of Chemistry & BiochemistryUniversity of North Carolina WilmingtonWilmingtonNC28409USA
| | - Markus Zweckstetter
- Structural Biology in DementiaGerman Center for Neurodegenerative Diseases (DZNE)Von-Siebold-Strasse 3a37075GöttingenGermany
- Department for NMR-based Structural BiologyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| |
Collapse
|
15
|
Fargason T, Wang T, De Silva NIU, Zhang Z, McKelvey H, Knapp T, Zaharias S, Zhang J. Amide additives improve RDC measurements in polyacrylamide. JOURNAL OF BIOMOLECULAR NMR 2020; 74:119-124. [PMID: 32056065 DOI: 10.1007/s10858-020-00305-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/08/2020] [Indexed: 06/10/2023]
Abstract
Residual dipolar couplings (RDCs) provide valuable NMR parameters that can be used for structural calculation and verification. Measuring RDCs requires aligning macromolecules using one of various types of alignment media. Of different alignment media options, stretched or compressed polyacrylamide gels are advantageous due to their chemical stability. However, polyacrylamide interacts with proteins and significantly broadens NMR resonances. In this study, we found that the amide-containing compounds asparagine, glutamine and propionamide improve spectral quality of proteins in polyacrylamide gel without significantly reducing the magnitude of RDC values. Moreover, we showed that propionamide is an attractive additive that increases protein solubility without interfering with protein stability, ligand binding or NMR pulse width, suggesting its potential applications for our NMR methods.
Collapse
Affiliation(s)
- Talia Fargason
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
| | - Ting Wang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
| | - Naiduwadura Ivon Upekala De Silva
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
| | - Zihan Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
| | - Heather McKelvey
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
| | - Taylor Knapp
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
| | - Steve Zaharias
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
| | - Jun Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA.
| |
Collapse
|
16
|
Zapletal V, Mládek A, Melková K, Louša P, Nomilner E, Jaseňáková Z, Kubáň V, Makovická M, Laníková A, Žídek L, Hritz J. Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions. Biophys J 2020; 118:1621-1633. [PMID: 32367806 DOI: 10.1016/j.bpj.2020.02.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 01/06/2020] [Accepted: 02/05/2020] [Indexed: 12/23/2022] Open
Abstract
Biomolecular force fields optimized for globular proteins fail to properly reproduce properties of intrinsically disordered proteins. In particular, parameters of the water model need to be modified to improve applicability of the force fields to both ordered and disordered proteins. Here, we compared performance of force fields recommended for intrinsically disordered proteins in molecular dynamics simulations of three proteins differing in the content of ordered and disordered regions (two proteins consisting of a well-structured domain and of a disordered region with and without a transient helical motif and one disordered protein containing a region of increased helical propensity). The obtained molecular dynamics trajectories were used to predict measurable parameters, including radii of gyration of the proteins and chemical shifts, residual dipolar couplings, paramagnetic relaxation enhancement, and NMR relaxation data of their individual residues. The predicted quantities were compared with experimental data obtained within this study or published previously. The results showed that the NMR relaxation parameters, rarely used for benchmarking, are particularly sensitive to the choice of force-field parameters, especially those defining the water model. Interestingly, the TIP3P water model, leading to an artificial structural collapse, also resulted in unrealistic relaxation properties. The TIP4P-D water model, combined with three biomolecular force-field parameters for the protein part, significantly improved reliability of the simulations. Additional analysis revealed only one particular force field capable of retaining the transient helical motif observed in NMR experiments. The benchmarking protocol used in our study, being more sensitive to imperfections than the commonly used tests, is well suited to evaluate the performance of newly developed force fields.
Collapse
Affiliation(s)
- Vojtěch Zapletal
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Arnošt Mládek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kateřina Melková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Petr Louša
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Erik Nomilner
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zuzana Jaseňáková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vojtěch Kubáň
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Markéta Makovická
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Alice Laníková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lukáš Žídek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| |
Collapse
|
17
|
Ibáñez de Opakua A, Klama F, Ndukwe IE, Martin GE, Williamson RT, Zweckstetter M. Bestimmung komplexer kleiner Molekülstrukturen mittels molekularer Ausrichtungssimulation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alain Ibáñez de Opakua
- Translationale Strukturelle Biologie der DemenzDeutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Deutschland
| | - Frederik Klama
- Abteilung für NMR-basierte StrukturbiologieMax-Planck-Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Deutschland
| | - Ikenna E. Ndukwe
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Complex Carbohydrate Research CenterUniversity of Georgia Athens GA 30602 USA
| | - Gary E. Martin
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Department of Chemistry and BiochemistrySeton Hall University South Orange NJ 07079 USA
| | - R. Thomas Williamson
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Department of Chemistry & BiochemistryUniversity of North Carolina Wilmington Wilmington NC 28409 USA
| | - Markus Zweckstetter
- Translationale Strukturelle Biologie der DemenzDeutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Deutschland
- Abteilung für NMR-basierte StrukturbiologieMax-Planck-Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Deutschland
| |
Collapse
|
18
|
Orton H, Huber T, Otting G. Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:1-12. [PMID: 37904891 PMCID: PMC10500712 DOI: 10.5194/mr-1-1-2020] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/20/2020] [Indexed: 11/01/2023]
Abstract
Paramagnetic metal ions with fast-relaxing electrons generate pseudocontact shifts (PCSs), residual dipolar couplings (RDCs), paramagnetic relaxation enhancements (PREs) and cross-correlated relaxation (CCR) in the nuclear magnetic resonance (NMR) spectra of the molecules they bind to. These effects offer long-range structural information in molecules equipped with binding sites for such metal ions. Here we present the new open-source software Paramagpy, which has been written in Python 3 with a graphic user interface. Paramagpy combines the functionalities of different currently available programs to support the fitting of magnetic susceptibility tensors using PCS, RDC, PRE and CCR data and molecular coordinates in Protein Data Bank (PDB) format, including a convenient graphical user interface. Paramagpy uses efficient fitting algorithms to avoid local minima and supports corrections to back-calculated PCS and PRE data arising from cross-correlation effects with chemical shift tensors. The source code is available from 10.5281/zenodo.3594568 .
Collapse
Affiliation(s)
- Henry William Orton
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
19
|
Ramanujam V, Shen Y, Ying J, Mobli M. Residual Dipolar Couplings for Resolving Cysteine Bridges in Disulfide-Rich Peptides. Front Chem 2020; 7:889. [PMID: 32039137 PMCID: PMC6987419 DOI: 10.3389/fchem.2019.00889] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 12/10/2019] [Indexed: 11/25/2022] Open
Abstract
Disulfide bridges in proteins are formed by the oxidation of pairs of cysteine residues. These cross-links play a critical role in stabilizing the 3D-structure of small disulfide rich polypeptides such as hormones and venom toxins. The arrangement of the multiple disulfide bonds directs the peptide fold into distinct structural motifs that have evolved for resistance against biochemical and physical insults. These structural scaffolds have, therefore, proven to be very attractive in bioengineering efforts to develop novel biologics with applications in health and agriculture. Structural characterization of small disulfide rich peptides (DRPs) presents unique challenges when using commonly applied biophysical methods. NMR is the most commonly used method for studying such molecules, where the relatively small size of these molecules results in highly precise structural ensembles defined by a large number of distance and dihedral angle restraints per amino acid. However, in NMR the sulfur atoms that are involved in three of the five dihedral angles in a disulfide bond cannot be readily measured. Given the central role of disulfide bonds in the structure of these molecules, it is unclear what the inherent resolution of such NMR structures is when using traditional NMR methods. Here, we use an extensive set of long-range residual dipolar couplings (RDCs) to assess the resolution of the NMR structure of a disulfide-rich peptide. We find that structures based primarily on NOEs, yield ensembles that are equivalent to a crystallographic resolution of 2-3 Å in resolution, and that incorporation of RDCs reduces this to ~1-1.5 Å resolution. At this resolution the sidechain of ordered amino acids can be defined accurately, allowing the geometry of the cysteine bridges to be better defined, and allowing for disulfide-bond connectivities to be determined with high confidence. The observed improvements in resolution when using RDCs is remarkable considering the small size of these peptides.
Collapse
Affiliation(s)
- Venkatraman Ramanujam
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia
| |
Collapse
|
20
|
Schirò A, Carlon A, Parigi G, Murshudov G, Calderone V, Ravera E, Luchinat C. On the complementarity of X-ray and NMR data. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100019. [PMID: 32647823 PMCID: PMC7337059 DOI: 10.1016/j.yjsbx.2020.100019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/28/2019] [Accepted: 01/02/2020] [Indexed: 12/20/2022]
Abstract
X-ray crystallography and NMR contain complementary information for the structural characterization of biological macromolecules. X-ray diffraction is primarily sensitive to the overall shape of the molecule, whereas NMR is mostly sensitive to the atomic detail. Their combination can therefore provide a stronger justification for the resulting structure. For their combination we have recently proposed REFMAC-NMR, which relies on primary data from both techniques for joint refinement. This possibility raises the compelling question of how far the complementarity can be extended. In this paper, we describe an integrative approach to the refinement with NMR data of four X-ray structures of hen-egg-white lysozyme, solved at atomic resolution in four different crystal forms, and we demonstrate that the outcome critically depends on the crystal form itself, reflecting the sensitivity of NMR to fine details.
Collapse
Affiliation(s)
- Antonio Schirò
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Azzurra Carlon
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Garib Murshudov
- MRC Laboratory for Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Vito Calderone
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| |
Collapse
|
21
|
Kooshapur H, Ma J, Tjandra N, Bermejo GA. NMR Analysis of Apo Glutamine‐Binding Protein Exposes Challenges in the Study of Interdomain Dynamics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hamed Kooshapur
- Laboratory of Structural BiophysicsBiochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of Health Bethesda MD 20892 USA
| | - Junhe Ma
- Laboratory of Structural BiophysicsBiochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of Health Bethesda MD 20892 USA
- Present address: Ashland Specialty Ingredients 500 Hercules Rd. Wilmington DE 19808 USA
| | - Nico Tjandra
- Laboratory of Structural BiophysicsBiochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of Health Bethesda MD 20892 USA
| | - Guillermo A. Bermejo
- Office of Intramural ResearchCenter for Information TechnologyNational Institutes of Health Bethesda MD 20892 USA
| |
Collapse
|
22
|
Bibow S. Opportunities and Challenges of Backbone, Sidechain, and RDC Experiments to Study Membrane Protein Dynamics in a Detergent-Free Lipid Environment Using Solution State NMR. Front Mol Biosci 2019; 6:103. [PMID: 31709261 PMCID: PMC6823230 DOI: 10.3389/fmolb.2019.00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/19/2019] [Indexed: 12/22/2022] Open
Abstract
Whereas solution state NMR provided a wealth of information on the dynamics landscape of soluble proteins, only few studies have investigated membrane protein dynamics in a detergent-free lipid environment. Recent developments of smaller nanodiscs and other lipid-scaffolding polymers, such as styrene maleic acid (SMA), however, open new and promising avenues to explore the function-dynamics relationship of membrane proteins as well as between membrane proteins and their surrounding lipid environment. Favorably sized lipid-bilayer nanodiscs, established membrane protein reconstitution protocols and sophisticated solution NMR relaxation methods probing dynamics over a wide range of timescales will eventually reveal unprecedented lipid-membrane protein interdependencies that allow us to explain things we have not been able to explain so far. In particular, methyl group dynamics resulting from CEST, CPMG, ZZ exchange, and RDC experiments are expected to provide new and surprising insights due to their proximity to lipids, their applicability in large 100+ kDa assemblies and their simple labeling due to the availability of commercial precursors. This review summarizes the recent developments of membrane protein dynamics with a special focus on membrane protein dynamics in lipid-bilayer nanodiscs. Opportunities and challenges of backbone, side chain and RDC dynamics applied to membrane proteins are discussed. Solution-state NMR and lipid nanodiscs bear great potential to change our molecular understanding of lipid-membrane protein interactions.
Collapse
Affiliation(s)
- Stefan Bibow
- Biozentrum, University of Basel, Basel, Switzerland
| |
Collapse
|
23
|
Ravula T, Ramamoorthy A. Magnetic Alignment of Polymer Macro-Nanodiscs Enables Residual-Dipolar-Coupling-Based High-Resolution Structural Studies by NMR Spectroscopy. Angew Chem Int Ed Engl 2019; 58:14925-14928. [PMID: 31310700 PMCID: PMC7161179 DOI: 10.1002/anie.201907655] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Indexed: 01/18/2023]
Abstract
Experimentally measured residual dipolar couplings (RDCs) are highly valuable for atomic-resolution structural and dynamic studies of molecular systems ranging from small molecules to large proteins by solution NMR spectroscopy. Here we demonstrate the first use of magnetic-alignment behavior of lyotropic liquid-crystalline polymer macro-nanodiscs (>20 nm in diameter) as a novel alignment medium for the measurement of RDCs using high-resolution NMR. The easy preparation of macro-nanodiscs, their high stability against pH changes and the presence of divalent metal ions, and their high homogeneity make them an efficient tool to investigate a wide range of molecular systems including natural products, proteins, and RNA.
Collapse
Affiliation(s)
- Thirupathi Ravula
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| |
Collapse
|
24
|
Ravula T, Ramamoorthy A. Magnetic Alignment of Polymer Macro‐Nanodiscs Enables Residual‐Dipolar‐Coupling‐Based High‐Resolution Structural Studies by NMR Spectroscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Thirupathi Ravula
- Department of Chemistry and Biophysics Biomedical Engineering, Macromolecular Science and Engineering University of Michigan Ann Arbor MI 48109-1055 USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics Biomedical Engineering, Macromolecular Science and Engineering University of Michigan Ann Arbor MI 48109-1055 USA
| |
Collapse
|
25
|
Kooshapur H, Ma J, Tjandra N, Bermejo GA. NMR Analysis of Apo Glutamine-Binding Protein Exposes Challenges in the Study of Interdomain Dynamics. Angew Chem Int Ed Engl 2019; 58:16899-16902. [PMID: 31515908 DOI: 10.1002/anie.201911015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Indexed: 02/06/2023]
Abstract
Glutamine-binding protein (GlnBP) displays an apo, "open" and a holo, "closed" crystal form, mutually related by a rigid-body reorientation of its domains. A fundamental question about such large-scale conformational transitions, whether the closed state exists in the absence of ligand, is controversial in the case of GlnBP. NMR observations have indicated no evidence of the closed form, whereas experimentally validated computations have suggested a remarkable ca. 40 % population. Herein, a paramagnetic NMR strategy designed to detect the putative apo-closed species shows that a major population of the latter is highly improbable. Further, NMR residual dipolar couplings collected under three anisotropic conditions do not reveal differential domain alignment and establish that the average solution conformation is satisfied by the apo-open crystal structure. Our results indicate that the computational prediction of large-scale interdomain motions is not trivial and may lead to erroneous conclusions without proper experimental validation.
Collapse
Affiliation(s)
- Hamed Kooshapur
- Laboratory of Structural Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Junhe Ma
- Laboratory of Structural Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Present address: Ashland Specialty Ingredients, 500 Hercules Rd., Wilmington, DE, 19808, USA
| | - Nico Tjandra
- Laboratory of Structural Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Guillermo A Bermejo
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD, 20892, USA
| |
Collapse
|
26
|
Lorieau JL. Partial alignment, residual dipolar couplings and molecular symmetry in solution NMR. JOURNAL OF BIOMOLECULAR NMR 2019; 73:477-491. [PMID: 31407205 DOI: 10.1007/s10858-019-00256-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
Residual dipolar couplings (RDCs) and residual anisotropic chemical shifts (RACSs) are produced by the partial alignment of solution NMR samples. RDCs and RACSs yield high-resolution structural and dynamic information on the orientation of bonds and chemical groups in molecules. Many molecules form oligomers or have intrinsic symmetries, which may simplify the analysis of their partial alignment datasets. In this report, we explore the theory of partial alignment using an irreducible spherical representation, and we investigate the impact of molecular symmetry on the alignment of molecules. Though previous studies have reported simplified relationships on the partial alignment of molecules bearing different symmetry groups, we show that these simplified relationships may not be universal and only apply to a limited set of systems.
Collapse
Affiliation(s)
- Justin L Lorieau
- Department of Chemistry, University of Illinois at Chicago, 4500 SES, 845 W Taylor St, Chicago, IL, 60607, USA.
| |
Collapse
|
27
|
Accuracy of MD solvent models in RNA structure refinement assessed via liquid-crystal NMR and spin relaxation data. J Struct Biol 2019; 207:250-259. [PMID: 31279068 DOI: 10.1016/j.jsb.2019.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 11/20/2022]
Abstract
Molecular dynamics (MD) simulations play an important role in characterizing Ribonucleic Acid (RNA) structure, augmenting information from experimental techniques such as Nuclear Magnetic Resonance (NMR). In this work, we examine the accuracy of structural representation resulting from application of a number of explicit and implicit solvent models and refinement protocols against experimental data ranging from high density of residual dipolar coupling (RDC) restraints to completely unrestrained simulations. For a prototype A-form RNA helix, our results indicate that AMBER RNA force field with either implicit or explicit solvent can produce a realistic dynamic representation of RNA helical structure, accurately cross-validating with respect to a diverse array of NMR observables. In refinement against NMR distance restraints, modern MD force fields are found to be equally adequate, with high fidelity cross-validation to the residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs), while slightly over-estimating structural order as monitored via NMR relaxation data. With restraints trimmed to encode only for base pairing information, cross-validation quality significantly deteriorates, now exhibiting a pronounced dependence on the choice of the solvent model. This deterioration is found to be partially reversible by increasing planarity restraints on the nucleobase geometry. For completely unrestrained MD simulations, the choice of water model becomes very important, with the best-performing TIP4P-Ew accurately reproducing both the RDC and RCSA data, while closely matching the NMR-derived order parameters. The information provided here will serve as a foundation for MD-based refinement of solution state NMR structures of RNA.
Collapse
|
28
|
Solution NMR Spectroscopy for the Determination of Structures of Membrane Proteins in a Lipid Environment. Methods Mol Biol 2019. [PMID: 31218634 DOI: 10.1007/978-1-4939-9512-7_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2023]
Abstract
NMR spectroscopy has harnessed the recent technical advances to emerge as a competitive, elegant, and eminently viable technique for determining the solution structures of membrane proteins at the level of atomic resolution. Once a good level of cell-based or cell-free expression and purification of a suitably sized membrane protein has been achieved, then NMR offers a combination of several versatile strategies, for example choice of appropriate deuterated or nondeuterated detergents, temperature, and ionic strength; isotope labeling with 2H, 13C, 15N, with or without protonation of Ile (δ1), Leu, and Val methyl protons; combinatorial labeling or unlabeling of specific amino acids; TROSY based-, nonuniform sampling (NUS) based-, and other NMR experiments; measurement of residual dipolar couplings using stretched polyacrylamide gels or DNA nanotubes; spin labeling and paramagnetic relaxation enhancements (PRE). Strategic combinations of these advancements together with availability of highly sensitive cryogenically cooled-probes equipped high-field NMR spectrometers (up to 1 GHz 1H frequency) have allowed the perseverant investigator to successfully overcome several of the conventional pitfalls associated with the NMR technique and membrane proteins, viz., low sensitivity, poor sample stability, spectral crowding, and a limited number of NOEs and other constraints for structure calculations. This has resulted in an unprecedented growth in the number of successfully determined NMR structures of large and complex membrane proteins over the last two decades, and this technique now holds great promise for the structure determination of an ever larger body of membrane proteins.
Collapse
|
29
|
Ndukwe IE, Brunskill A, Gauthier DR, Zhong YL, Martin GE, Williamson RT, Reibarkh M, Liu Y. 13C NMR-Based Approaches for Solving Challenging Stereochemical Problems. Org Lett 2019; 21:4072-4076. [PMID: 31117703 DOI: 10.1021/acs.orglett.9b01248] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Determining the configuration of proton-deficient molecules is challenging using conventional NMR methods including nuclear Overhauser effect (NOE) and the proton-dependent J-based configuration analysis (JBCA). The problem is exacerbated when only one stereoisomer is available. Alternative methods based on the utilization of 13C NMR chemical shifts, 13C-13C homonuclear couplings measured at natural abundance, and residual chemical shift anisotropy measurements in conjunction with density functional theory calculations are illustrated with a proton-deficient model compound.
Collapse
Affiliation(s)
- Ikenna E Ndukwe
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Andrew Brunskill
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Donald R Gauthier
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Yong-Li Zhong
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Gary E Martin
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - R Thomas Williamson
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Mikhail Reibarkh
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Yizhou Liu
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| |
Collapse
|
30
|
Bergonzo C, Grishaev A. Maximizing accuracy of RNA structure in refinement against residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2019; 73:117-139. [PMID: 31049778 DOI: 10.1007/s10858-019-00236-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 02/12/2019] [Indexed: 06/09/2023]
Abstract
Structural information about ribonucleic acid (RNA) is lagging behind that of proteins, in part due to its high charge and conformational variability. Molecular dynamics (MD) has played an important role in describing RNA structure, complementing information from both nuclear magnetic resonance (NMR), or X-ray crystallography. We examine the impact of the choice of the empirical force field for RNA structure refinement using cross-validation against residual dipolar couplings (RDCs) as structural accuracy reporter. Four force fields, representing both the state-of-the art in RNA simulation and the most popular selections in NMR structure determination, are compared for a prototypical A-RNA helix. RNA structural accuracy is also evaluated as a function of both density and nature of input NMR data including RDCs, anisotropic chemical shifts, and distance restraints. Our results show a complex interplay between the experimental restraints and the force fields indicating two best-performing choices: high-fidelity refinement in explicit solvent, and the conformational database-derived potentials. Accuracy of RNA models closely tracks the density of 1-bond C-H RDCs, with other data types having beneficial, but smaller effects. At lower RDC density, or when refining against NOEs only, the two selected force fields are capable of accurately describing RNA helices with little or no experimental RDC data, making them available for the higher order structure assembly or better quantification of the intramolecular dynamics. Unrestrained simulations of simple RNA motifs with state-of-the art MD force fields appear to capture the flexibility inherent in nucleic acids while also maintaining a good agreement with the experimental observables.
Collapse
Affiliation(s)
- Christina Bergonzo
- National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Alexander Grishaev
- National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
| |
Collapse
|
31
|
Application of anisotropic NMR parameters to the confirmation of molecular structure. Nat Protoc 2018; 14:217-247. [DOI: 10.1038/s41596-018-0091-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
32
|
Nichols PJ, Born A, Henen MA, Strotz D, Celestine CN, Güntert P, Vögeli B. Extending the Applicability of Exact Nuclear Overhauser Enhancements to Large Proteins and RNA. Chembiochem 2018; 19:1695-1701. [PMID: 29883016 DOI: 10.1002/cbic.201800237] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Indexed: 01/24/2023]
Abstract
Distance-dependent nuclear Overhauser enhancements (NOEs) are one of the most popular and important experimental restraints for calculating NMR structures. Despite this, they are mostly employed as semiquantitative upper distance bounds, and this discards the wealth of information that is encoded in the cross-relaxation rate constant. Information that is lost includes exact distances between protons and dynamics that occur on the sub-millisecond timescale. Our recently introduced exact measurement of the NOE (eNOE) requires little additional experimental effort relative to other NMR observables. So far, we have used eNOEs to calculate multistate ensembles of proteins up to approximately 150 residues. Here, we briefly revisit eNOE methodology and present two new directions for the use of eNOEs: applications to large proteins and RNA.
Collapse
Affiliation(s)
- Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Chi N Celestine
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123, Uppsala, Sweden
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
- Institute of Biophysical Chemistry, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438, Frankfurt am Main, Germany
- Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| |
Collapse
|
33
|
Enhanced Sampling of Interdomain Motion Using Map-Restrained Langevin Dynamics and NMR: Application to Pin1. J Mol Biol 2018; 430:2164-2180. [PMID: 29775635 DOI: 10.1016/j.jmb.2018.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/04/2018] [Accepted: 05/05/2018] [Indexed: 11/20/2022]
Abstract
Many signaling proteins consist of globular domains connected by flexible linkers that allow for substantial domain motion. Because these domains often serve as complementary functional modules, the possibility of functionally important domain motions arises. To explore this possibility, we require knowledge of the ensemble of protein conformations sampled by interdomain motion. Measurements of NMR residual dipolar couplings (RDCs) of backbone HN bonds offer a per-residue characterization of interdomain dynamics, as the couplings are sensitive to domain orientation. A challenge in reaching this potential is the need to interpret the RDCs as averages over dynamic ensembles of domain conformations. Here, we address this challenge by introducing an efficient protocol for generating conformational ensembles appropriate for flexible, multi-domain proteins. The protocol uses map-restrained self-guided Langevin dynamics simulations to promote collective, interdomain motion while restraining the internal domain motion to near rigidity. Critically, the simulations retain an all-atom description for facile inclusion of site-specific NMR RDC restraints. The result is the rapid generation of conformational ensembles consistent with the RDC data. We illustrate this protocol on human Pin1, a two-domain peptidyl-prolyl isomerase relevant for cancer and Alzheimer's disease. The results include the ensemble of domain orientations sampled by Pin1, as well as those of a dysfunctional variant, I28A-Pin1. The differences between the ensembles corroborate our previous spin relaxation results that showed weakened interdomain contact in the I28A variant relative to wild type. Our protocol extends our abilities to explore the functional significance of protein domain motions.
Collapse
|
34
|
Iwahara J, Zandarashvili L, Kemme CA, Esadze A. NMR-based investigations into target DNA search processes of proteins. Methods 2018; 148:57-66. [PMID: 29753002 DOI: 10.1016/j.ymeth.2018.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022] Open
Abstract
To perform their function, transcription factors and DNA-repair/modifying enzymes must first locate their targets in the vast presence of nonspecific, but structurally similar sites on genomic DNA. Before reaching their targets, these proteins stochastically scan DNA and dynamically move from one site to another on DNA. Solution NMR spectroscopy provides unique atomic-level insights into the dynamic DNA-scanning processes, which are difficult to gain by any other experimental means. In this review, we provide an introductory overview on the NMR methods for the structural, dynamic, and kinetic investigations of target DNA search by proteins. We also discuss advantages and disadvantages of these NMR methods over other methods such as single-molecule techniques and biochemical approaches.
Collapse
Affiliation(s)
- Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, United States.
| | - Levani Zandarashvili
- Department of Biochemistry and Biophysics, University of Pennsylvania, United States
| | - Catherine A Kemme
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, United States
| | - Alexandre Esadze
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, United States
| |
Collapse
|
35
|
Gao Q, Yang JY, Moremen KW, Flanagan JG, Prestegard JH. Structural Characterization of a Heparan Sulfate Pentamer Interacting with LAR-Ig1-2. Biochemistry 2018; 57:2189-2199. [PMID: 29570275 DOI: 10.1021/acs.biochem.8b00241] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Leukocyte common antigen-related (LAR) protein is one of the type IIa receptor protein tyrosine phosphatases (RPTPs) that are important for signal transduction in biological processes, including axon growth and regeneration. Glycosaminoglycan chains, including heparan sulfate (HS) and chondroitin sulfate (CS), act as ligands that regulate LAR signaling. Here, we report the structural characterization of the first two immunoglobulin domains (Ig1-2) of LAR interacting with an HS pentasaccharide (GlcNS6S-GlcA-GlcNS3,6S-IdoA2S-GlcNS6S-OME, fondaparinux) using multiple solution-based NMR methods. In the course of the study, we extended an assignment strategy useful for sparsely labeled proteins expressed in mammalian cell culture supplemented with a single type of isotopically enriched amino acid ([15N]-Lys in this case) by including paramagnetic perturbations to NMR resonances. The folded two-domain structure for LAR-Ig1-2 seen in previous crystal structures has been validated in solution using residual dipolar coupling data, and a combination of chemical shift perturbation on titration of LAR-Ig1-2 with fondaparinux, saturation transfer difference (STD) spectra, and transferred nuclear Overhauser effects (trNOEs) have been employed in the docking program HADDOCK to generate models for the LAR-fondaparinux complex. These models are further analyzed by postprocessing energetic analysis to identify key binding interactions. In addition to providing insight into the ligand interaction mechanisms of type IIa RPTPs and the origin of opposing effects of CS and HS ligands, these results may assist in future design of therapeutic compounds for nervous system repair.
Collapse
Affiliation(s)
- Qi Gao
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Kelley W Moremen
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - John G Flanagan
- Department of Cell Biology and Program in Neuroscience , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - James H Prestegard
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| |
Collapse
|
36
|
Kovalevskiy O, Nicholls RA, Long F, Carlon A, Murshudov GN. Overview of refinement procedures within REFMAC5: utilizing data from different sources. Acta Crystallogr D Struct Biol 2018; 74:215-227. [PMID: 29533229 PMCID: PMC5947762 DOI: 10.1107/s2059798318000979] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/16/2018] [Indexed: 01/10/2023] Open
Abstract
Refinement is a process that involves bringing into agreement the structural model, available prior knowledge and experimental data. To achieve this, the refinement procedure optimizes a posterior conditional probability distribution of model parameters, including atomic coordinates, atomic displacement parameters (B factors), scale factors, parameters of the solvent model and twin fractions in the case of twinned crystals, given observed data such as observed amplitudes or intensities of structure factors. A library of chemical restraints is typically used to ensure consistency between the model and the prior knowledge of stereochemistry. If the observation-to-parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented in REFMAC5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary-structure formation and even data obtained using different experimental methods, for example NMR. The refinement procedure also generates the `best' weighted electron-density maps, which are useful for further model (re)building. Here, the refinement of macromolecular structures using REFMAC5 and related tools distributed as part of the CCP4 suite is discussed.
Collapse
Affiliation(s)
- Oleg Kovalevskiy
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Robert A. Nicholls
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Fei Long
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Azzurra Carlon
- Magnetic Resonance Center (CERM), University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Garib N. Murshudov
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| |
Collapse
|
37
|
Chiliveri SC, Louis JM, Ghirlando R, Baber JL, Bax A. Tilted, Uninterrupted, Monomeric HIV-1 gp41 Transmembrane Helix from Residual Dipolar Couplings. J Am Chem Soc 2017; 140:34-37. [PMID: 29277995 DOI: 10.1021/jacs.7b10245] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cryo-electron microscopy and X-ray crystallography have shown that the pre- and postfusion states of the HIV-1 gp41 viral coat protein, although very different from one another, each adopt C3 symmetric structures. A stable homotrimeric structure for the transmembrane domain (TM) also was modeled and supported by experimental data. For a C3 symmetric structure, alignment in an anisotropic medium must be axially symmetric, with the unique axis of the alignment tensor coinciding with the C3 axis. However, NMR residual dipolar couplings (RDCs) measured under three different alignment conditions were found to be incompatible with C3 symmetry. Subsequent measurements by paramagnetic relaxation enhancement, analytical ultracentrifugation, and DEER EPR, indicate that the transmembrane domain is monomeric. 15N NMR relaxation data and RDCs show that TM is highly ordered and uninterrupted for a total length of 32 residues, extending well into the membrane proximal external region.
Collapse
Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - John M Louis
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Rodolfo Ghirlando
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - James L Baber
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| |
Collapse
|
38
|
Liu Y, Saurí J, Mevers E, Peczuh MW, Hiemstra H, Clardy J, Martin GE, Williamson RT. Unequivocal determination of complex molecular structures using anisotropic NMR measurements. Science 2017; 356:356/6333/eaam5349. [PMID: 28385960 DOI: 10.1126/science.aam5349] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/16/2017] [Indexed: 11/02/2022]
Abstract
Assignment of complex molecular structures from nuclear magnetic resonance (NMR) data can be prone to interpretational mistakes. Residual dipolar couplings and residual chemical shift anisotropy provide a spatial view of the relative orientations between bonds and chemical shielding tensors, respectively, regardless of separation. Consequently, these data constitute a reliable reporter of global structural validity. Anisotropic NMR parameters can be used to evaluate investigators' structure proposals or structures generated by computer-assisted structure elucidation. Application of the method to several complex structure assignment problems shows promising results that signal a potential paradigm shift from conventional NMR data interpretation, which may be of particular utility for compounds not amenable to x-ray crystallography.
Collapse
Affiliation(s)
- Yizhou Liu
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Josep Saurí
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Mark W Peczuh
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Unit 3060, Storrs, CT 06269, USA
| | - Henk Hiemstra
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Gary E Martin
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, NJ 07065, USA.
| | - R Thomas Williamson
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, NJ 07065, USA.
| |
Collapse
|
39
|
Lorieau JL. Mollib: a molecular and NMR data analysis software. JOURNAL OF BIOMOLECULAR NMR 2017; 69:69-80. [PMID: 29032520 DOI: 10.1007/s10858-017-0142-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/07/2017] [Indexed: 06/07/2023]
Abstract
Mollib is a software framework for the analysis of molecular structures, properties and data with an emphasis on data collected by NMR. It uses an open source model and a plugin framework to promote community-driven development of new and enhanced features. Mollib includes tools for the automatic retrieval and caching of protein databank (PDB) structures, the hydrogenation of biomolecules, the analysis of backbone dihedral angles and hydrogen bonds, and the fitting of residual dipolar coupling (RDC) and residual anisotropic chemical shift (RACS) data. In this article, we release version 1.0 of mollib and demonstrate its application to common molecular and NMR data analyses.
Collapse
Affiliation(s)
- Justin L Lorieau
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL, 60607, USA.
| |
Collapse
|
40
|
Li Y, Kang C. Solution NMR Spectroscopy in Target-Based Drug Discovery. Molecules 2017; 22:E1399. [PMID: 28832542 PMCID: PMC6151424 DOI: 10.3390/molecules22091399] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/18/2017] [Accepted: 08/18/2017] [Indexed: 12/14/2022] Open
Abstract
Solution NMR spectroscopy is a powerful tool to study protein structures and dynamics under physiological conditions. This technique is particularly useful in target-based drug discovery projects as it provides protein-ligand binding information in solution. Accumulated studies have shown that NMR will play more and more important roles in multiple steps of the drug discovery process. In a fragment-based drug discovery process, ligand-observed and protein-observed NMR spectroscopy can be applied to screen fragments with low binding affinities. The screened fragments can be further optimized into drug-like molecules. In combination with other biophysical techniques, NMR will guide structure-based drug discovery. In this review, we describe the possible roles of NMR spectroscopy in drug discovery. We also illustrate the challenges encountered in the drug discovery process. We include several examples demonstrating the roles of NMR in target-based drug discoveries such as hit identification, ranking ligand binding affinities, and mapping the ligand binding site. We also speculate the possible roles of NMR in target engagement based on recent processes in in-cell NMR spectroscopy.
Collapse
Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore.
| | - Congbao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore.
| |
Collapse
|
41
|
Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. Nat Commun 2017; 8:145. [PMID: 28747759 PMCID: PMC5529581 DOI: 10.1038/s41467-017-00165-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/07/2017] [Indexed: 01/25/2023] Open
Abstract
Proteins perform their functions in solution but their structures are most frequently studied inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using solid-state NMR measurements and multi-microsecond MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance relaxation dispersion (NERRD) experiments probe angular backbone motion, while Bloch–McConnell relaxation dispersion data report on fluctuations of the local electronic environment. These experiments and simulations reveal that the packing of the protein can significantly alter the thermodynamics and kinetics of local conformational exchange. Moreover, we report small-amplitude reorientational motion of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds time scale in one of the crystals, but not in others. An intriguing possibility arises that overall motion is to some extent coupled to local dynamics. Our study highlights the importance of considering the packing when analyzing dynamics of crystalline proteins. X-ray crystallography is the main method for protein structure determination. Here the authors combine solid-state NMR measurements and molecular dynamics simulations and show that crystal packing alters the thermodynamics and kinetics of local conformational exchange as well as overall rocking motion of protein molecules in the crystal lattice.
Collapse
|
42
|
Pederson K, Chalmers GR, Gao Q, Elnatan D, Ramelot TA, Ma LC, Montelione GT, Kennedy MA, Agard DA, Prestegard JH. NMR characterization of HtpG, the E. coli Hsp90, using sparse labeling with 13C-methyl alanine. JOURNAL OF BIOMOLECULAR NMR 2017; 68:225-236. [PMID: 28653216 PMCID: PMC5546222 DOI: 10.1007/s10858-017-0123-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/22/2017] [Indexed: 05/03/2023]
Abstract
A strategy for acquiring structural information from sparsely isotopically labeled large proteins is illustrated with an application to the E. coli heat-shock protein, HtpG (high temperature protein G), a 145 kDa dimer. It uses 13C-alanine methyl labeling in a perdeuterated background to take advantage of the sensitivity and resolution of Methyl-TROSY spectra, as well as the backbone-centered structural information from 1H-13C residual dipolar couplings (RDCs) of alanine methyl groups. In all, 40 of the 47 expected crosspeaks were resolved and 36 gave RDC data. Assignments of crosspeaks were partially achieved by transferring assignments from those made on individual domains using triple resonance methods. However, these were incomplete and in many cases the transfer was ambiguous. A genetic algorithm search for consistency between predictions based on domain structures and measurements for chemical shifts and RDCs allowed 60% of the 40 resolved crosspeaks to be assigned with confidence. Chemical shift changes of these crosspeaks on adding an ATP analog to the apo-protein are shown to be consistent with structural changes expected on comparing previous crystal structures for apo- and complex- structures. RDCs collected on the assigned alanine methyl peaks are used to generate a new solution model for the apo-protein structure.
Collapse
Affiliation(s)
- Kari Pederson
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
| | - Gordon R Chalmers
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
- Department of Computer Science, University of Georgia, Athens, USA
| | - Qi Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
| | - Daniel Elnatan
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, USA
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, Miami University, Oxford, USA
| | - Li-Chung Ma
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA.
| |
Collapse
|
43
|
Thiagarajan-Rosenkranz P, Draney AW, Lorieau JL. Hybrid NMR: A Union of Solution- and Solid-State NMR. J Am Chem Soc 2017; 139:4715-4723. [PMID: 28287254 DOI: 10.1021/jacs.6b11402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hybrid NMR (hdNMR) is a powerful new tool that combines the strengths of solution- and solid-state NMR to measure dipolar, chemical shift, and quadrupolar tensors in aqueous solution. We introduce the theory of hdNMR and partially randomly oriented (PRO) crystalline hydrogel samples. PRO samples produce randomly oriented spectra with characteristic Pake patterns from the solid state, yet they maintain the high-resolution dispersion of solution NMR experiments. With new pulse sequences, we show how hdNMR can be used to measure with high precision the 1Hα-13Cα dipolar tensor and carboxylate chemical shift anisotropy tensor of aspartate. These measurements contain detailed information on the distribution of electron density, interatomic distances, and the orientation dependence of molecular motion.
Collapse
Affiliation(s)
- Pallavi Thiagarajan-Rosenkranz
- Department of Chemistry, University of Illinois at Chicago , 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Adrian W Draney
- Department of Chemistry, University of Illinois at Chicago , 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Justin L Lorieau
- Department of Chemistry, University of Illinois at Chicago , 845 West Taylor Street, Chicago, Illinois 60607, United States
| |
Collapse
|
44
|
García ME, Woodruff SR, Hellemann E, Tsarevsky NV, Gil RR. Di(ethylene glycol) methyl ether methacrylate (DEGMEMA)-derived gels align small organic molecules in methanol. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:206-209. [PMID: 26763068 DOI: 10.1002/mrc.4400] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 10/20/2015] [Accepted: 11/24/2015] [Indexed: 05/28/2023]
Abstract
Residual dipolar couplings (RDCs) constitute an important NMR parameter for structural elucidation in all areas of chemistry. In this study, di(ethylene glycol) methyl ether methacrylate (DEGMEMA)-based gels are introduced as alignment media for the measurement of RDCs of small organic molecules in polar solvents such as methanol. The low viscosity of methanol permits the execution of J-scaled BIRD HSQC experiments that yield very sharp lines in anisotropic conditions. The gels have excellent mechanical properties, and their compression and expansion in the swollen state can be reversed and performed multiple times. This process enables the easy loading and release of analytes. The excellent performance of these new aligning gels is demonstrated by analyzing the structure of the alkaloid retrorsine. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Manuela E García
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
- Department of Organic Chemistry, National University of Cordoba, Medina Allende y Haya de La Torre, Cordoba, 5000, Argentina
| | - Shannon R Woodruff
- Department of Chemistry, Southern Methodist University, Dallas, TX, USA
- Center for Drug Discovery, Design, and Delivery in Dedman College, Southern Methodist University, Dallas, TX, USA
| | - Erich Hellemann
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Nicolay V Tsarevsky
- Department of Chemistry, Southern Methodist University, Dallas, TX, USA
- Center for Drug Discovery, Design, and Delivery in Dedman College, Southern Methodist University, Dallas, TX, USA
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| |
Collapse
|
45
|
Pilla KB, Otting G, Huber T. Protein Structure Determination by Assembling Super-Secondary Structure Motifs Using Pseudocontact Shifts. Structure 2017; 25:559-568. [DOI: 10.1016/j.str.2017.01.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/17/2017] [Accepted: 01/29/2017] [Indexed: 11/26/2022]
|
46
|
Hybrid Applications of Solution Scattering to Aid Structural Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:215-227. [PMID: 29218562 DOI: 10.1007/978-981-10-6038-0_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biomolecular applications of solution X-ray and neutron scattering (SAXS and SANS, respectively) started in late 1960s - early 1970s but were relatively limited in their ability to provide a detailed structural picture and lagged behind what became the two primary methods of experimental structural biology - X-ray crystallography and NMR. However, improvements in both data analysis and instrumentation led to an explosive growth in the number of studies that used small-angle scattering (SAS) for investigation of macromolecular structure, often in combination with other biophysical techniques. Such hybrid applications are nowadays quickly becoming a norm whenever scattering data are used for two reasons. First, it is generally accepted that SAS data on their own cannot lead to a uniquely defined high-resolution structural model, creating a need for supplementing them with information from complementary techniques. Second, solution scattering data are frequently applied in situations when a method such NMR or X-ray crystallography cannot provide a satisfactory structural picture, which makes these additional restraints highly desirable. Maturation of the hybrid bio-SAS approaches brings to light new questions including completeness of the conformational space sampling, model validation, and data compatibility.
Collapse
|
47
|
Zydziak N, Konrad W, Feist F, Afonin S, Weidner S, Barner-Kowollik C. Coding and decoding libraries of sequence-defined functional copolymers synthesized via photoligation. Nat Commun 2016; 7:13672. [PMID: 27901024 PMCID: PMC5141382 DOI: 10.1038/ncomms13672] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 10/23/2016] [Indexed: 12/23/2022] Open
Abstract
Designing artificial macromolecules with absolute sequence order represents a considerable challenge. Here we report an advanced light-induced avenue to monodisperse sequence-defined functional linear macromolecules up to decamers via a unique photochemical approach. The versatility of the synthetic strategy-combining sequential and modular concepts-enables the synthesis of perfect macromolecules varying in chemical constitution and topology. Specific functions are placed at arbitrary positions along the chain via the successive addition of monomer units and blocks, leading to a library of functional homopolymers, alternating copolymers and block copolymers. The in-depth characterization of each sequence-defined chain confirms the precision nature of the macromolecules. Decoding of the functional information contained in the molecular structure is achieved via tandem mass spectrometry without recourse to their synthetic history, showing that the sequence information can be read. We submit that the presented photochemical strategy is a viable and advanced concept for coding individual monomer units along a macromolecular chain.
Collapse
Affiliation(s)
- Nicolas Zydziak
- Soft Matter Synthesis Laboratory, Institut für Biologische Grenzflächen, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Preparative Macromolecular Chemistry, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstrasse 18, 76131 Karlsruhe, Germany
| | - Waldemar Konrad
- Soft Matter Synthesis Laboratory, Institut für Biologische Grenzflächen, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Preparative Macromolecular Chemistry, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstrasse 18, 76131 Karlsruhe, Germany
| | - Florian Feist
- Soft Matter Synthesis Laboratory, Institut für Biologische Grenzflächen, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Preparative Macromolecular Chemistry, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstrasse 18, 76131 Karlsruhe, Germany
| | - Sergii Afonin
- Department of Molecular Biophysics (IGB-2), Institut für Biologische Grenzflächen, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Steffen Weidner
- BAM-Federal Institute for Materials Research and Testing, Richard-Willstätter-Strasse 11, 12489 Berlin, Germany
| | - Christopher Barner-Kowollik
- Soft Matter Synthesis Laboratory, Institut für Biologische Grenzflächen, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Preparative Macromolecular Chemistry, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstrasse 18, 76131 Karlsruhe, Germany
| |
Collapse
|
48
|
Abstract
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.
Collapse
|
49
|
Zhuo Y, Yang JY, Moremen KW, Prestegard JH. Glycosylation Alters Dimerization Properties of a Cell-surface Signaling Protein, Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1). J Biol Chem 2016; 291:20085-95. [PMID: 27471271 DOI: 10.1074/jbc.m116.740050] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Indexed: 12/12/2022] Open
Abstract
Human carcinoembryonic antigen-related cell adhesion molecule 1 (C?/Au: EACAM1) is a cell-surface signaling molecule involved in cell adhesion, proliferation, and immune response. It is also implicated in cancer angiogenesis, progression, and metastasis. This diverse set of effects likely arises as a result of the numerous homophilic and heterophilic interactions that CEACAM1 can have with itself and other molecules. Its N-terminal Ig variable (IgV) domain has been suggested to be a principal player in these interactions. Previous crystal structures of the β-sandwich-like IgV domain have been produced using Escherichia coli-expressed material, which lacks native glycosylation. These have led to distinctly different proposals for dimer interfaces, one involving interactions of ABED β-strands and the other involving GFCC'C″ β-strands, with the former burying one prominent glycosylation site. These structures raise questions as to which form may exist in solution and what the effect of glycosylation may have on this form. Here, we use NMR cross-correlation measurements to examine the effect of glycosylation on CEACAM1-IgV dimerization and use residual dipolar coupling (RDC) measurements to characterize the solution structure of the non-glycosylated form. Our findings demonstrate that even addition of a single N-linked GlcNAc at potential glycosylation sites inhibits dimer formation. Surprisingly, RDC data collected on E. coli expressed material in solution indicate that a dimer using the non-glycosylated GFCC'C″ interface is preferred even in the absence of glycosylation. The results open new questions about what other factors may facilitate dimerization of CEACAM1 in vivo, and what roles glycosylation may play in heterophylic interactions.
Collapse
Affiliation(s)
- You Zhuo
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Jeong-Yeh Yang
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Kelley W Moremen
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - James H Prestegard
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| |
Collapse
|
50
|
Borkar AN, Bardaro MF, Camilloni C, Aprile FA, Varani G, Vendruscolo M. Structure of a low-population binding intermediate in protein-RNA recognition. Proc Natl Acad Sci U S A 2016; 113:7171-6. [PMID: 27286828 PMCID: PMC4932932 DOI: 10.1073/pnas.1521349113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interaction of the HIV-1 protein transactivator of transcription (Tat) and its cognate transactivation response element (TAR) RNA transactivates viral transcription and represents a paradigm for the widespread occurrence of conformational rearrangements in protein-RNA recognition. Although the structures of free and bound forms of TAR are well characterized, the conformations of the intermediates in the binding process are still unknown. By determining the free energy landscape of the complex using NMR residual dipolar couplings in replica-averaged metadynamics simulations, we observe two low-population intermediates. We then rationally design two mutants, one in the protein and another in the RNA, that weaken specific nonnative interactions that stabilize one of the intermediates. By using surface plasmon resonance, we show that these mutations lower the release rate of Tat, as predicted. These results identify the structure of an intermediate for RNA-protein binding and illustrate a general strategy to achieve this goal with high resolution.
Collapse
Affiliation(s)
- Aditi N Borkar
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michael F Bardaro
- Department of Chemistry, University of Washington, Seattle, WA 98197-1700
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98197-1700
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| |
Collapse
|