1
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Du Y, Li J, Suryanarayanan R, Su Y. Probing Chemical Equilibrium in Frozen Sodium Phosphate Buffer Solution by 31P Solid-State NMR. J Phys Chem Lett 2024; 15:5714-5720. [PMID: 38768559 DOI: 10.1021/acs.jpclett.4c00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Phosphate buffers are crucial for cryopreservative stability in pharmaceuticals, food processing, biomedical sciences, and biology. However, their freeze concentrates lack quantitative characterization, especially regarding the physicochemical properties of phosphate salt species in equilibrium at subzero temperatures. This study employs 31P solid-state NMR (ssNMR) to analyze frozen sodium phosphate (NaP) solutions, providing insights into phase composition, ionic strength, and pH. For the first time, we have directly quantified phosphate species in frozen NaP buffer, including crystallized disodium phosphate dodecahydrate (Na2HPO4·12H2O) content and the concentrations of H2PO4- and HPO42- in the freeze concentrate. This enabled the calculation of the pH as well as the ionic strength in the freeze concentrate. Trehalose effectively mitigated pH shifts in buffer solutions by preventing the selective crystallization of salt, a spectroscopic phenomenon not previously observed experimentally.
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Affiliation(s)
- Yong Du
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jinghan Li
- Department of Pharmaceutics College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Raj Suryanarayanan
- Department of Pharmaceutics College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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2
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Du Y, Su Y. Quantification of Residual Water in Pharmaceutical Frozen Solutions Via 1H Solid-State NMR. J Pharm Sci 2024:S0022-3549(24)00144-8. [PMID: 38643897 DOI: 10.1016/j.xphs.2024.04.013] [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: 10/26/2023] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 04/23/2024]
Abstract
Freezing is essential for the stability of biological drug substances and products, particularly in frozen solution formulations and during the primary drying of lyophilized preparations. However, the unfrozen segment within the frozen matrix can alter solute concentration, ionic strength, and stabilizer crystallization, posing risks of increased biophysical instability and faster chemical degradation. While quantifying the unfrozen water content is important for designing stable biopharmaceuticals, there is a lack of analytical techniques for in situ quantitative measurements. In this study, we introduce a 1H magic angle spinning NMR technique to identify the freezing point (Tice) and quantify mobile water content in frozen biologics, applying this method to analyze the freezing of a commercial high-concentration drug product, Dupixent®. Our results demonstrate that water freezing is influenced by buffer salt properties and formulation composition, including the presence of sugar cryoprotectants and protein concentration. Additionally, the 1H chemical shift can probe pH in the unfrozen phase, potentially predicting the microenvironmental acidity in the frozen state. Our proposed methodology provides fresh insights into the analysis of freeze-concentrated solutions, enhancing our understanding of the stability of frozen and lyophilized biopharmaceuticals.
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Affiliation(s)
- Yong Du
- Analytical Research and Development, Merck & Co. Inc., Rahway, NJ 07065, USA
| | - Yongchao Su
- Analytical Research and Development, Merck & Co. Inc., Rahway, NJ 07065, USA; Pharmaceutical Sciences and Clinical Supply, Merck & Co. Inc., West Point, PA 19486, USA.
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3
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Du Y, Li J, Xu W, Cote A, Lay-Fortenbery A, Suryanarayanan R, Su Y. Solid-State NMR Spectroscopy to Probe State and Phase Transitions in Frozen Solutions. Mol Pharm 2023; 20:6380-6390. [PMID: 37947441 DOI: 10.1021/acs.molpharmaceut.3c00764] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Freezing is commonly encountered during the processing and storage of biomacromolecule products. Therefore, understanding the phase and state transitions in pharmaceutical frozen solutions is crucial for the rational development of biopharmaceuticals. Solid-state nuclear magnetic resonance spectroscopy (ssNMR) was used to analyze solutions containing sodium phosphate buffer, histidine, and trehalose. Upon freezing, crystallization of disodium phosphate hydrogen dodecahydrate (Na2HPO4·12H2O, DPDH) and histidine was identified using 31P and 13C ssNMR, respectively, and confirmed by synchrotron X-ray diffractometry (SXRD). Using histidine as a molecular probe and based on the chemical shifts of atoms of interest, the pH of the freeze concentrate was measured. The unfrozen water content in freeze concentrates was quantified by 1H single pulse experiments. 13C-insensitive nuclei enhancement by polarization transfer (INEPT) and cross-polarization (CP) experiments were used as orthogonal tools to characterize the solutes in a "mobile" and a more "solid-like" state in the freeze-concentrated solutions, respectively. The above analyses were applied to a commercial monoclonal antibody (mAb) formulation of dupilumab. This work further establishes ssNMR spectroscopy as a highly capable biophysical tool to investigate the attributes of biopharmaceuticals and thereby provide insights into process optimization and formulation development.
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Affiliation(s)
- Yong Du
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jinghan Li
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Wei Xu
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Aaron Cote
- Biologics Process Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Ashley Lay-Fortenbery
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Raj Suryanarayanan
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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4
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Beriashvili D, Yao R, D'Amico F, Krafčíková M, Gurinov A, Safeer A, Cai X, Mulder MPC, Liu Y, Folkers GE, Baldus M. A high-field cellular DNP-supported solid-state NMR approach to study proteins with sub-cellular specificity. Chem Sci 2023; 14:9892-9899. [PMID: 37736634 PMCID: PMC10510770 DOI: 10.1039/d3sc02117c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
Studying the structural aspects of proteins within sub-cellular compartments is of growing interest. Dynamic nuclear polarization supported solid-state NMR (DNP-ssNMR) is uniquely suited to provide such information, but critically lacks the desired sensitivity and resolution. Here we utilize SNAPol-1, a novel biradical, to conduct DNP-ssNMR at high-magnetic fields (800 MHz/527 GHz) inside HeLa cells and isolated cell nuclei electroporated with [13C,15N] labeled ubiquitin. We report that SNAPol-1 passively diffuses and homogenously distributes within whole cells and cell nuclei providing ubiquitin spectra of high sensitivity and remarkably improved spectral resolution. For cell nuclei, physical enrichment facilitates a further 4-fold decrease in measurement time and provides an exclusive structural view of the nuclear ubiquitin pool. Taken together, these advancements enable atomic interrogation of protein conformational plasticity at atomic resolution and with sub-cellular specificity.
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Affiliation(s)
- David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Ru Yao
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Francesca D'Amico
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Michaela Krafčíková
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Andrei Gurinov
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Adil Safeer
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Xinyi Cai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
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5
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Kragelj J, Dumarieh R, Xiao Y, Frederick KK. Conformational ensembles explain NMR spectra of frozen intrinsically disordered proteins. Protein Sci 2023; 32:e4628. [PMID: 36930141 PMCID: PMC10108432 DOI: 10.1002/pro.4628] [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: 11/15/2022] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023]
Abstract
Protein regions which are intrinsically disordered, exist as an ensemble of rapidly interconverting structures. Cooling proteins to cryogenic temperatures for dynamic nuclear polarization (DNP) magic angle spinning (MAS) NMR studies suspends most of the motions, resulting in peaks that are broad but not featureless. To demonstrate that detailed conformational restraints can be retrieved from the peak shapes of frozen proteins alone, we developed and used a simulation framework to assign peak features to conformers in the ensemble. We validated our simulations by comparing them to spectra of α-synuclein acquired under different experimental conditions. Our assignments of peaks to discrete dihedral angle populations suggest that structural constraints are attainable under cryogenic conditions. The ability to infer ensemble populations from peak shapes has important implications for DNP MAS NMR studies of proteins with regions of disorder in living cells because chemical shifts are the most accessible measured parameter.
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Affiliation(s)
- Jaka Kragelj
- Department of BiophysicsUT Southwestern Medical CenterDallasTexas75390‐8816USA
- Present address:
National Institute of ChemistryHajdrihova 191001LjubljanaSlovenia
| | - Rania Dumarieh
- Department of BiophysicsUT Southwestern Medical CenterDallasTexas75390‐8816USA
| | - Yiling Xiao
- Department of BiophysicsUT Southwestern Medical CenterDallasTexas75390‐8816USA
| | - Kendra K. Frederick
- Department of BiophysicsUT Southwestern Medical CenterDallasTexas75390‐8816USA
- Center for Alzheimer's and Neurodegenerative DiseaseUT Southwestern Medical CenterDallasTexas75390USA
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6
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Burakova E, Vasa SK, Linser R. Characterization of conformational heterogeneity via higher-dimensionality, proton-detected solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2022; 76:197-212. [PMID: 36149571 PMCID: PMC9712413 DOI: 10.1007/s10858-022-00405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Site-specific heterogeneity of solid protein samples can be exploited as valuable information to answer biological questions ranging from thermodynamic properties determining fibril formation to protein folding and conformational stability upon stress. In particular, for proteins of increasing molecular weight, however, site-resolved assessment without residue-specific labeling is challenging using established methodology, which tends to rely on carbon-detected 2D correlations. Here we develop purely chemical-shift-based approaches for assessment of relative conformational heterogeneity that allows identification of each residue via four chemical-shift dimensions. High dimensionality diminishes the probability of peak overlap in the presence of multiple, heterogeneously broadened resonances. Utilizing backbone dihedral-angle reconstruction from individual contributions to the peak shape either via suitably adapted prediction routines or direct association with a relational database, the methods may in future studies afford assessment of site-specific heterogeneity of proteins without site-specific labeling.
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Affiliation(s)
- Ekaterina Burakova
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Suresh K Vasa
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
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7
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Cerofolini L, Parigi G, Ravera E, Fragai M, Luchinat C. Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101828. [PMID: 36240720 DOI: 10.1016/j.ssnmr.2022.101828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.
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Affiliation(s)
- Linda Cerofolini
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy; Florence Data Science, Università degli Studi di Firenze, Italy.
| | - Marco Fragai
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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8
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Jeon J, Blake Wilson C, Yau WM, Thurber KR, Tycko R. Time-resolved solid state NMR of biomolecular processes with millisecond time resolution. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 342:107285. [PMID: 35998398 PMCID: PMC9463123 DOI: 10.1016/j.jmr.2022.107285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 05/21/2023]
Abstract
We review recent efforts to develop and apply an experimental approach to the structural characterization of transient intermediate states in biomolecular processes that involve large changes in molecular conformation or assembly state. This approach depends on solid state nuclear magnetic resonance (ssNMR) measurements that are performed at very low temperatures, typically 25-30 K, with signal enhancements from dynamic nuclear polarization (DNP). This approach also involves novel technology for initiating the process of interest, either by rapid mixing of two solutions or by a rapid inverse temperature jump, and for rapid freezing to trap intermediate states. Initiation by rapid mixing or an inverse temperature jump can be accomplished in approximately-one millisecond. Freezing can be accomplished in approximately 100 microseconds. Thus, millisecond time resolution can be achieved. Recent applications to the process by which the biologically essential calcium sensor protein calmodulin forms a complex with one of its target proteins and the process by which the bee venom peptide melittin converts from an unstructured monomeric state to a helical, tetrameric state after a rapid change in pH or temperature are described briefly. Future applications of millisecond time-resolved ssNMR are also discussed briefly.
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Affiliation(s)
- Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - C Blake Wilson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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9
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Takamuku M, Sugishita T, Tamaki H, Dong L, So M, Fujiwara T, Matsuki Y. Evolution of α-synuclein conformation ensemble toward amyloid fibril via liquid-liquid phase separation (LLPS) as investigated by dynamic nuclear polarization-enhanced solid-state MAS NMR. Neurochem Int 2022; 157:105345. [DOI: 10.1016/j.neuint.2022.105345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/11/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
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10
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Porat-Dahlerbruch G, Goldbourt A, Polenova T. Virus Structures and Dynamics by Magic-Angle Spinning NMR. Annu Rev Virol 2021; 8:219-237. [PMID: 34586870 DOI: 10.1146/annurev-virology-011921-064653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Techniques for atomic-resolution structural biology have evolved during the past several decades. Breakthroughs in instrumentation, sample preparation, and data analysis that occurred in the past decade have enabled characterization of viruses with an unprecedented level of detail. Here we review the recent advances in magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy for structural analysis of viruses and viral assemblies. MAS NMR is a powerful method that yields information on 3D structures and dynamics in a broad range of experimental conditions. After a brief introduction, we discuss recent structural and functional studies of several viruses investigated with atomic resolution at various levels of structural organization, from individual domains of a membrane protein reconstituted into lipid bilayers to virus-like particles and intact viruses. We present examples of the unique information revealed by MAS NMR about drug binding, conduction mechanisms, interactions with cellular host factors, and DNA packaging in biologically relevant environments that are inaccessible by other methods.
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Affiliation(s)
- Gal Porat-Dahlerbruch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA;
| | - Amir Goldbourt
- School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA; .,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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11
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Andrews B, Long K, Urbanc B. Soluble State of Villin Headpiece Protein as a Tool in the Assessment of MD Force Fields. J Phys Chem B 2021; 125:6897-6911. [PMID: 34143637 DOI: 10.1021/acs.jpcb.1c04589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein self-assembly plays an important role in cellular processes. Whereas molecular dynamics (MD) represents a powerful tool in studying assembly mechanisms, its predictions depend on the accuracy of underlying force fields, which are known to overly promote protein assembly. We here examine villin headpiece domain, HP36, which remains soluble at concentrations amenable to MD studies. The experimental characterization of soluble HP36 at concentrations of 0.05 to 1 mM reveals concentration-independent 90% monomeric and 10% dimeric populations. Extensive all-atom MD simulations at two protein concentrations, 0.9 and 8.5 mM, probe the HP36 dimer population, stability, and kinetics of dimer formation within two MD force fields, Amber ff14SB and CHARMM36m. MD results demonstrate that whereas CHARMM36m captures experimental HP36 monomer populations at the lower concentration, both force fields overly promote HP36 association at the higher concentration. Moreover, contacts stabilizing HP36 dimers are force-field-dependent. CHARMM36m produces consistently higher HP36 monomer populations, lower association rates, and weaker dependence of these quantities on the protein concentration than Amber ff14SB. Nonetheless, the highest monomer populations and dissociation constants are observed when the TIP3P water model in Amber ff14SB is replaced by TIP4P/2005, showcasing the critical role of the water model in addressing the protein solubility problem in MD.
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Affiliation(s)
- Brian Andrews
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Kaho Long
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
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12
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Zou J, Xiao S, Simmerling C, Raleigh DP. Quantitative Analysis of Protein Unfolded State Energetics: Experimental and Computational Studies Demonstrate That Non-Native Side-Chain Interactions Stabilize Local Native Backbone Structure. J Phys Chem B 2021; 125:3269-3277. [PMID: 33779182 DOI: 10.1021/acs.jpcb.0c08922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins fold on relatively smooth free energy landscapes which are biased toward the native state, but even simple topologies which fold rapidly can experience roughness on their free energy landscape. The details of these interactions are difficult to elucidate experimentally. Closely related to the problem of deciphering the details of the free energy landscape is the problem of defining the interactions in the denatured state ensemble (DSE) which is populated under native conditions, that is, under conditions where the native state is stable. The DSE of many proteins deviates from random coil models, but quantifying and defining the energetics of the transiently populated interactions in this ensemble is extremely challenging. Characterization of the DSE of proteins which fold to compact structures is also relevant to studies of intrinsically disordered proteins (IDPs) since interactions in the dynamic ensemble populated by IDPs can modulate their behavior. Here we show how experimental thermodynamic and pKa measurements can be combined with computational thermodynamic integration to quantify interactions in the DSE. We show that non-native side chain interactions can stabilize native backbone structure in the DSE and demonstrate that that even rapidly folding proteins can form energetically significant non-native interactions in their DSE. As an example, we characterize a non-native salt bridge that stabilizes local native backbone structure in the DSE of a widely studied fast-folding protein, the villin headpiece helical domain. The combined computational experimental approach is applicable to other protein unfolded states and provides insight that is impossible to obtain with either method alone.
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Affiliation(s)
- Junjie Zou
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Shifeng Xiao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Daniel P Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
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13
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Siemer AB. Advances in studying protein disorder with solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 106:101643. [PMID: 31972419 PMCID: PMC7202078 DOI: 10.1016/j.ssnmr.2020.101643] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 05/26/2023]
Abstract
Solution NMR is a key tool to study intrinsically disordered proteins (IDPs), whose importance for biological function is widely accepted. However, disordered proteins are not limited to solution and are also found in non-soluble systems such as fibrils and membrane proteins. In this Trends article, I will discuss how solid-state NMR can be used to study disorder in non-soluble proteins. Techniques based on dipolar couplings can study static protein disorder which either occurs naturally as e.g. in spider silk or can be induced by freeze trapping IDPs or unfolded proteins. In this case, structural ensembles are directly reflected by a static distribution of dihedral angels that can be determined by the distribution of chemical shifts or other methods. Techniques based on J-couplings can detect dynamic protein disorder under MAS. In this case, only average chemical shifts are measured but disorder can be characterized with a variety of data including secondary chemical shifts, relaxation rates, paramagnetic relaxation enhancements, or residual dipolar couplings. I describe both technical aspects and examples of solid-state NMR on protein disorder and end the article with a discussion of challenges and opportunities of this emerging field.
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Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Univeristy of Southern California, 1501 San Pablo Street, Los Angeles, CA, 90033, USA.
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14
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Geraets JA, Pothula KR, Schröder GF. Integrating cryo-EM and NMR data. Curr Opin Struct Biol 2020; 61:173-181. [PMID: 32028106 DOI: 10.1016/j.sbi.2020.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 01/06/2023]
Abstract
Single-particle cryo-electron microscopy (cryo-EM) is increasingly used as a technique to determine the atomic structure of challenging biological systems. Recent advances in microscope engineering, electron detection, and image processing have allowed the structural determination of bigger and more flexible targets than possible with the complementary techniques X-ray crystallography and NMR spectroscopy. However, there exist many biological targets for which atomic resolution cannot be currently achieved with cryo-EM, making unambiguous determination of the protein structure impossible. Although determining the structure of large biological systems using solely NMR is often difficult, highly complementary experimental atomic-level data for each molecule can be derived from the spectra, and used in combination with cryo-EM data. We review here strategies with which both techniques can be synergistically combined, in order to reach detail and understanding unattainable by each technique acting alone; and the types of biological systems for which such an approach would be desirable.
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Affiliation(s)
- James A Geraets
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Karunakar R Pothula
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
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15
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Application of millisecond time-resolved solid state NMR to the kinetics and mechanism of melittin self-assembly. Proc Natl Acad Sci U S A 2019; 116:16717-16722. [PMID: 31387974 DOI: 10.1073/pnas.1908006116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Common experimental approaches for characterizing structural conversion processes such as protein folding and self-assembly do not report on all aspects of the evolution from an initial state to the final state. Here, we demonstrate an approach that is based on rapid mixing, freeze-trapping, and low-temperature solid-state NMR (ssNMR) with signal enhancements from dynamic nuclear polarization (DNP). Experiments on the folding and tetramerization of the 26-residue peptide melittin following a rapid pH jump show that multiple aspects of molecular structure can be followed with millisecond time resolution, including secondary structure at specific isotopically labeled sites, intramolecular and intermolecular contacts between specific pairs of labeled residues, and overall structural order. DNP-enhanced ssNMR data reveal that conversion of conformationally disordered melittin monomers at low pH to α-helical conformations at neutral pH occurs on nearly the same timescale as formation of antiparallel melittin dimers, about 6 to 9 ms for 0.3 mM melittin at 24 °C in aqueous solution containing 20% (vol/vol) glycerol and 75 mM sodium phosphate. Although stopped-flow fluorescence data suggest that melittin tetramers form quickly after dimerization, ssNMR spectra show that full structural order within melittin tetramers develops more slowly, in ∼60 ms. Time-resolved ssNMR is likely to find many applications to biomolecular structural conversion processes, including early stages of amyloid formation, viral capsid formation, and protein-protein recognition.
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16
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Gupta R, Zhang H, Lu M, Hou G, Caporini M, Rosay M, Maas W, Struppe J, Ahn J, Byeon IJL, Oschkinat H, Jaudzems K, Barbet-Massin E, Emsley L, Pintacuda G, Lesage A, Gronenborn AM, Polenova T. Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies. J Phys Chem B 2019; 123:5048-5058. [PMID: 31125232 DOI: 10.1021/acs.jpcb.9b02293] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) NMR spectroscopy in viral capsids from HIV-1 and bacteriophage AP205. Viruses regulate their life cycles and infectivity through modulation of their structures and dynamics. While static structures of capsids from several viruses are now accessible with near-atomic-level resolution, atomic-level understanding of functionally important motions in assembled capsids is lacking. We observed up to 64-fold signal enhancements by DNP, which permitted in-depth analysis of these assemblies. For the HIV-1 CA assemblies, a remarkably high spectral resolution in the 3D and 2D heteronuclear data sets permitted the assignment of a significant fraction of backbone and side-chain resonances. Using an integrated DNP MAS NMR and molecular dynamics (MD) simulation approach, the conformational space sampled by the assembled capsid at cryogenic temperatures was mapped. Qualitatively, a remarkable agreement was observed for the experimental 13C/15N chemical shift distributions and those calculated from substructures along the MD trajectory. Residues that are mobile at physiological temperatures are frozen out in multiple conformers at cryogenic conditions, resulting in broad experimental and calculated chemical shift distributions. Overall, our results suggest that DNP MAS NMR measurements in combination with MD simulations facilitate a thorough understanding of the dynamic signatures of viral capsids.
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Affiliation(s)
- Rupal Gupta
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Huilan Zhang
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Manman Lu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Guangjin Hou
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Marc Caporini
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Melanie Rosay
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Werner Maas
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Jochem Struppe
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | | | | | - Hartmut Oschkinat
- Leibniz-Institut für Molekulare Pharmakologie , Robert-Roessle-Str. 10 , 13125 Berlin , Germany
| | - Kristaps Jaudzems
- Centre de RMN à Très Hauts Champs , Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon , 5 Rue de la Doua , Villeurbanne, 69100 Lyon , France
| | - Emeline Barbet-Massin
- Centre de RMN à Très Hauts Champs , Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon , 5 Rue de la Doua , Villeurbanne, 69100 Lyon , France
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimques , Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne , Switzerland
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs , Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon , 5 Rue de la Doua , Villeurbanne, 69100 Lyon , France
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs , Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon , 5 Rue de la Doua , Villeurbanne, 69100 Lyon , France
| | | | - Tatyana Polenova
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
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17
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Uluca B, Viennet T, Petrović D, Shaykhalishahi H, Weirich F, Gönülalan A, Strodel B, Etzkorn M, Hoyer W, Heise H. DNP-Enhanced MAS NMR: A Tool to Snapshot Conformational Ensembles of α-Synuclein in Different States. Biophys J 2019; 114:1614-1623. [PMID: 29642031 PMCID: PMC5954275 DOI: 10.1016/j.bpj.2018.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/04/2018] [Accepted: 02/07/2018] [Indexed: 11/06/2022] Open
Abstract
Intrinsically disordered proteins dynamically sample a wide conformational space and therefore do not adopt a stable and defined three-dimensional conformation. The structural heterogeneity is related to their proper functioning in physiological processes. Knowledge of the conformational ensemble is crucial for a complete comprehension of this kind of proteins. We here present an approach that utilizes dynamic nuclear polarization-enhanced solid-state NMR spectroscopy of sparsely isotope-labeled proteins in frozen solution to take snapshots of the complete structural ensembles by exploiting the inhomogeneously broadened line-shapes. We investigated the intrinsically disordered protein α-synuclein (α-syn), which plays a key role in the etiology of Parkinson’s disease, in three different physiologically relevant states. For the free monomer in frozen solution we could see that the so-called “random coil conformation” consists of α-helical and β-sheet-like conformations, and that secondary chemical shifts of neighboring amino acids tend to be correlated, indicative of frequent formation of secondary structure elements. Based on these results, we could estimate the number of disordered regions in fibrillar α-syn as well as in α-syn bound to membranes in different protein-to-lipid ratios. Our approach thus provides quantitative information on the propensity to sample transient secondary structures in different functional states. Molecular dynamics simulations rationalize the results.
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Affiliation(s)
- Boran Uluca
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Thibault Viennet
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Dušan Petrović
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Hamed Shaykhalishahi
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Franziska Weirich
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Ayşenur Gönülalan
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Manuel Etzkorn
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Henrike Heise
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
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18
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König A, Schölzel D, Uluca B, Viennet T, Akbey Ü, Heise H. Hyperpolarized MAS NMR of unfolded and misfolded proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 98:1-11. [PMID: 30641444 DOI: 10.1016/j.ssnmr.2018.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/28/2018] [Accepted: 12/30/2018] [Indexed: 05/09/2023]
Abstract
In this article we give an overview over the use of DNP-enhanced solid-state NMR spectroscopy for the investigation of unfolded, disordered and misfolded proteins. We first provide an overview over studies in which DNP spectroscopy has successfully been applied for the structural investigation of well-folded amyloid fibrils formed by short peptides as well as full-length proteins. Sample cooling to cryogenic temperatures often leads to severe line broadening of resonance signals and thus a loss in resolution. However, inhomogeneous line broadening at low temperatures provides valuable information about residual dynamics and flexibility in proteins, and, in combination with appropriate selective isotope labeling techniques, inhomogeneous linewidths in disordered proteins or protein regions may be exploited for evaluation of conformational ensembles. In the last paragraph we highlight some recent studies where DNP-enhanced MAS-NMR-spectroscopy was applied to the study of disordered proteins/protein regions and inhomogeneous sample preparations.
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Affiliation(s)
- Anna König
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Daniel Schölzel
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Boran Uluca
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Thibault Viennet
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Ümit Akbey
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Henrike Heise
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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19
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Nagarajan S, Xiao S, Raleigh DP, Dyer RB. Heterogeneity in the Folding of Villin Headpiece Subdomain HP36. J Phys Chem B 2018; 122:11640-11648. [PMID: 30118232 DOI: 10.1021/acs.jpcb.8b07683] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small single domain proteins that fold on the microsecond time scale have been the subject of intense interest as models for probing the complexity of folding energy landscapes. The villin headpiece subdomain (HP36) has been extensively studied because of its simple three helix structure, ultrafast folding lifetime of a few microseconds, and stable native fold. We have previously shown that folding as measured by a single 13C═18O isotopic label on residue A57 in helix 2 occurs at a different rate than that measured by global probes of folding, indicating noncooperative complexity in the folding of HP36. In order to determine whether this complexity reflects intermediates or parallel pathways over a small activation barrier, 13C═18O labels were individually incorporated at six different positions in HP36, including into all 3 helices. The equilibrium thermal unfolding transitions and the folding/unfolding dynamics were monitored using the unique IR signature of the 13C═18O label by temperature dependent FTIR and temperature jump IR spectroscopy, respectively. Equilibrium experiments reveal that the 13C═18O labels at different positions in HP36 show drastic differences in the midpoint of their transitions ( Tm), ranging from 45 to 67 °C. Heterogeneity is also observed in the relaxation kinetics; there are differences in the microsecond phase when different labeled positions are probed. At a final temperature of 45 °C, the relaxation rate for 13C═18O A57 is 2.4e + 05 s-1 whereas for 13C═18O L69 HP36 the relaxation rate is 5.1e + 05 s-1, two times faster. The observation of site-dependent midpoints for the equilibrium unfolding transitions and differences in the relaxation rates of the labeled positions enables us to probe the progressive accumulation of the folded structure, providing insight into the microscopic details of the folding mechanism.
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Affiliation(s)
- Sureshbabu Nagarajan
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Shifeng Xiao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography , Shenzhen University , Shenzhen 518060 , China
| | - Daniel P Raleigh
- Department of Chemistry , State University of New York at Stony Brook , Stony Brook , New York 11794 , United States.,Institute of Structural and Molecular Biology , University College London , Gower Street , London WC1E 6BT , United Kingdom
| | - R Brian Dyer
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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20
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Bauer T, Gath J, Hunkeler A, Ernst M, Böckmann A, Meier BH. Hexagonal ice in pure water and biological NMR samples. JOURNAL OF BIOMOLECULAR NMR 2017; 67:15-22. [PMID: 28028745 DOI: 10.1007/s10858-016-0080-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/07/2016] [Indexed: 06/06/2023]
Abstract
Ice, in addition to "liquid" water and protein, is an important component of protein samples for NMR spectroscopy at subfreezing temperatures but it has rarely been observed spectroscopically in this context. We characterize its spectroscopic behavior in the temperature range from 100 to 273 K, and find that it behaves like pure water ice. The interference of magic-angle spinning (MAS) as well as rf multiple-pulse sequences with Bjerrum-defect motion greatly influences the ice spectra.
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Affiliation(s)
- Thomas Bauer
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Julia Gath
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Andreas Hunkeler
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS, Université de Lyon 1, 7 passage du Vercors, 69367, Lyon, France.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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21
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Calligari P, Gerolin M, Abergel D, Polimeno A. Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions. J Chem Theory Comput 2016; 13:309-319. [DOI: 10.1021/acs.jctc.6b00702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Paolo Calligari
- Dipartimento
di Scienze Chimiche, Università di Padova, via Marzolo, 1, I-35131 Padova, Italy
| | - Marco Gerolin
- Dipartimento
di Scienze Chimiche, Università di Padova, via Marzolo, 1, I-35131 Padova, Italy
- Département
de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
| | - Daniel Abergel
- Département
de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
| | - Antonino Polimeno
- Dipartimento
di Scienze Chimiche, Università di Padova, via Marzolo, 1, I-35131 Padova, Italy
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22
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Abstract
AbstractIncreasing evidence suggests that most proteins occur and function in complexes rather than as isolated entities when embedded in cellular membranes. Nuclear magnetic resonance (NMR) provides increasing possibilities to study structure, dynamics and assembly of such systems. In our review, we discuss recent methodological progress to study membrane–protein complexes (MPCs) by NMR, starting with expression, isotope-labeling and reconstitution protocols. We review approaches to deal with spectral complexity and limited spectral spectroscopic sensitivity that are usually encountered in NMR-based studies of MPCs. We highlight NMR applications in various classes of MPCs, including G-protein-coupled receptors, ion channels and retinal proteins and extend our discussion to protein–protein complexes that span entire cellular compartments or orchestrate processes such as protein transport across or within membranes. These examples demonstrate the growing potential of NMR-based studies of MPCs to provide critical insight into the energetics of protein–ligand and protein–protein interactions that underlie essential biological functions in cellular membranes.
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23
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Thurber K, Tycko R. Low-temperature dynamic nuclear polarization with helium-cooled samples and nitrogen-driven magic-angle spinning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 264:99-106. [PMID: 26920835 PMCID: PMC4769783 DOI: 10.1016/j.jmr.2016.01.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 05/05/2023]
Abstract
We describe novel instrumentation for low-temperature solid state nuclear magnetic resonance (NMR) with dynamic nuclear polarization (DNP) and magic-angle spinning (MAS), focusing on aspects of this instrumentation that have not been described in detail in previous publications. We characterize the performance of an extended interaction oscillator (EIO) microwave source, operating near 264 GHz with 1.5 W output power, which we use in conjunction with a quasi-optical microwave polarizing system and a MAS NMR probe that employs liquid helium for sample cooling and nitrogen gas for sample spinning. Enhancement factors for cross-polarized (13)C NMR signals in the 100-200 range are demonstrated with DNP at 25K. The dependences of signal amplitudes on sample temperature, as well as microwave power, polarization, and frequency, are presented. We show that sample temperatures below 30K can be achieved with helium consumption rates below 1.3 l/h. To illustrate potential applications of this instrumentation in structural studies of biochemical systems, we compare results from low-temperature DNP experiments on a calmodulin-binding peptide in its free and bound states.
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Affiliation(s)
- Kent Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
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24
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Harpole KW, O'Brien ES, Clark MA, McKnight CJ, Vugmeyster L, Wand AJ. The unusual internal motion of the villin headpiece subdomain. Protein Sci 2015; 25:423-32. [PMID: 26473993 DOI: 10.1002/pro.2831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 10/12/2015] [Indexed: 11/06/2022]
Abstract
The thermostable 36-residue subdomain of the villin headpiece (HP36) is the smallest known cooperatively folding protein. Although the folding and internal dynamics of HP36 and close variants have been extensively studied, there has not been a comprehensive investigation of side-chain motion in this protein. Here, the fast motion of methyl-bearing amino acid side chains is explored over a range of temperatures using site-resolved solution nuclear magnetic resonance deuterium relaxation. The squared generalized order parameters of methyl groups extensively spatially segregate according to motional classes. This has not been observed before in any protein studied using this methodology. The class segregation is preserved from 275 to 305 K. Motions detected in Helix 3 suggest a fast timescale of conformational heterogeneity that has not been previously observed but is consistent with a range of folding and dynamics studies. Finally, a comparison between the order parameters in solution with previous results based on solid-state nuclear magnetic resonance deuterium line shape analysis of HP36 in partially hydrated powders shows a clear disagreement for half of the sites. This result has significant implications for the interpretation of data derived from a variety of approaches that rely on partially hydrated protein samples.
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Affiliation(s)
- Kyle W Harpole
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104-6059
| | - Evan S O'Brien
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104-6059
| | - Matthew A Clark
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska, 99508
| | - C James McKnight
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts, 02118
| | - Liliya Vugmeyster
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska, 99508.,Department of Chemistry, University of Colorado at Denver, Denver, Colorado, 80204
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104-6059
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25
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Potapov A, Yau WM, Ghirlando R, Thurber KR, Tycko R. Successive Stages of Amyloid-β Self-Assembly Characterized by Solid-State Nuclear Magnetic Resonance with Dynamic Nuclear Polarization. J Am Chem Soc 2015; 137:8294-307. [PMID: 26068174 PMCID: PMC5559291 DOI: 10.1021/jacs.5b04843] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Self-assembly of amyloid-β (Aβ) peptides in human brain tissue leads to neurodegeneration in Alzheimer's disease (AD). Amyloid fibrils, whose structures have been extensively characterized by solid state nuclear magnetic resonance (ssNMR) and other methods, are the thermodynamic end point of Aβ self-assembly. Oligomeric and protofibrillar assemblies, whose structures are less well-understood, are also observed as intermediates in the assembly process in vitro and have been implicated as important neurotoxic species in AD. We report experiments in which the structural evolution of 40-residue Aβ (Aβ40) is monitored by ssNMR measurements on frozen solutions prepared at four successive stages of the self-assembly process. Measurements on transient intermediates are enabled by ssNMR signal enhancements from dynamic nuclear polarization (DNP) at temperatures below 30 K. DNP-enhanced ssNMR data reveal a monotonic increase in conformational order from an initial state comprised primarily of monomers and small oligomers in solution at high pH, to larger oligomers near neutral pH, to metastable protofibrils, and finally to fibrils. Surprisingly, the predominant molecular conformation, indicated by (13)C NMR chemical shifts and by side chain contacts between F19 and L34 residues, is qualitatively similar at all stages. However, the in-register parallel β-sheet supramolecular structure, indicated by intermolecular (13)C spin polarization transfers, does not develop before the fibril stage. This work represents the first application of DNP-enhanced ssNMR to the characterization of peptide or protein self-assembly intermediates.
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Affiliation(s)
- Alexey Potapov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Kent R. Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
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26
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Ravera E, Schubeis T, Martelli T, Fragai M, Parigi G, Luchinat C. NMR of sedimented, fibrillized, silica-entrapped and microcrystalline (metallo)proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:60-70. [PMID: 25797005 DOI: 10.1016/j.jmr.2014.12.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/06/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
Resolution and sensitivity in solid state NMR (SSNMR) can rival the results achieved by solution NMR, and even outperform them in the case of large systems. However, several factors affect the spectral quality in SSNMR samples, and not all systems turn out to be equally amenable for this methodology. In this review we attempt at analyzing the causes of this variable behavior and at providing hints to increase the chances of experimental success.
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Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Tobias Schubeis
- Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Tommaso Martelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
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27
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Koers EJ, van der Cruijsen EAW, Rosay M, Weingarth M, Prokofyev A, Sauvée C, Ouari O, van der Zwan J, Pongs O, Tordo P, Maas WE, Baldus M. NMR-based structural biology enhanced by dynamic nuclear polarization at high magnetic field. JOURNAL OF BIOMOLECULAR NMR 2014; 60:157-68. [PMID: 25284462 DOI: 10.1007/s10858-014-9865-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/23/2014] [Indexed: 05/04/2023]
Abstract
Dynamic nuclear polarization (DNP) has become a powerful method to enhance spectroscopic sensitivity in the context of magnetic resonance imaging and nuclear magnetic resonance spectroscopy. We show that, compared to DNP at lower field (400 MHz/263 GHz), high field DNP (800 MHz/527 GHz) can significantly enhance spectral resolution and allows exploitation of the paramagnetic relaxation properties of DNP polarizing agents as direct structural probes under magic angle spinning conditions. Applied to a membrane-embedded K(+) channel, this approach allowed us to refine the membrane-embedded channel structure and revealed conformational substates that are present during two different stages of the channel gating cycle. High-field DNP thus offers atomic insight into the role of molecular plasticity during the course of biomolecular function in a complex cellular environment.
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Affiliation(s)
- Eline J Koers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
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28
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Andrews CT, Elcock AH. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids. J Chem Theory Comput 2014; 10:5178-5194. [PMID: 25400526 PMCID: PMC4230375 DOI: 10.1021/ct5006328] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Indexed: 02/06/2023]
Abstract
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We describe the derivation of a set
of bonded and nonbonded coarse-grained
(CG) potential functions for use in implicit-solvent Brownian dynamics
(BD) simulations of proteins derived from all-atom explicit-solvent
molecular dynamics (MD) simulations of amino acids. Bonded potential
functions were derived from 1 μs MD simulations of each of the
20 canonical amino acids, with histidine modeled in both its protonated
and neutral forms; nonbonded potential functions were derived from
1 μs MD simulations of every possible pairing of the amino acids
(231 different systems). The angle and dihedral probability distributions
and radial distribution functions sampled during MD were used to optimize
a set of CG potential functions through use of the iterative Boltzmann
inversion (IBI) method. The optimized set of potential functions—which
we term COFFDROP (COarse-grained Force Field for Dynamic Representation
Of Proteins)—quantitatively reproduced all of the “target”
MD distributions. In a first test of the force field, it was used
to predict the clustering behavior of concentrated amino acid solutions;
the predictions were directly compared with the results of corresponding
all-atom explicit-solvent MD simulations and found to be in excellent
agreement. In a second test, BD simulations of the small protein villin
headpiece were carried out at concentrations that have recently been
studied in all-atom explicit-solvent MD simulations by Petrov and
Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions
seen in the MD study were reproduced in the COFFDROP simulations;
a simple scaling of COFFDROP’s nonbonded parameters, however,
produced results in better accordance with experiment. Overall, our
results suggest that potential functions derived from simulations
of pairwise amino acid interactions might be of quite broad applicability,
with COFFDROP likely to be especially useful for modeling unfolded
or intrinsically disordered proteins.
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Affiliation(s)
- Casey T Andrews
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
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29
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Roessl U, Leitgeb S, Pieters S, De Beer T, Nidetzky B. In Situ Protein Secondary Structure Determination in Ice: Raman Spectroscopy-Based Process Analytical Tool for Frozen Storage of Biopharmaceuticals. J Pharm Sci 2014; 103:2287-95. [DOI: 10.1002/jps.24072] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/18/2014] [Accepted: 06/09/2014] [Indexed: 01/09/2023]
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30
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Are current atomistic force fields accurate enough to study proteins in crowded environments? PLoS Comput Biol 2014; 10:e1003638. [PMID: 24854339 PMCID: PMC4031056 DOI: 10.1371/journal.pcbi.1003638] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 04/08/2014] [Indexed: 01/30/2023] Open
Abstract
The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the picture of protein behavior in biologically relevant crowded environments. Protein behavior is strongly affected by highly crowded and interaction-rich environments, i.e., typical conditions in both biologically relevant systems, such as the cellular interior, and solution-based structural experiments, including NMR and different spectroscopies. On the other hand, primarily because of limited computational power, molecular dynamics (MD) simulations, a premier high-resolution method for analyzing structure, dynamics and interactions of proteins, have been predominantly used to study individual proteins at infinite dilution. To fill this gap, we use MD simulations to study the behavior of wild-type (aggregation-resistant) and oxidatively damaged (aggregation-prone) forms of villin headpiece at high concentration, and reveal unexpected limitations and inaccuracies of modern-day MD force fields when it comes to modeling proteins at physiologically or experimentally relevant concentrations.
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31
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Duan LL, Zhu T, Zhang QG, Tang B, Zhang JZH. Electronic polarization stabilizes tertiary structure prediction of HP-36. J Mol Model 2014; 20:2195. [PMID: 24715046 PMCID: PMC3996369 DOI: 10.1007/s00894-014-2195-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 03/02/2014] [Indexed: 01/10/2023]
Abstract
Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although some intermediates were close to the native structure, the overall conformation was not stable. Further analysis revealed that the large structure fluctuation of loop and hydrophobic core regions was devoted mostly to the instability of the structure during MD simulation. The backbone root-mean-square deviation (RMSD) of the loop and hydrophobic core regions showed strong correlation with the backbone RMSD of the whole protein. The free energy landscape indicated that the distribution of main chain torsions in loop and turn regions was far away from the native state. Starting from an intermediate structure extracted from the initial AMBER simulation, HP-36 was found to generally fold to the native state under the dynamically adjusted polarized protein-specific charge (DPPC) simulation, while the peptide did not fold into the native structure when AMBER force filed was used. The two best folded structures were extracted and taken into further simulations in water employing AMBER03 charge and DPPC for 25 ns. Result showed that introducing polarization effect into interacting potential could stabilize the near-native protein structure.
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Affiliation(s)
- Li L Duan
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
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32
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Emani PS, Bardaro MF, Huang W, Aragon S, Varani G, Drobny GP. Elucidating molecular motion through structural and dynamic filters of energy-minimized conformer ensembles. J Phys Chem B 2014; 118:1726-42. [PMID: 24479561 PMCID: PMC3983377 DOI: 10.1021/jp409386t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
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Complex RNA structures are constructed
from helical segments connected
by flexible loops that move spontaneously and in response to binding
of small molecule ligands and proteins. Understanding the conformational
variability of RNA requires the characterization of the coupled time
evolution of interconnected flexible domains. To elucidate the collective
molecular motions and explore the conformational landscape of the
HIV-1 TAR RNA, we describe a new methodology that utilizes energy-minimized
structures generated by the program “Fragment Assembly of RNA
with Full-Atom Refinement (FARFAR)”. We apply structural filters
in the form of experimental residual dipolar couplings (RDCs) to select
a subset of discrete energy-minimized conformers and carry out principal
component analyses (PCA) to corroborate the choice of the filtered
subset. We use this subset of structures to calculate solution T1 and T1ρ relaxation times for 13C spins in multiple residues in different domains of the molecule
using two simulation protocols that we previously published. We match
the experimental T1 times to within 2% and the T1ρ times to within less than 10% for helical residues. These results
introduce a protocol to construct viable dynamic trajectories for
RNA molecules that accord well with experimental NMR data and support
the notion that the motions of the helical portions of this small
RNA can be described by a relatively small number of discrete conformations
exchanging over time scales longer than 1 μs.
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Affiliation(s)
- Prashant S Emani
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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33
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Fragai M, Luchinat C, Parigi G, Ravera E. Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 57:155-66. [PMID: 23990200 DOI: 10.1007/s10858-013-9776-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 08/23/2013] [Indexed: 05/09/2023]
Abstract
Great theoretical and methodological advances are pushing the limits of resolution and sensitivity in solid state NMR (SSNMR). However, sample preparation remains a critical issue for the success of an experiment. The factors affecting spectral quality in SSNMR samples are discussed, examining cases encountered in the literature and presenting new experimental data. A discussion on resolution and sensitivity in sedimented solutes is framed in this context.
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Affiliation(s)
- Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
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34
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Vugmeyster L, Ostrovsky D, Lipton AS. Origin of abrupt rise in deuteron NMR longitudinal relaxation times of protein methyl groups below 90 K. J Phys Chem B 2013; 117:6129-37. [PMID: 23627365 DOI: 10.1021/jp4021596] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In order to examine the origin of the abrupt change in the temperature dependence of (2)H NMR longitudinal relaxation times observed previously for methyl groups of L69 in the hydrophobic core of villin headpiece protein at around 90 K (Vugmeyster et al. J. Am. Chem. Soc. 2010, 132, 4038-4039), we extended the measurements to several other methyl groups in the hydrophobic core. We show that, for all methyl groups, relaxation times experience a dramatic jump several orders of magnitude around this temperature. Theoretical modeling supports the conclusion that the origin of the apparent transition in the relaxation times is due to the existence of the distribution of conformers distinguished by their activation energy for methyl three-site hops. It is also crucial to take into account the differential contribution of individual conformers into overall signal intensity. When a particular conformer approaches the regime at which its three-site hop rate constant is on the order of the quadrupolar coupling interaction constant, the intensity of the signal due to this conformer experiences a sharp drop, thus changing the balance of the contributions of different conformers into the overall signal. As a result, the observed apparent transition in the relaxation rates can be explained without the assumption of an underlying transition in the rate constants. This work in combination with earlier results also shows that the model based on the distribution of conformers explains the relaxation behavior in the entire temperature range between 300 and 70 K.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, Alaska 99508, United States.
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35
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Ikeda K, Egawa A, Fujiwara T. Secondary structural analysis of proteins based on (13)C chemical shift assignments in unresolved solid-state NMR spectra enhanced by fragmented structure database. JOURNAL OF BIOMOLECULAR NMR 2013; 55:189-200. [PMID: 23271376 DOI: 10.1007/s10858-012-9701-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 12/21/2012] [Indexed: 06/01/2023]
Abstract
Magic-angle-spinning solid-state (13)C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-(13)C,(15)N labeled samples. To overcome this problem, we present a method for assigning (13)C chemical shifts and secondary structures from unresolved two-dimensional (13)C-(13)C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to (13)C(α), (13)C(β), and (13)C' chemical shifts and cross-peak intensities. The experimental (13)C-(13)C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific C(α), C(β), and C' chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50-200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved (13)C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.
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Affiliation(s)
- Keisuke Ikeda
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
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36
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Vugmeyster L, Ostrovsky D, Penland K, Hoatson GL, Vold RL. Glassy dynamics of protein methyl groups revealed by deuteron NMR. J Phys Chem B 2013; 117:1051-61. [PMID: 23301823 DOI: 10.1021/jp311112j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated site-specific dynamics of key methyl groups in the hydrophobic core of chicken villin headpiece subdomain (HP36) over the temperature range between 298 and 140 K using deuteron solid-state NMR longitudinal relaxation measurements. The relaxation of the longitudinal magnetization is weakly nonexponential (glassy) at high temperatures and exhibits a stronger degree of nonexponentiality below about 175 K. In addition, the characteristic relaxation times deviate from the simple Arrhenius law. We interpret this behavior via the existence of distribution of activation energy barriers for the three-site methyl jumps, which originates from somewhat different methyl environments within the local energy landscape. The width of the distribution of the activation barriers for methyl jumps is rather significant, about 1.4 kJ/mol. Our experimental results and modeling allow for the description of the apparent change at about 175 K without invoking a specific transition temperature. For most residues in the core, the relaxation behavior at high temperatures points to the existence of conformational exchange between the substates of the landscape, and our model takes into account the kinetics of this process. The observed dynamics are the same for dry and hydrated protein. We also looked at the effect of F58L mutation inside the hydrophobic core on the dynamics of one of the residues and observed a significant increase in its conformational exchange rate constant at high temperatures.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska 99508, USA.
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37
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Abstract
Solid-state NMR spectroscopy proved to be a versatile tool for characterization of structure and dynamics of complex biochemical systems. In particular, magic angle spinning (MAS) solid-state NMR came to maturity for application towards structural elucidation of biological macromolecules. Current challenges in applying solid-state NMR as well as progress achieved recently will be discussed in the following chapter focusing on conceptual aspects important for structural elucidation of proteins.
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Affiliation(s)
- Henrik Müller
- Institute of Physical Biology, Heinrich-Heine-University of Düsseldorf, 40225, Düsseldorf, Germany
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38
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Siemer AB, Huang KY, McDermott AE. Protein linewidth and solvent dynamics in frozen solution NMR. PLoS One 2012; 7:e47242. [PMID: 23077575 PMCID: PMC3471952 DOI: 10.1371/journal.pone.0047242] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 09/11/2012] [Indexed: 11/17/2022] Open
Abstract
Solid-state NMR of proteins in frozen aqueous solution is a potentially powerful technique in structural biology, especially if it is combined with dynamic nuclear polarization signal enhancement strategies. One concern regarding NMR studies of frozen solution protein samples at low temperatures is that they may have poor linewidths, thus preventing high-resolution studies. To learn more about how the solvent shell composition and temperature affects the protein linewidth, we recorded ¹H, ²H, and ¹³C spectra of ubiquitin in frozen water and frozen glycerol-water solutions at different temperatures. We found that the ¹³C protein linewidths generally increase with decreasing temperature. This line broadening was found to be inhomogeneous and independent of proton decoupling. In pure water, we observe an abrupt line broadening with the freezing of the bulk solvent, followed by continuous line broadening at lower temperatures. In frozen glycerol-water, we did not observe an abrupt line broadening and the NMR lines were generally narrower than for pure water at the same temperature. ¹H and ²H measurements characterizing the dynamics of water that is in exchange with the protein showed that the ¹³C line broadening is relatively independent from the arrest of isotropic water motions.
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Affiliation(s)
- Ansgar B Siemer
- Department of Chemistry, Columbia University, New York, New York, United States of America.
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39
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Comellas G, Lemkau LR, Zhou DH, George JM, Rienstra CM. Structural intermediates during α-synuclein fibrillogenesis on phospholipid vesicles. J Am Chem Soc 2012; 134:5090-9. [PMID: 22352310 PMCID: PMC3331674 DOI: 10.1021/ja209019s] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
α-Synuclein (AS) fibrils are the main protein component of Lewy bodies, the pathological hallmark of Parkinson's disease and other related disorders. AS forms helices that bind phospholipid membranes with high affinity, but no atomic level data for AS aggregation in the presence of lipids is yet available. Here, we present direct evidence of a conversion from α-helical conformation to β-sheet fibrils in the presence of anionic phospholipid vesicles and direct conversion to β-sheet fibrils in their absence. We have trapped intermediate states throughout the fibril formation pathways to examine the structural changes using solid-state NMR spectroscopy and electron microscopy. The comparison between mature AS fibrils formed in aqueous buffer and those derived in the presence of anionic phospholipids demonstrates no major changes in the overall fibril fold. However, a site-specific comparison of these fibrillar states demonstrates major perturbations in the N-terminal domain with a partial disruption of the long β-strand located in the 40s and small perturbations in residues located in the "non-β amyloid component" (NAC) domain. Combining all these results, we propose a model for AS fibrillogenesis in the presence of phospholipid vesicles.
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Affiliation(s)
- Gemma Comellas
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Luisel R. Lemkau
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Donghua H. Zhou
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Julia M. George
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Chad M. Rienstra
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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40
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Vugmeyster L, Ostrovsky D, Khadjinova A, Ellden J, Hoatson GL, Vold RL. Slow motions in the hydrophobic core of chicken villin headpiece subdomain and their contributions to configurational entropy and heat capacity from solid-state deuteron NMR measurements. Biochemistry 2011; 50:10637-46. [PMID: 22085262 PMCID: PMC3366553 DOI: 10.1021/bi201515b] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated microsecond to millisecond time scale dynamics in several key hydrophobic core methyl groups of chicken villin headpiece subdomain protein (HP36) using a combination of single-site labeling, deuteron solid-state NMR line shape analysis, and computational modeling. Deuteron line shapes of hydrated powder samples are dominated by rotameric jumps and show a large variability of rate constants, activation energies, and rotameric populations. Site-specific activation energies vary from 6 to 38 kJ/mol. An additional mode of diffusion on a restricted arc is significant for some sites. In dry samples, the dynamics is quenched. Parameters of the motional models allow for calculations of configurational entropy and heat capacity, which, together with the rate constants, allow for observation of interplay between thermodynamic and kinetic picture of the landscape. Mutations at key phenylalanine residues at both distal (F47L&F51L) and proximal (F58L) locations to a relatively rigid side chain of L69 have a pronounced effect on alleviating the rigidity of this side chain at room temperature and demonstrate the sensitivity of the hydrophobic core environment to such perturbations.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Alaska, Anchorage, Alaska 99508, United States.
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41
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Sutto L, Mereu I, Gervasio FL. A Hybrid All-Atom Structure-Based Model for Protein Folding and Large Scale Conformational Transitions. J Chem Theory Comput 2011; 7:4208-17. [DOI: 10.1021/ct200547m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ludovico Sutto
- Spanish National Cancer Research Center (CNIO), Structural Biology and Biocomputing Programme, Melchor Fernandez Almagro, 3, E-28029 Madrid, Spain
| | - Ilaria Mereu
- Spanish National Cancer Research Center (CNIO), Structural Biology and Biocomputing Programme, Melchor Fernandez Almagro, 3, E-28029 Madrid, Spain
| | - Francesco Luigi Gervasio
- Spanish National Cancer Research Center (CNIO), Structural Biology and Biocomputing Programme, Melchor Fernandez Almagro, 3, E-28029 Madrid, Spain
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42
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Saladino G, Marenchino M, Pieraccini S, Campos-Olivas R, Sironi M, Gervasio FL. A Simple Mechanism Underlying the Effect of Protecting Osmolytes on Protein Folding. J Chem Theory Comput 2011; 7:3846-52. [PMID: 26598273 DOI: 10.1021/ct200471w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Osmolytes are small organic compounds that confer to the cell an enhanced adaptability to external conditions. Many osmolytes not only protect the cell from osmotic stress but also stabilize the native structure of proteins. While simplified models able to predict changes to protein stability are available, a general physicochemical explanation of the underlying microscopic mechanism is still missing. Here, we address this issue by performing very long all-atom MD simulations, free energy calculations, and experiments on a well-characterized mini-protein, the villin headpiece. Comparisons between the folding free energy landscapes in pure water and osmolyte solutions, together with experimental validation by means of circular dichroism, unfolding experiments, and NMR, led us to formulate a simple hypothesis for the protecting mechanism. Taken together, our results support a novel mechanistic explanation according to which the main driving force behind native state protection is a change in the solvent rotational diffusion.
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Affiliation(s)
- G Saladino
- Dipartimento di Chimica Fisica ed Elettrochimica, Universita' degli Studi di Milano , Via Golgi 19, 20133 Milano, Italy
| | - M Marenchino
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - S Pieraccini
- Dipartimento di Chimica Fisica ed Elettrochimica, Universita' degli Studi di Milano , Via Golgi 19, 20133 Milano, Italy.,INSTM Research Unit , Via Golgi 19, 20133 Milano, Italy
| | - R Campos-Olivas
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - M Sironi
- Dipartimento di Chimica Fisica ed Elettrochimica, Universita' degli Studi di Milano , Via Golgi 19, 20133 Milano, Italy.,INSTM Research Unit , Via Golgi 19, 20133 Milano, Italy.,Institute of Molecular Science and Technology , Via Golgi 19, 20133 Milano
| | - F L Gervasio
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez Almagro 3, 28029, Madrid, Spain
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43
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Su Y, Hong M. Conformational disorder of membrane peptides investigated from solid-state NMR line widths and line shapes. J Phys Chem B 2011; 115:10758-67. [PMID: 21806038 PMCID: PMC3222302 DOI: 10.1021/jp205002n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A challenge in the application of solid-state NMR spectroscopy to membrane peptides and proteins is the relatively broad line widths compared to those for solution NMR spectra. To understand the linewidth contributions to membrane protein NMR spectra, we have measured the inhomogeneous and homogeneous line widths of several well-studied membrane peptides under immobilized conditions. (13)C T(2) relaxation times of uniformly (13)C-labeled residues show that the homogeneous line widths of the peptides are comparable to those of crystalline model compounds under identical (1)H decoupling and magic angle spinning conditions, indicating that the homogeneous line widths are determined by conformation-independent factors, including residual dipolar coupling, J-coupling, and intrinsic T(2) relaxation. However, the membrane peptides exhibit larger apparent line widths than the crystalline compounds, indicating conformational disorder. A cationic cell-penetrating peptide, the human immunodeficiency virus TAT, exhibits the largest apparent line widths, which are about five-fold larger than the homogeneous line widths, while the transmembrane helix of the influenza M2 peptide and the β-hairpin antimicrobial peptide PG-1 show moderately larger apparent line widths than the crystalline compounds. These results are consistent with the random coil nature of the TAT peptide, which contrasts with the intramolecularly hydrogen bonded M2 and PG-1. Cross peak line shapes of 2D double-quantum correlation spectra show that the conformational disorder can occur at the residue level and can result from three origins, lipid-peptide interaction, intrinsic conformational disorder encoded in the amino acid sequence, and side-chain rotameric averaging. A particularly important lipid-peptide interaction for cationic membrane peptides is guanidinium-phosphate ion pair interaction. Thus, NMR line widths and line shapes are useful for understanding the conformational disorder of membrane peptides and proteins.
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Affiliation(s)
- Yongchao Su
- Department of Chemistry, Iowa State University, Ames, IA 50011
| | - Mei Hong
- Department of Chemistry, Iowa State University, Ames, IA 50011
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44
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Saladino G, Marenchino M, Gervasio FL. Bridging the Gap between Folding Simulations and Experiments: The Case of the Villin Headpiece. J Chem Theory Comput 2011; 7:2675-80. [PMID: 26605458 DOI: 10.1021/ct2002489] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The increasing accuracy of molecular dynamics force fields parameters and the increasing resolution of experimental results allow one to carefully compare and complement in silico data with experimental observations. Here, we study the human villin headpiece C-terminal helical subdomain (HP35) with the recent highly optimized Amber99SB*-ILDN force field and compare the results with recent high resolution triplet-triplet energy transfer (TTET) experiments. The correct reproduction of the main structural features reveals a good agreement between experimental data and simulations.
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Affiliation(s)
- G Saladino
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO) , c/Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - M Marenchino
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO) , c/Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - F L Gervasio
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO) , c/Melchor Fernandez Almagro 3, 28029, Madrid, Spain
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45
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Vugmeyster L, Ostrovsky D. Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain. JOURNAL OF BIOMOLECULAR NMR 2011; 50:119-27. [PMID: 21416162 PMCID: PMC3366550 DOI: 10.1007/s10858-011-9500-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 03/02/2011] [Indexed: 05/03/2023]
Abstract
Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: (13)C' longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms, (13)C'/(13)C'-(13)C(α) CSA/dipolar and (13)C'/(13)C'-(15)N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the time scales of internal and molecular motions in the 2-16°C temperature range. There is a gradual deviation from this assumption from lower to higher temperatures, such that above 16°C the separation of the time scales is inconsistent with the experimental data and, thus, the Lipari-Szabo formalism can not be applied. While there are variations among the residues, on the average the order parameters indicate a markedly steeper temperature dependence at backbone carbonyl carbons compared to that probed at amide nitrogens in an earlier study. This strongly advocates for probing sites other than amide nitrogen for accurate characterization of the potential and other thermodynamics characteristics of protein backbone.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry and Environment and Natural Resources Institute, University of Alaska at Anchorage, Providence Drive, Anchorage, AK 99508, USA.
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46
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Etzkorn M, Böckmann A, Baldus M. Kinetic analysis of protein aggregation monitored by real-time 2D solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2011; 49:121-129. [PMID: 21253842 PMCID: PMC3042102 DOI: 10.1007/s10858-011-9468-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 01/01/2011] [Indexed: 05/30/2023]
Abstract
It is shown that real-time 2D solid-state NMR can be used to obtain kinetic and structural information about the process of protein aggregation. In addition to the incorporation of kinetic information involving intermediate states, this approach can offer atom-specific resolution for all detectable species. The analysis was carried out using experimental data obtained during aggregation of the 10.4 kDa Crh protein, which has been shown to involve a partially unfolded intermediate state prior to aggregation. Based on a single real-time 2D (13)C-(13)C transition spectrum, kinetic information about the refolding and aggregation step could be extracted. In addition, structural rearrangements associated with refolding are estimated and several different aggregation scenarios were compared to the experimental data.
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Affiliation(s)
- Manuel Etzkorn
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Present Address: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115 USA
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS-UCBL, Université de Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Marc Baldus
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 Utrecht, The Netherlands
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47
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Yoda T, Sugita Y, Okamoto Y. Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations. Biophys J 2010; 99:1637-44. [PMID: 20816077 DOI: 10.1016/j.bpj.2010.06.045] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 06/05/2010] [Accepted: 06/22/2010] [Indexed: 11/30/2022] Open
Abstract
Despite its small size, chicken villin headpiece subdomain HP36 folds into the native structure with a stable hydrophobic core within several microseconds. How such a small protein keeps up its conformational stability and fast folding in solution is an important issue for understanding molecular mechanisms of protein folding. In this study, we performed multicanonical replica-exchange simulations of HP36 in explicit water, starting from a fully extended conformation. We observed at least five events of HP36 folding into nativelike conformations. The smallest backbone root mean-square deviation from the crystal structure was 1.1 A. In the nativelike conformations, the stably formed hydrophobic core was fully dehydrated. Statistical analyses of the simulation trajectories show the following sequential events in folding of HP36: 1), Helix 3 is formed at the earliest stage; 2), the backbone and the side chains near the loop between Helices 2 and 3 take nativelike conformations; and 3), the side-chain packing at the hydrophobic core and the dehydration of the core side chains take place simultaneously at the later stage of folding. This sequence suggests that the initial folding nucleus is not necessarily the same as the hydrophobic core, consistent with a recent experimental phi-value analysis.
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Affiliation(s)
- Takao Yoda
- Nagahama Institute of Bio-Science and Technology, Tamura, Nagahama, Shiga, Japan.
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48
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Siemer AB, Huang KY, McDermott AE. Protein-ice interaction of an antifreeze protein observed with solid-state NMR. Proc Natl Acad Sci U S A 2010; 107:17580-5. [PMID: 20884853 PMCID: PMC2955146 DOI: 10.1073/pnas.1009369107] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
NMR on frozen solutions is an ideal method to study fundamental questions of macromolecular hydration, because the hydration shell of many biomolecules does not freeze together with bulk solvent. In the present study, we present previously undescribed NMR methods to study the interactions of proteins with their hydration shell and the ice lattice in frozen solution. We applied these methods to compare solvent interaction of an ice-binding type III antifreeze protein (AFP III) and ubiquitin a non-ice-binding protein in frozen solution. We measured (1)H-(1)H cross-saturation and cross-relaxation to provide evidence for a molecular contact surface between ice and AFP III at moderate freezing temperatures of -35 °C. This phenomenon is potentially unique for AFPs because ubiquitin shows no such cross relaxation or cross saturation with ice. On the other hand, we detected liquid hydration water and strong water-AFP III and water-ubiquitin cross peaks in frozen solution using relaxation filtered (2)H and HETCOR spectra with additional (1)H-(1)H mixing. These results are consistent with the idea that ubiquitin is surrounded by a hydration shell, which separates it from the bulk ice. For AFP III, the water cross peaks indicate that only a portion of its hydration shell (i.e., at the ice-binding surface) is in contact with the ice lattice. The rest of AFP III's hydration shell behaves similarly to the hydration shell of non-ice-interacting proteins such as ubiquitin and does not freeze together with the bulk water.
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Affiliation(s)
- Ansgar B. Siemer
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027
| | - Kuo-Ying Huang
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027
| | - Ann E. McDermott
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027
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49
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Hu F, Luo W, Cady SD, Hong M. Conformational plasticity of the influenza A M2 transmembrane helix in lipid bilayers under varying pH, drug binding, and membrane thickness. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:415-23. [PMID: 20883664 DOI: 10.1016/j.bbamem.2010.09.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 09/05/2010] [Accepted: 09/21/2010] [Indexed: 12/14/2022]
Abstract
Membrane proteins change their conformations to respond to environmental cues, thus conformational plasticity is important for function. The influenza A M2 protein forms an acid-activated proton channel important for the virus lifecycle. Here we have used solid-state NMR spectroscopy to examine the conformational plasticity of membrane-bound transmembrane domain of M2 (M2TM). (13)C and (15)N chemical shifts indicate coupled conformational changes of several pore-facing residues due to changes in bilayer thickness, drug binding, and pH. The structural changes are attributed to the formation of a well-defined helical kink at G34 in the drug-bound state and in thick lipid bilayers, nonideal backbone conformation of the secondary-gate residue V27 in the presence of drug, and nonideal conformation of the proton-sensing residue H37 at high pH. The chemical shifts constrained the (ϕ, ψ) torsion angles for three "basis" states, the equilibrium among which explains the multiple resonances per site in the NMR spectra under different combinations of bilayer thickness, drug binding, and pH conditions. Thus, conformational plasticity is important for the proton conduction and inhibition of M2TM. The study illustrates the utility of NMR chemical shifts for probing the structural plasticity and folding of membrane proteins.
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Affiliation(s)
- Fanghao Hu
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
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50
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Klenin K, Strodel B, Wales DJ, Wenzel W. Modelling proteins: conformational sampling and reconstruction of folding kinetics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:977-1000. [PMID: 20851219 DOI: 10.1016/j.bbapap.2010.09.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 09/03/2010] [Accepted: 09/05/2010] [Indexed: 01/08/2023]
Abstract
In the last decades biomolecular simulation has made tremendous inroads to help elucidate biomolecular processes in-silico. Despite enormous advances in molecular dynamics techniques and the available computational power, many problems involve long time scales and large-scale molecular rearrangements that are still difficult to sample adequately. In this review we therefore summarise recent efforts to fundamentally improve this situation by decoupling the sampling of the energy landscape from the description of the kinetics of the process. Recent years have seen the emergence of many advanced sampling techniques, which permit efficient characterisation of the relevant family of molecular conformations by dispensing with the details of the short-term kinetics of the process. Because these methods generate thermodynamic information at best, they must be complemented by techniques to reconstruct the kinetics of the process using the ensemble of relevant conformations. Here we review recent advances for both types of methods and discuss their perspectives to permit efficient and accurate modelling of large-scale conformational changes in biomolecules. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Konstantin Klenin
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, P.O. Box 3640, D-76021 Karlsruhe, Germany
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