1
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He JH, Cheng WW, Zhang AQ, Qin SY. Tandem "One-Shot" Measurement of Residual Chemical Shift Anisotropy and Residual Dipolar Coupling using Biphasic Supramolecular Peptide Liquid Crystals. Anal Chem 2024; 96:11881-11889. [PMID: 38976239 DOI: 10.1021/acs.analchem.4c01558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Both solitary and tandem applications of residual chemical shift anisotropy (RCSA) and residual dipolar coupling (RDC) show great potential for the structural and configurational determination of organic molecules. A critical component of both RDC and RCSA methodologies is the alignment medium, whose availability is limited, especially for RCSA measurement. Moreover, reported RDC and RCSA acquisitions mainly rely on two experiments conducted under two different conditions, which are relatively time-consuming and easily cause experimental errors. Herein, a biphasic supramolecular lyotropic liquid crystalline (LLC) system was developed through the self-assembly of C21H43-CONH-V4K3-CONH2, which could act as an alignment medium for not only RDC but also RCSA extraction in DMSO-d6. Notably, the RCSA extraction was easily achieved via one-shot measurement from a single one-dimensional 13C NMR experiment, with no need for special instruments, devices, and correction. Relying on the biphasic LLC medium, meanwhile, RDC data were simply extracted from a single F1-coupled HSQC experiment, different from the standard protocol that requires two spectral acquisitions corresponding to the isotropic and anisotropic conditions. Collectively, the biphasic LLC medium is applicable for tandem RCSA and RDC measurements in one single sample, advancing the stereochemical elucidation of molecules of interest.
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Affiliation(s)
- Jin-Hao He
- Hubei Engineering Technology Research Centre of Energy Polymer Materials, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Wei-Wei Cheng
- Hubei Engineering Technology Research Centre of Energy Polymer Materials, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Ai-Qing Zhang
- Hubei Engineering Technology Research Centre of Energy Polymer Materials, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Si-Yong Qin
- Hubei Engineering Technology Research Centre of Energy Polymer Materials, Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, South-Central Minzu University, Wuhan 430074, P. R. China
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2
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Schroder R, Dorsey PJ, Vanderburgh J, Xu W, D'Addio SM, Klein L, Gindy M, Su Y. Probing Molecular Packing of Lipid Nanoparticles from 31P Solution and Solid-State NMR. Anal Chem 2024; 96:2464-2473. [PMID: 38306310 DOI: 10.1021/acs.analchem.3c04430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
Lipid nanoparticles (LNPs) are intricate multicomponent systems widely recognized for their efficient delivery of oligonucleotide cargo to host cells. Gaining insights into the molecular properties of LNPs is crucial for their effective design and characterization. However, analysis of their internal structure at the molecular level presents a significant challenge. This study introduces 31P nuclear magnetic resonance (NMR) methods to acquire structural and dynamic information about the phospholipid envelope of LNPs. Specifically, we demonstrate that the 31P chemical shift anisotropy (CSA) parameters serve as a sensitive indicator of the molecular assembly of distearoylphosphatidylcholine (DSPC) lipids within the particles. An analytical protocol for measuring 31P CSA is developed, which can be implemented using either solution NMR or solid-state NMR, offering wide accessibility and adaptability. The capability of this method is demonstrated using both model DSPC liposomes and real-world pharmaceutical LNP formulations. Furthermore, our method can be employed to investigate the impact of formulation processes and composition on the assembly of specifically LNP particles or, more generally, phospholipid-based delivery systems. This makes it an indispensable tool for evaluating critical pharmaceutical properties such as structural homogeneity, batch-to-batch reproducibility, and the stability of the particles.
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Affiliation(s)
- Ryan Schroder
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Phillip J Dorsey
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Joe Vanderburgh
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Wei Xu
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Suzanne M D'Addio
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Lee Klein
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Marian Gindy
- Small Molecule Science and Technology, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yongchao Su
- Analytical Research & 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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3
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Burns DC, Reynolds WF. Minimizing the risk of deducing wrong natural product structures from NMR data. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:500-533. [PMID: 33855734 DOI: 10.1002/mrc.4933] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 06/12/2023]
Abstract
There continues to be a disturbing number of natural products reported in the literature whose structures are incorrect. At least in part, this reflects the fact that many natural product chemists have limited formal nuclear magnetic resonance training. Gaps in training and lack of awareness regarding the challenges and ambiguities associated with two-dimensional nuclear magnetic resonance data interpretation can easily lead to errors in structure elucidation. The purpose of this tutorial is to point out some of these issues, highlight the kinds of errors that have been made and provide specific advice on how to avoid these missteps such that the risk of reporting a wrong structure is minimized.
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Affiliation(s)
- Darcy C Burns
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - William F Reynolds
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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4
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Das A, Nath N. Elucidating natural product structures using a robust measurement of carbon residual chemical shift anisotropy combined with DFT. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:569-576. [PMID: 31758720 DOI: 10.1002/mrc.4975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/20/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
Determination of configurations and conformations is an important step in the structural characterization of small molecules. Apart from utilizing isotropic J-couplings and nuclear overhauser effect (NOEs) measured in isotropic solution, anisotropic Nuclear Magnetic resonance (NMR) data such as residual dipolar couplings and residual chemical shift anisotropies (RCSAs) were also used to elucidate complex small molecule structures. Measuring RCSA has always been historically difficult due to the isotropic shift effect accompanied by molecular alignment and therefore only occasionally applied in a few examples. Here, we present a robust measurement of carbon RCSAs using a smaller gel-stretching device to determine the structures of a few small molecules. A systematic study on how different density functional theory computed anisotropies of the chemical shift anisotropy tensors impact RCSA data interpretation has also been discussed. We also discuss the effect of utilizing various carbons as reference nuclei for RCSA data extraction as well as the orientation behavior of estrone in orthogonal alignment media.
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Affiliation(s)
- Akhi Das
- Department of Chemistry, Gauhati University, Guwahati, India
| | - Nilamoni Nath
- Department of Chemistry, Gauhati University, Guwahati, India
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5
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Relative configuration of micrograms of natural compounds using proton residual chemical shift anisotropy. Nat Commun 2020; 11:4372. [PMID: 32873801 PMCID: PMC7463026 DOI: 10.1038/s41467-020-18093-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 07/28/2020] [Indexed: 01/12/2023] Open
Abstract
3D molecular structure determination is a challenge for organic compounds or natural products available in minute amounts. Proton/proton and proton/carbon correlations yield the constitution. J couplings and NOEs oftentimes supported by one-bond 1H,13C residual dipolar couplings (RDCs) or by 13C residual chemical shift anisotropies (RCSAs) provide the relative configuration. However, these RDCs or carbon RCSAs rely on 1% natural abundance of 13C preventing their use for compounds available only in quantities of a few 10’s of µgs. By contrast, 1H RCSAs provide similar information on spatial orientation of structural moieties within a molecule, while using the abundant 1H spin. Herein, 1H RCSAs are accurately measured using constrained aligning gels or liquid crystals and applied to the 3D structural determination of molecules with varying complexities. Even more, deuterated alignment media allow the elucidation of the relative configuration of around 35 µg of a briarane compound isolated from Briareum asbestinum. Determination of 3D molecular structures remains challenging for natural products or organic compounds available in minute amounts. Here, the authors determine the structure of complex molecules, including few micrograms of briarane B-3 isolated from Briareum asbestinums, through measurement of 1H residual chemical shift anisotropy.
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6
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Upadhyay SK, Mackereth CD. Structural basis of UCUU RNA motif recognition by splicing factor RBM20. Nucleic Acids Res 2020; 48:4538-4550. [PMID: 32187365 PMCID: PMC7192616 DOI: 10.1093/nar/gkaa168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/28/2020] [Accepted: 03/07/2020] [Indexed: 12/16/2022] Open
Abstract
The vertebrate splicing factor RBM20 (RNA binding motif protein 20) regulates protein isoforms important for heart development and function, with mutations in the gene linked to cardiomyopathy. Previous studies have identified the four nucleotide RNA motif UCUU as a common element in pre-mRNA targeted by RBM20. Here, we have determined the structure of the RNA Recognition Motif (RRM) domain from mouse RBM20 bound to RNA containing a UCUU sequence. The atomic details show that the RRM domain spans a larger region than initially proposed in order to interact with the complete UCUU motif, with a well-folded C-terminal helix encoded by exon 8 critical for high affinity binding. This helix only forms upon binding RNA with the final uracil, and removing the helix reduces affinity as well as specificity. We therefore find that RBM20 uses a coupled folding-binding mechanism by the C-terminal helix to specifically recognize the UCUU RNA motif.
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Affiliation(s)
| | - Cameron D Mackereth
- Univ. Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac Cedex, France.,Inserm U1212, CNRS UMR5320, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
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7
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Marceau AH, Brison CM, Nerli S, Arsenault HE, McShan AC, Chen E, Lee HW, Benanti JA, Sgourakis NG, Rubin SM. An order-to-disorder structural switch activates the FoxM1 transcription factor. eLife 2019; 8:e46131. [PMID: 31134895 PMCID: PMC6538375 DOI: 10.7554/elife.46131] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/08/2019] [Indexed: 12/15/2022] Open
Abstract
Intrinsically disordered transcription factor transactivation domains (TADs) function through structural plasticity, adopting ordered conformations when bound to transcriptional co-regulators. Many transcription factors contain a negative regulatory domain (NRD) that suppresses recruitment of transcriptional machinery through autoregulation of the TAD. We report the solution structure of an autoinhibited NRD-TAD complex within FoxM1, a critical activator of mitotic gene expression. We observe that while both the FoxM1 NRD and TAD are primarily intrinsically disordered domains, they associate and adopt a structured conformation. We identify how Plk1 and Cdk kinases cooperate to phosphorylate FoxM1, which releases the TAD into a disordered conformation that then associates with the TAZ2 or KIX domains of the transcriptional co-activator CBP. Our results support a mechanism of FoxM1 regulation in which the TAD undergoes switching between disordered and different ordered structures.
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Affiliation(s)
- Aimee H Marceau
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
| | - Caileen M Brison
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
| | - Santrupti Nerli
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
- Department of Computer ScienceUniversity of California, Santa CruzSanta CruzUnited States
| | - Heather E Arsenault
- Department of Molecular, Cell and Cancer BiologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Andrew C McShan
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
| | - Eefei Chen
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
| | - Hsiau-Wei Lee
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
| | - Jennifer A Benanti
- Department of Molecular, Cell and Cancer BiologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Nikolaos G Sgourakis
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
| | - Seth M Rubin
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
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8
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Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen. J Comput Aided Mol Des 2019; 33:531-558. [PMID: 31054028 PMCID: PMC6554267 DOI: 10.1007/s10822-019-00203-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/20/2019] [Indexed: 11/24/2022]
Abstract
ForceGen is a template-free, non-stochastic approach for 2D to 3D structure generation and conformational elaboration for small molecules, including both non-macrocycles and macrocycles. For conformational search of non-macrocycles, ForceGen is both faster and more accurate than the best of all tested methods on a very large, independently curated benchmark of 2859 PDB ligands. In this study, the primary results are on macrocycles, including results for 431 unique examples from four separate benchmarks. These include complex peptide and peptide-like cases that can form networks of internal hydrogen bonds. By making use of new physical movements (“flips” of near-linear sub-cycles and explicit formation of hydrogen bonds), ForceGen exhibited statistically significantly better performance for overall RMS deviation from experimental coordinates than all other approaches. The algorithmic approach offers natural parallelization across multiple computing-cores. On a modest multi-core workstation, for all but the most complex macrocycles, median wall-clock times were generally under a minute in fast search mode and under 2 min using thorough search. On the most complex cases (roughly cyclic decapeptides and larger) explicit exploration of likely hydrogen bonding networks yielded marked improvements, but with calculation times increasing to several minutes and in some cases to roughly an hour for fast search. In complex cases, utilization of NMR data to constrain conformational search produces accurate conformational ensembles representative of solution state macrocycle behavior. On macrocycles of typical complexity (up to 21 rotatable macrocyclic and exocyclic bonds), design-focused macrocycle optimization can be practically supported by computational chemistry at interactive time-scales, with conformational ensemble accuracy equaling what is seen with non-macrocyclic ligands. For more complex macrocycles, inclusion of sparse biophysical data is a helpful adjunct to computation.
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9
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Carvalho DS, da Silva DGB, Hallwass F, Navarro-Vázquez A. Chemically cross-linked polyacrylonitrile. A DMSO compatible NMR alignment medium for measurement of residual dipolar couplings and residual chemical shift anisotropies. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 302:21-27. [PMID: 30933840 DOI: 10.1016/j.jmr.2019.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/09/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
Chemically cross-linked polyacrylontrile polymer gels, have been prepared as an alignment medium compatible with DMSO-d6. These gels allow measurement of residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) with good accuracy as tested with brucine and α-santonin natural compounds. The gels can be reversibly compressed allowing easy measurement of RCSAs. They also present good physical homogeneity, clean HSQC spectra with little background 1H signals, and allow unambiguous referencing of 13C spectra for RCSA extraction.
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Affiliation(s)
- Daiane S Carvalho
- Universidade Federal de Pernambuco, Departamento de Química Fundamental, CCEN, Recife, Pernambuco 50670-901, Brazil
| | - Danilo G B da Silva
- Universidade Federal de Pernambuco, Departamento de Química Fundamental, CCEN, Recife, Pernambuco 50670-901, Brazil
| | - Fernando Hallwass
- Universidade Federal de Pernambuco, Departamento de Química Fundamental, CCEN, Recife, Pernambuco 50670-901, Brazil
| | - Armando Navarro-Vázquez
- Universidade Federal de Pernambuco, Departamento de Química Fundamental, CCEN, Recife, Pernambuco 50670-901, Brazil.
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10
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Zhang W, Meredith R, Yoon MK, Wang X, Woods RJ, Carmichael I, Serianni AS. Synthesis and O-Glycosidic Linkage Conformational Analysis of 13C-Labeled Oligosaccharide Fragments of an Antifreeze Glycolipid. J Org Chem 2019; 84:1706-1724. [PMID: 30624062 DOI: 10.1021/acs.joc.8b01411] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
NMR studies of two 13C-labeled disaccharides and a tetrasaccharide were undertaken that comprise the backbone of a novel thermal hysteresis glycolipid containing a linear glycan sequence of alternating [βXyl p-(1→4)-βMan p-(1→4)] n dimers. Experimental trans-glycoside NMR J-couplings, parameterized equations obtained from density functional theory (DFT) calculations, and an in-house circular statistics package ( MA'AT) were used to derive conformational models of linkage torsion angles ϕ and ψ in solution, which were compared to those obtained from molecular dynamics simulations. Modeling using different probability distribution functions showed that MA'AT models of ϕ in βMan(1→4)βXyl and βXyl(1→4)βMan linkages are very similar in the disaccharide building blocks, whereas MA'AT models of ψ differ. This pattern is conserved in the tetrasaccharide, showing that linkage context does not influence linkage geometry in this linear system. Good agreement was observed between the MA'AT and MD models of ψ with respect to mean values and circular standard deviations. Significant differences were observed for ϕ, indicating that revision of the force-field employed by GLYCAM is probably needed. Incorporation of the experimental models of ϕ and ψ into the backbone of an octasaccharide fragment leads to a helical amphipathic topography that may affect the thermal hysteresis properties of the glycolipid.
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Affiliation(s)
| | | | | | - Xiaocong Wang
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Robert J Woods
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
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11
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Zhang W, Meredith R, Pan Q, Wang X, Woods RJ, Carmichael I, Serianni AS. Use of Circular Statistics To Model αMan-(1→2)-αMan and αMan-(1→3)-α/βMan O-Glycosidic Linkage Conformation in 13C-Labeled Disaccharides and High-Mannose Oligosaccharides. Biochemistry 2019; 58:546-560. [PMID: 30605318 DOI: 10.1021/acs.biochem.8b01050] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new experimental method, MA' AT analysis, has been applied to investigate the conformational properties of O-glycosidic linkages in several biologically important mannose-containing di- and oligosaccharides. Methyl α-d-mannopyranosyl-(1→2)-α-d-mannopyranoside (2), methyl α-d-mannopyranosyl-(1→3)-α-d-mannopyranoside (3), and methyl α-d-mannopyranosyl-(1→3)-β-d-mannopyranoside (4) were prepared with selective 13C-enrichment to enable the measurement of NMR scalar couplings across their internal O-glycosidic linkages. Density functional theory (DFT) was used to parameterize equations for JCH and JCC values in 2-4 that are sensitive to phi (ϕ) and psi (ψ). The experimental J-couplings and parameterized equations were treated using a circular statistics algorithm encoded in the MA' AT program. Conformations about ϕ and ψ treated using single-state von Mises models gave excellent fits to the ensembles of redundant J-couplings. Mean values and circular standard deviations (CSDs) for each linkage torsion angle ϕ (CSD) and ψ (CSD) in 2, -29° (25°) and 20° (22°); in 3, -36° (36°) and 8° (27°); in 4, -37° (34°) and 10° (26°); ϕ = H1'-C1'-O1'-CX and ψ = C1'-O1'-CX-HX (CX = aglycone carbon) were compared to histograms obtained from 1 μs aqueous molecular dynamics (MD) simulations and X-ray database statistical analysis. MA' AT-derived models of ψ were in very good agreement with the MD and X-ray data, but not those of ϕ, suggesting a need for force field revision. The effect of structural context on linkage conformation was also investigated in four selectively 13C-labeled homomannose tri- and tetrasaccharides using the MA' AT method. In the cases examined, context effects were found to be small.
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Affiliation(s)
| | | | | | - Xiaocong Wang
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 United States
| | - Robert J Woods
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 United States
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12
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Burns DC, Mazzola EP, Reynolds WF. The role of computer-assisted structure elucidation (CASE) programs in the structure elucidation of complex natural products. Nat Prod Rep 2019; 36:919-933. [DOI: 10.1039/c9np00007k] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Computer-assisted structure elucidation can help to determine the structures of complex natural products while minimizing the risk of structure errors.
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Affiliation(s)
- Darcy C. Burns
- Department of Chemistry
- University of Toronto
- Toronto
- Canada
| | - Eugene P. Mazzola
- Department of Chemistry & Biochemistry
- University of Maryland
- College Park
- USA
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13
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Application of anisotropic NMR parameters to the confirmation of molecular structure. Nat Protoc 2018; 14:217-247. [DOI: 10.1038/s41596-018-0091-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Nath N, Bordoloi P, Barman B, Baishya B, Chaudhari SR. Insight into old and new pure shift nuclear magnetic resonance methods for enantiodiscrimination. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:876-892. [PMID: 29411898 DOI: 10.1002/mrc.4719] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 01/20/2018] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
Enantiodiscrimination and their quantification using nuclear magnetic resonance (NMR) spectroscopy has always been a subject of great interest. Proton is the nucleus of choice for enantiodiscrimination due to its high sensitivity and ubiquitous presence in nature. Despite its advantages, enantiodiscrimination suffers from extensive signal splitting by the proton-proton scalar couplings, which give complex multiplets that spread over a frequency range of some tens of hertz. These multiplets often overlap, further complicating interpretation of the spectra and quantifications. In the present review, we discuss some of the recent developments in the pure shift 1 H NMR based methods for enantiomer resolution and enantiodiscrimination. We also compare various pure shift methods used for enantiodiscrimination and measurement of enantiomeric excess, considering the fact that conventional 1 H NMR fails to provide any detailed insight.
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Affiliation(s)
- Nilamoni Nath
- Department of Chemistry, Gauhati University, Guwahati, Assam, 781014, India
| | - Priyakshi Bordoloi
- Department of Chemistry, Gauhati University, Guwahati, Assam, 781014, India
| | - Bhaskar Barman
- Department of Chemistry, Gauhati University, Guwahati, Assam, 781014, India
| | - Bikash Baishya
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, Uttar Pradesh, 226014, India
| | - Sachin R Chaudhari
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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15
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Hallwass F, Teles RR, Hellemann E, Griesinger C, Gil RR, Navarro-Vázquez A. Measurement of residual chemical shift anisotropies in compressed polymethylmethacrylate gels. Automatic compensation of gel isotropic shift contribution. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:321-328. [PMID: 29327368 DOI: 10.1002/mrc.4711] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/29/2017] [Accepted: 12/31/2017] [Indexed: 05/28/2023]
Abstract
Mechanical compression of polymer gels provides a simple way for the measurement of residual chemical shift anisotropies, which then can be employed, on its own, or in combination with residual dipolar couplings, for structural elucidation purposes. Residual chemical shift anisotropies measured using compression devices needed a posteriori correction to account for the increase of the polymer to solvent ratio inside the swollen gel. This correction has been cast before in terms of a single-free parameter which, as shown here, can be simultaneously optimized along with the components of the alignment tensor while still retaining discriminating power of the different relative configurations as illustrated in the stereochemical analysis of α-santonin and 10-epi-8-deoxycumambrin B.
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Affiliation(s)
- Fernando Hallwass
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Avenida Professor Moraes Rego, 1235, Cidade Universitária, 50670-901, Recife, Pernambuco, Brazil
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Fassberg 11, Göttingen, 37077, Germany
| | - Rubens R Teles
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Avenida Professor Moraes Rego, 1235, Cidade Universitária, 50670-901, Recife, Pernambuco, Brazil
- Instituto Federal da Paraíba, Campus Princesa Isabel, Rodovia PB 426, s/no, Princesa Isabel, CEP 58755-000, Paraíba, Brazil
| | - Erich Hellemann
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Fassberg 11, Göttingen, 37077, Germany
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Avenida Professor Moraes Rego, 1235, Cidade Universitária, 50670-901, Recife, Pernambuco, Brazil
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16
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Liu Y, Cohen RD, Gustafson KR, Martin GE, Williamson RT. Enhanced measurement of residual chemical shift anisotropy for small molecule structure elucidation. Chem Commun (Camb) 2018; 54:4254-4257. [PMID: 29505044 PMCID: PMC6322199 DOI: 10.1039/c8cc00552d] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A method is introduced to measure residual chemical shift anisotropies conveniently and accurately in the mesophase of poly-γ-(benzyl-l-glutamate). The alignment amplitude is substantially enhanced over common methods which greatly benefits measurements particularly on sp3 carbons. The approach offers significant improvements in data accuracy and utility for small molecule structure determination.
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Affiliation(s)
- Yizhou Liu
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co. Inc., 126 East Lincoln Avenue, Rahway, NJ 07065, USA.
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17
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Hellemann E, Gil RR. New Stretching Method for Aligning Gels: Its Application to the Measurement Residual Chemical Shift Anisotropies (RCSAs) without the Need for Isotropic Shift Correction. Chemistry 2018; 24:3689-3693. [DOI: 10.1002/chem.201704541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Erich Hellemann
- Department of Chemistry Carnegie Mellon University 4400 Fifth Ave. Pittsburgh PA 15213 USA
| | - Roberto R. Gil
- Department of Chemistry Carnegie Mellon University 4400 Fifth Ave. Pittsburgh PA 15213 USA
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18
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Liu Y, Saurí J, Mevers E, Peczuh MW, Hiemstra H, Clardy J, Martin GE, Williamson RT. Unequivocal determination of complex molecular structures using anisotropic NMR measurements. Science 2017; 356:356/6333/eaam5349. [PMID: 28385960 DOI: 10.1126/science.aam5349] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/16/2017] [Indexed: 11/02/2022]
Abstract
Assignment of complex molecular structures from nuclear magnetic resonance (NMR) data can be prone to interpretational mistakes. Residual dipolar couplings and residual chemical shift anisotropy provide a spatial view of the relative orientations between bonds and chemical shielding tensors, respectively, regardless of separation. Consequently, these data constitute a reliable reporter of global structural validity. Anisotropic NMR parameters can be used to evaluate investigators' structure proposals or structures generated by computer-assisted structure elucidation. Application of the method to several complex structure assignment problems shows promising results that signal a potential paradigm shift from conventional NMR data interpretation, which may be of particular utility for compounds not amenable to x-ray crystallography.
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Affiliation(s)
- Yizhou Liu
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Josep Saurí
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Mark W Peczuh
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Unit 3060, Storrs, CT 06269, USA
| | - Henk Hiemstra
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Gary E Martin
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, NJ 07065, USA.
| | - R Thomas Williamson
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, NJ 07065, USA.
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19
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Lorieau JL. Mollib: a molecular and NMR data analysis software. JOURNAL OF BIOMOLECULAR NMR 2017; 69:69-80. [PMID: 29032520 DOI: 10.1007/s10858-017-0142-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/07/2017] [Indexed: 06/07/2023]
Abstract
Mollib is a software framework for the analysis of molecular structures, properties and data with an emphasis on data collected by NMR. It uses an open source model and a plugin framework to promote community-driven development of new and enhanced features. Mollib includes tools for the automatic retrieval and caching of protein databank (PDB) structures, the hydrogenation of biomolecules, the analysis of backbone dihedral angles and hydrogen bonds, and the fitting of residual dipolar coupling (RDC) and residual anisotropic chemical shift (RACS) data. In this article, we release version 1.0 of mollib and demonstrate its application to common molecular and NMR data analyses.
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Affiliation(s)
- Justin L Lorieau
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL, 60607, USA.
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20
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Zhang W, Turney T, Meredith R, Pan Q, Sernau L, Wang X, Hu X, Woods RJ, Carmichael I, Serianni AS. Conformational Populations of β-(1→4) O-Glycosidic Linkages Using Redundant NMR J-Couplings and Circular Statistics. J Phys Chem B 2017; 121:3042-3058. [PMID: 28296420 DOI: 10.1021/acs.jpcb.7b02252] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Twelve disaccharides containing β-(1→4) linkages and displaying systematic structural variations in the vicinity of these linkages were selectively labeled with 13C to facilitate measurements of multiple NMR spin-spin (scalar; J) coupling constants (JCH and JCC values) across their O-glycosidic linkages. Ensembles of spin-couplings (2JCOC, 3JCOCH, 3JCOCC) sensitive to the two linkage torsion angles, phi (ϕ) and psi (ψ), were analyzed by using parametrized equations obtained from density functional theory (DFT) calculations, Fredholm theory, and circular statistics to calculate experiment-based rotamer populations for ϕ and ψ in each disaccharide. With the statistical program MA'AT, torsion angles ϕ and ψ were modeled as a single von Mises distribution, which yielded two parameters, the mean position and the circular standard deviation (CSD) for each angle. The NMR-derived rotamer populations were compared to those obtained from 1 μs aqueous molecular dynamics (MD) simulations and crystallographic database statistical analyses. Conformer populations obtained exclusively from the MA'AT treatment of redundant J-couplings were in very good agreement with those obtained from the MD simulations, providing evidence that conformational populations can be determined by NMR for mobile molecular elements such as O-glycosidic linkages with minimal input from theory. The approach also provides an experimental means to validate the conformational preferences predicted from MD simulations. The conformational behaviors of ϕ in the 12 disaccharides were very similar, but those of ψ varied significantly, allowing a classification of the 12 disaccharides based on preferred linkage conformation in solution.
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Affiliation(s)
- Wenhui Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556-5670, United States
| | - Toby Turney
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556-5670, United States
| | - Reagan Meredith
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556-5670, United States
| | - Qingfeng Pan
- Omicron Biochemicals Inc. , South Bend, Indiana 46617-2701, United States
| | - Luke Sernau
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556-5670, United States
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Xiaosong Hu
- Department of Chemistry, Wuhan University of Technology , Wuhan 430070, China
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Ian Carmichael
- Radiation Laboratory, University of Notre Dame , Notre Dame, Indiana 46556-5670, United States
| | - Anthony S Serianni
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556-5670, United States
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21
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Nath N, Schmidt M, Gil RR, Williamson RT, Martin GE, Navarro-Vázquez A, Griesinger C, Liu Y. Determination of Relative Configuration from Residual Chemical Shift Anisotropy. J Am Chem Soc 2016; 138:9548-56. [DOI: 10.1021/jacs.6b04082] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nilamoni Nath
- Department
of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Manuel Schmidt
- Department
of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Roberto R. Gil
- Department
of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - R. Thomas Williamson
- Process Research and Development, NMR Structure Elucidation Group, Merck & Co., Inc., 126 E Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Gary E. Martin
- Process Research and Development, NMR Structure Elucidation Group, Merck & Co., Inc., 126 E Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Armando Navarro-Vázquez
- Departamento
de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária, Recife, PE 50740-560, Brazil
- Institute
of Organic Chemistry and Institute for Biological Interfaces Karlsruhe, Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Christian Griesinger
- Department
of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Yizhou Liu
- Process Research and Development, NMR Structure Elucidation Group, Merck & Co., Inc., 126 E Lincoln Avenue, Rahway, New Jersey 07065, United States
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22
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Park Y, Jowitt TA, Day AJ, Prestegard JH. Nuclear Magnetic Resonance Insight into the Multiple Glycosaminoglycan Binding Modes of the Link Module from Human TSG-6. Biochemistry 2016; 55:262-76. [PMID: 26685054 PMCID: PMC5073374 DOI: 10.1021/acs.biochem.5b01148] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tumor necrosis factor-stimulated gene-6 (TSG-6) is a hyaluronan (HA)-binding protein that is essential for stabilizing and remodeling the extracellular matrix (ECM) during ovulation and inflammatory disease processes such as arthritis. The Link module, one of the domains of TSG-6, is responsible for binding hyaluronan and other glycosaminoglycans found in the ECM. In this study, we used a well-defined chondroitin sulfate (CS) hexasaccharide (ΔC444S) to determine the structure of the Link module, in solution, in its chondroitin sulfate-bound state. A variety of nuclear magnetic resonance techniques were employed, including chemical shift perturbation, residual dipolar couplings (RDCs), nuclear Overhauser effects, spin relaxation measurements, and paramagnetic relaxation enhancements from a spin-labeled analogue of ΔC444S. The binding site for ΔC444S on the Link module overlapped with that of HA. Surprisingly, ΔC444S binding induced dimerization of the Link module (as confirmed by analytical ultracentrifugation), and a second weak binding site that partially overlapped with a previously identified heparin site was detected. A dimer model was generated using chemical shift perturbations and RDCs as restraints in the docking program HADDOCK. We postulate that the molecular cross-linking enhanced by the multiple binding modes of the Link module might be critical for remodeling the ECM during inflammation/ovulation and might contribute to other functions of TSG-6.
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Affiliation(s)
- Younghee Park
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, USA
| | - Thomas A. Jowitt
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Anthony J. Day
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - James H. Prestegard
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, USA
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23
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Vammi V, Song G. Ensembles of a small number of conformations with relative populations. JOURNAL OF BIOMOLECULAR NMR 2015; 63:341-351. [PMID: 26474790 DOI: 10.1007/s10858-015-9993-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 10/14/2015] [Indexed: 06/05/2023]
Abstract
In our previous work, we proposed a new way to represent protein native states, using ensembles of a small number of conformations with relative Populations, or ESP in short. Using Ubiquitin as an example, we showed that using a small number of conformations could greatly reduce the potential of overfitting and assigning relative populations to protein ensembles could significantly improve their quality. To demonstrate that ESP indeed is an excellent alternative to represent protein native states, in this work we compare the quality of two ESP ensembles of Ubiquitin with several well-known regular ensembles or average structure representations. Extensive amount of significant experimental data are employed to achieve a thorough assessment. Our results demonstrate that ESP ensembles, though much smaller in size comparing to regular ensembles, perform equally or even better sometimes in all four different types of experimental data used in the assessment, namely, the residual dipolar couplings, residual chemical shift anisotropy, hydrogen exchange rates, and solution scattering profiles. This work further underlines the significance of having relative populations in describing the native states.
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Affiliation(s)
- Vijay Vammi
- Bioinformatics and Computational Biology Program, Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA, 50011, USA.
| | - Guang Song
- Bioinformatics and Computational Biology Program, Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA, 50011, USA
- Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA, USA
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24
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Martin RW, Kelly JE, Collier KA. Spatial reorientation experiments for NMR of solids and partially oriented liquids. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 90-91:92-122. [PMID: 26592947 PMCID: PMC6936739 DOI: 10.1016/j.pnmrs.2015.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 10/13/2015] [Accepted: 10/15/2015] [Indexed: 06/05/2023]
Abstract
Motional reorientation experiments are extensions of Magic Angle Spinning (MAS) where the rotor axis is changed in order to average out, reintroduce, or scale anisotropic interactions (e.g. dipolar couplings, quadrupolar interactions or chemical shift anisotropies). This review focuses on Variable Angle Spinning (VAS), Switched Angle Spinning (SAS), and Dynamic Angle Spinning (DAS), all of which involve spinning at two or more different angles sequentially, either in successive experiments or during a multidimensional experiment. In all of these experiments, anisotropic terms in the Hamiltonian are scaled by changing the orientation of the spinning sample relative to the static magnetic field. These experiments vary in experimental complexity and instrumentation requirements. In VAS, many one-dimensional spectra are collected as a function of spinning angle. In SAS, dipolar couplings and/or chemical shift anisotropies are reintroduced by switching the sample between two different angles, often 0° or 90° and the magic angle, yielding a two-dimensional isotropic-anisotropic correlation spectrum. Dynamic Angle Spinning (DAS) is a related experiment that is used to simultaneously average out the first- and second-order quadrupolar interactions, which cannot be accomplished by spinning at any unique rotor angle in physical space. Although motional reorientation experiments generally require specialized instrumentation and data analysis schemes, some are accessible with only minor modification of standard MAS probes. In this review, the mechanics of each type of experiment are described, with representative examples. Current and historical probe and coil designs are discussed from the standpoint of how each one accomplishes the particular objectives of the experiment(s) it was designed to perform. Finally, applications to inorganic materials and liquid crystals, which present very different experimental challenges, are discussed. The review concludes with perspectives on how motional reorientation experiments can be applied to current problems in chemistry, molecular biology, and materials science, given the many advances in high-field NMR magnets, fast spinning, and sample preparation realized in recent years.
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Affiliation(s)
- Rachel W Martin
- Department of Chemistry, University of California, Irvine 92697-2025, United States; Department of Molecular Biology and Biochemistry, University of California, Irvine 92697-3900, United States.
| | - John E Kelly
- Department of Chemistry, University of California, Irvine 92697-2025, United States
| | - Kelsey A Collier
- Department of Physics and Astronomy, University of California, Irvine 92697-4575, United States
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25
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Torchia DA. NMR studies of dynamic biomolecular conformational ensembles. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 84-85:14-32. [PMID: 25669739 PMCID: PMC4325279 DOI: 10.1016/j.pnmrs.2014.11.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 11/19/2014] [Accepted: 11/19/2014] [Indexed: 05/06/2023]
Abstract
Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: "Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?" This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA.
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Affiliation(s)
- Dennis A Torchia
- National Institutes of Health (NIH), 5 Memorial Drive, Bethesda, MD 20892, USA.
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26
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Lemak A, Wu B, Yee A, Houliston S, Lee HW, Gutmanas A, Fang X, Garcia M, Semesi A, Wang YX, Prestegard JH, Arrowsmith CH. Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data. Structure 2014; 22:1862-1874. [PMID: 25456817 PMCID: PMC5046226 DOI: 10.1016/j.str.2014.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 09/10/2014] [Accepted: 09/12/2014] [Indexed: 01/09/2023]
Abstract
Multidomain proteins in which individual domains are connected by linkers often possess inherent interdomain flexibility that significantly complicates their structural characterization in solution using either nuclear magnetic resonance (NMR) spectroscopy or small-angle X-ray scattering (SAXS) alone. Here, we report a protocol for joint refinement of flexible multidomain protein structures against NMR distance and angular restraints, residual dipolar couplings, and SAXS data. The protocol is based on the ensemble optimization method principle (Bernadó et al., 2007) and is compared with different refinement strategies for the structural characterization of the flexible two-domain protein sf3636 from Shigella flexneri 2a. The results of our refinement suggest the existence of a dominant population of configurational states in solution possessing an overall elongated shape and restricted relative twisting of the two domains.
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Affiliation(s)
- Alexander Lemak
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Bin Wu
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Adelinda Yee
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Aleksandras Gutmanas
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Xianyang Fang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA
| | - Maite Garcia
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Anthony Semesi
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
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27
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Simin M, Irausquin S, Cole CA, Valafar H. Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2014; 60:241-264. [PMID: 25403759 DOI: 10.1007/s10858-014-9871-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/30/2014] [Indexed: 06/04/2023]
Abstract
Within the past two decades, there has been an increase in the acquisition of residual dipolar couplings (RDC) for investigations of biomolecular structures. Their use however is still not as widely adopted as the traditional methods of structure determination by NMR, despite their potential for extending the limits in studies that examine both the structure and dynamics of biomolecules. This is in part due to the difficulties associated with the analysis of this information-rich data type. The software analysis tool REDCRAFT was previously introduced to address some of these challenges. Here we describe and evaluate a number of additional features that have been incorporated in order to extend its computational and analytical capabilities. REDCRAFT's more traditional enhancements integrate a modified steric collision term, as well as structural refinement in the rotamer space. Other, non-traditional improvements include: the filtering of viable structures based on relative order tensor estimates, decimation of the conformational space based on structural similarity, and forward/reverse folding of proteins. Utilizing REDCRAFT's newest features we demonstrate de-novo folding of proteins 1D3Z and 1P7E to within less than 1.6 Å of the corresponding X-ray structures, using as many as four RDCs per residue and as little as two RDCs per residue, in two alignment media. We also show the successful folding of a structure to less than 1.6 Å of the X-ray structure using {C(i-1)-N(i), N(i)-H(i), and C(i-1)-H(i)} RDCs in one alignment medium, and only {N(i)-H(i)} in the second alignment medium (a set of data which can be collected on deuterated samples). The program is available for download from our website at http://ifestos.cse.sc.edu .
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Affiliation(s)
- Mikhail Simin
- Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, 29208, USA
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28
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Schmidt C, Irausquin SJ, Valafar H. Advances in the REDCAT software package. BMC Bioinformatics 2013; 14:302. [PMID: 24098943 PMCID: PMC3840585 DOI: 10.1186/1471-2105-14-302] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 09/13/2013] [Indexed: 12/24/2022] Open
Abstract
Background Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. The REDCAT software package was previously introduced for the analysis of molecular structures using RDC data. Here we report additional features that have been included in this software package in order to expand the scope of its analyses. We first discuss the features that enhance REDCATs user-friendly nature, such as the integration of a number of analyses into one single operation and enabling convenient examination of a structural ensemble in order to identify the most suitable structure. We then describe the new features which expand the scope of RDC analyses, performing exercises that utilize both synthetic and experimental data to illustrate and evaluate different features with regard to structure refinement and structure validation. Results We establish the seamless interaction that takes place between REDCAT, VMD, and Xplor-NIH in demonstrations that utilize our newly developed REDCAT-VMD and XplorGUI interfaces. These modules enable visualization of RDC analysis results on the molecular structure displayed in VMD and refinement of structures with Xplor-NIH, respectively. We also highlight REDCAT’s Error-Analysis feature in reporting the localized fitness of a structure to RDC data, which provides a more effective means of recognizing local structural anomalies. This allows for structurally sound regions of a molecule to be identified, and for any refinement efforts to be focused solely on locally distorted regions. Conclusions The newly engineered REDCAT software package, which is available for download via the WWW from http://ifestos.cse.sc.edu, has been developed in the Object Oriented C++ environment. Our most recent enhancements to REDCAT serve to provide a more complete RDC analysis suite, while also accommodating a more user-friendly experience, and will be of great interest to the community of researchers and developers since it hides the complications of software development.
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Affiliation(s)
- Chris Schmidt
- Department of Computer Science & Engineering, University of South Carolina, Columbia, SC 29208, USA.
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29
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Chemokine oligomerization in cell signaling and migration. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:531-78. [PMID: 23663982 DOI: 10.1016/b978-0-12-386931-9.00020-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chemokines are small proteins best known for their role in controlling the migration of diverse cells, particularly leukocytes. Upon binding to their G-protein-coupled receptors on the leukocytes, chemokines stimulate the signaling events that cause cytoskeletal rearrangements involved in cell movement, and migration of the cells along chemokine gradients. Depending on the cell type, chemokines also induce many other types of cellular responses including those related to defense mechanisms, cell proliferation, survival, and development. Historically, most research efforts have focused on the interaction of chemokines with their receptors, where monomeric forms of the ligands are the functionally relevant state. More recently, however, the importance of chemokine interactions with cell surface glycosaminoglycans has come to light, and in most cases appears to involve oligomeric chemokine structures. This review summarizes existing knowledge relating to the structure and function of chemokine oligomers, and emerging methodology for determining structures of complex chemokine assemblies in the future.
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30
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Barb AW, Freedberg DI, Battistel MD, Prestegard JH. NMR detection and characterization of sialylated glycoproteins and cell surface polysaccharides. JOURNAL OF BIOMOLECULAR NMR 2011; 51:163-71. [PMID: 21947924 PMCID: PMC3199143 DOI: 10.1007/s10858-011-9550-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 06/25/2011] [Indexed: 05/03/2023]
Abstract
Few solution NMR pulse sequences exist that are explicitly designed to characterize carbohydrates (glycans). This is despite the essential role carbohydrate motifs play in cell-cell communication, microbial pathogenesis, autoimmune disease progression and cancer metastasis, and despite that fact that glycans, often shed to extra-cellular fluids, can be diagnostic of disease. Here we present a suite of two dimensional coherence experiments to measure three different correlations (H3-C2, H3-C1, and C1-C2) on sialic acids, a group of nine-carbon carbohydrates found on eukaryotic cell surfaces that often play a key role in disease processes. The chemical shifts of the H3, C2, and C1 nuclei of sialic acids are sensitive to carbohydrate linkage, linkage conformation, and ionization state of the C1 carboxylate. The experiments reported include rigorous filter elements to enable detection and characterization of isotopically labeled sialic acids with high sensitivity in living cells and crude isolates with minimal interference from unwanted signals arising from the ~1% (13)C-natural abundance of cellular metabolites. Application is illustrated with detection of sialic acids on living cells, in unpurified mixtures, and at the terminus of the N-glycan on the 55 kDa immunoglobulin G Fc.
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Affiliation(s)
- Adam W. Barb
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602
| | - Darón I. Freedberg
- Laboratory of Bacterial Polysaccharides, Building 29, Room 115 Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, HFM-419, Rockville, MD 20852
| | - Marcos D. Battistel
- Laboratory of Bacterial Polysaccharides, Building 29, Room 115 Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, HFM-419, Rockville, MD 20852
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31
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Wang X, Watson C, Sharp JS, Handel TM, Prestegard JH. Oligomeric structure of the chemokine CCL5/RANTES from NMR, MS, and SAXS data. Structure 2011; 19:1138-48. [PMID: 21827949 PMCID: PMC3159919 DOI: 10.1016/j.str.2011.06.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 06/06/2011] [Accepted: 06/07/2011] [Indexed: 12/20/2022]
Abstract
CCL5 (RANTES) is a proinflammatory chemokine known to activate leukocytes through its receptor, CCR5. Although the monomeric form of CCL5 is sufficient to cause cell migration in vitro, CCL5's propensity for aggregation is essential for migration in vivo, T cell activation and apoptosis, and HIV entry into cells. However, there is currently no structural information on CCL5 oligomers larger than the canonical CC chemokine dimer. In this study the solution structure of a CCL5 oligomer was investigated using an integrated approach, including NMR residual dipolar couplings to determine allowed relative orientations of the component monomers, SAXS to restrict overall shape, and hydroxyl radical footprinting and NMR cross-saturation experiments to identify interface residues. The resulting model of the CCL5 oligomer provides a basis for explaining the disaggregating effect of E66 and E26 mutations and suggests mechanisms by which glycosaminoglycan binding may promote oligomer formation and facilitate cell migration in vivo.
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Affiliation(s)
- Xu Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Caroline Watson
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Joshua S. Sharp
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Tracy M. Handel
- Skaggs School of Pharm & Pharmaceut Sci, Univ. Calif., San Diego, La Jolla, CA 92093 USA
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
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Ramelot TA, Smola MJ, Lee HW, Ciccosanti C, Hamilton K, Acton TB, Xiao R, Everett JK, Prestegard JH, Montelione GT, Kennedy MA. Solution structure of 4'-phosphopantetheine - GmACP3 from Geobacter metallireducens: a specialized acyl carrier protein with atypical structural features and a putative role in lipopolysaccharide biosynthesis. Biochemistry 2011; 50:1442-53. [PMID: 21235239 PMCID: PMC3063093 DOI: 10.1021/bi101932s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
GmACP3 from Geobacter metallireducens is a specialized acyl carrier protein (ACP) whose gene, gmet_2339, is located near genes encoding many proteins involved in lipopolysaccharide (LPS) biosynthesis, indicating a likely function for GmACP3 in LPS production. By overexpression in Escherichia coli, about 50% holo-GmACP3 and 50% apo-GmACP3 were obtained. Apo-GmACP3 exhibited slow precipitation and non-monomeric behavior by (15)N NMR relaxation measurements. Addition of 4'-phosphopantetheine (4'-PP) via enzymatic conversion by E. coli holo-ACP synthase resulted in stable >95% holo-GmACP3 that was characterized as monomeric by (15)N relaxation measurements and had no indication of conformational exchange. We have determined a high-resolution solution structure of holo-GmACP3 by standard NMR methods, including refinement with two sets of NH residual dipolar couplings, allowing for a detailed structural analysis of the interactions between 4'-PP and GmACP3. Whereas the overall four helix bundle topology is similar to previously solved ACP structures, this structure has unique characteristics, including an ordered 4'-PP conformation that places the thiol at the entrance to a central hydrophobic cavity near a conserved hydrogen-bonded Trp-His pair. These residues are part of a conserved WDSLxH/N motif found in GmACP3 and its orthologs. The helix locations and the large hydrophobic cavity are more similar to medium- and long-chain acyl-ACPs than to other apo- and holo-ACP structures. Taken together, structural characterization along with bioinformatic analysis of nearby genes suggests that GmACP3 is involved in lipid A acylation, possibly by atypical long-chain hydroxy fatty acids, and potentially is involved in synthesis of secondary metabolites.
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Affiliation(s)
- Theresa A. Ramelot
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States and the Northeast Structural Genomics Consortium
| | - Matthew J. Smola
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States and the Northeast Structural Genomics Consortium
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States and the Northeast Structural Genomics Consortium
| | - Colleen Ciccosanti
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - Keith Hamilton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - Thomas B. Acton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - John K. Everett
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States and the Northeast Structural Genomics Consortium
| | - Gaetano T. Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey, 08854, United States
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States and the Northeast Structural Genomics Consortium
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Wang X, Lee HW, Liu Y, Prestegard JH. Structural NMR of protein oligomers using hybrid methods. J Struct Biol 2011; 173:515-29. [PMID: 21074622 PMCID: PMC3040251 DOI: 10.1016/j.jsb.2010.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 10/03/2010] [Accepted: 11/04/2010] [Indexed: 11/19/2022]
Abstract
Solving structures of native oligomeric protein complexes using traditional high-resolution NMR techniques remains challenging. However, increased utilization of computational platforms, and integration of information from less traditional NMR techniques with data from other complementary biophysical methods, promises to extend the boundary of NMR-applicable targets. This article reviews several of the techniques capable of providing less traditional and complementary structural information. In particular, the use of orientational constraints coming from residual dipolar couplings and residual chemical shift anisotropy offsets are shown to simplify the construction of models for oligomeric complexes, especially in cases of weak homo-dimers. Combining this orientational information with interaction site information supplied by computation, chemical shift perturbation, paramagnetic surface perturbation, cross-saturation and mass spectrometry allows high resolution models of the complexes to be constructed with relative ease. Non-NMR techniques, such as mass spectrometry, EPR and small angle X-ray scattering, are also expected to play increasingly important roles by offering alternative methods of probing the overall shape of the complex. Computational platforms capable of integrating information from multiple sources in the modeling process are also discussed in the article. And finally a new, detailed example on the determination of a chemokine tetramer structure will be used to illustrate how a non-traditional approach to oligomeric structure determination works in practice.
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Affiliation(s)
- Xu Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602. USA
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602. USA
| | - Yizhou Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602. USA
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602. USA
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Qureshi T, Goto NK. Contemporary methods in structure determination of membrane proteins by solution NMR. Top Curr Chem (Cham) 2011; 326:123-85. [PMID: 22160391 DOI: 10.1007/128_2011_306] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Integral membrane proteins are vital to life, being responsible for information and material exchange between a cell and its environment. Although high-resolution structural information is needed to understand how these functions are achieved, membrane proteins remain an under-represented subset of the protein structure databank. Solution NMR is increasingly demonstrating its ability to help address this knowledge shortfall, with the development of a diverse array of techniques to counter the challenges presented by membrane proteins. Here we document the advances that are helping to define solution NMR as an effective tool for membrane protein structure determination. Developments introduced over the last decade in the production of isotope-labeled samples, reconstitution of these samples into the growing selection of NMR-compatible membrane-mimetic systems, and the approaches used for the acquisition and application of structural restraints from these complexes are reviewed.
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Affiliation(s)
- Tabussom Qureshi
- Department of Chemistry, University of Ottawa, Ottawa, ON, Canada
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Chen K, Tjandra N. The use of residual dipolar coupling in studying proteins by NMR. Top Curr Chem (Cham) 2011; 326:47-67. [PMID: 21952837 DOI: 10.1007/128_2011_215] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The development of residual dipolar coupling (RDC) in protein NMR spectroscopy, over a decade ago, has become a useful and almost routine tool for accurate protein solution structure determination. RDCs provide orientation information of magnetic dipole-dipole interaction vectors within a common reference frame. Its measurement requires a nonisotropic orientation, through a direct or indirect magnetic field alignment, of the protein in solution. There has been recent progress in the developments of alignment methods to allow the measurement of RDC and of methods to analyze the resulting data. In this chapter we briefly go through the mathematical expressions for the RDC and common descriptions of the alignment tensor, which may be represented using either Saupe order or the principal order matrix. Then we review the latest developments in alignment media. In particular we looked at the lipid-compatible media that allow the measurement of RDCs for membrane proteins. Other methods including conservative surface residue mutation have been invented to obtain up to five orthogonal alignment tensors that provide a potential for de novo structure and dynamics study using RDCs exclusively. We then discuss approximations assumed in RDC interpretations and different views on dynamics uncovered from the RDC method. In addition to routine usage of RDCs in refining a single structure, novel applications such as ensemble refinement against RDCs have been implemented to represent protein structure and dynamics in solution. The RDC application also extends to the study of protein-substrate interaction as well as to solving quaternary structure of oligomer in equilibrium with a monomer, opening an avenue for RDCs in high-order protein structure determination.
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Affiliation(s)
- Kang Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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