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Vögeli B, Vugmeyster L. Distance-independent Cross-correlated Relaxation and Isotropic Chemical Shift Modulation in Protein Dynamics Studies. Chemphyschem 2019; 20:178-196. [PMID: 30110510 PMCID: PMC9206835 DOI: 10.1002/cphc.201800602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 01/09/2023]
Abstract
Cross-correlated relaxation (CCR) in multiple-quantum coherences differs from other relaxation phenomena in its theoretical ability to be mediated across an infinite distance. The two interfering relaxation mechanisms may be dipolar interactions, chemical shift anisotropies, chemical shift modulations or quadrupolar interactions. These properties make multiple-quantum CCR an attractive probe for structure and dynamics of biomacromolecules not accessible from other measurements. Here, we review the use of multiple-quantum CCR measurements in dynamics studies of proteins. We compile a list of all experiments proposed for CCR rate measurements, provide an overview of the theory with a focus on protein dynamics, and present applications to various protein systems.
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Affiliation(s)
- Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, 12801 East 17 Avenue, Aurora, CO 80045, United States
| | - Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, 1201 Laurimer Street Denver, CO 80204, United States
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Dunker AK, Oldfield CJ. Back to the Future: Nuclear Magnetic Resonance and Bioinformatics Studies on Intrinsically Disordered Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:1-34. [PMID: 26387098 DOI: 10.1007/978-3-319-20164-1_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
From the 1970s to the present, regions of missing electron density in protein structures determined by X-ray diffraction and the characterization of the functions of these regions have suggested that not all protein regions depend on prior 3D structure to carry out function. Motivated by these observations, in early 1996 we began to use bioinformatics approaches to study these intrinsically disordered proteins (IDPs) and IDP regions. At just about the same time, several laboratory groups began to study a collection of IDPs and IDP regions using nuclear magnetic resonance. The temporal overlap of the bioinformatics and NMR studies played a significant role in the development of our understanding of IDPs. Here the goal is to recount some of this history and to project from this experience possible directions for future work.
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Affiliation(s)
- A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202, Indianapolis, IN, USA.
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202, Indianapolis, IN, USA.
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Deschamps M, Bodenhausen G. Anisotropy of rotational diffusion, dipole-dipole cross-correlated NMR relaxation and angles between bond vectors in proteins. Chemphyschem 2013; 2:539-43. [PMID: 23686993 DOI: 10.1002/1439-7641(20010917)2:8/9<539::aid-cphc539>3.0.co;2-m] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2001] [Indexed: 11/08/2022]
Abstract
Cross correlations between the fluctuations of dipolar (13)C(α)-(1)H(α) interactions yield information about the relative orientation of successive (13)C(α)-(1)H(α) bond vectors in proteins, in turn providing a direct handle on their structure and dynamics in solution. However, overall anisotropic reorientation must be taken into account in the interpretation of cross-correlation rates. The protein shown, human ubiquitin, has amino acid residues in white where the cross-correlation rates deviate from those predicted for a rigid structure.
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Affiliation(s)
- M Deschamps
- Département de Chimie, associé au CNRS, Ecole Normale Supérieure, Paris, France
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Ota M, Koike R, Amemiya T, Tenno T, Romero PR, Hiroaki H, Dunker AK, Fukuchi S. An assignment of intrinsically disordered regions of proteins based on NMR structures. J Struct Biol 2012; 181:29-36. [PMID: 23142703 DOI: 10.1016/j.jsb.2012.10.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 10/26/2012] [Accepted: 10/30/2012] [Indexed: 11/24/2022]
Abstract
Intrinsically disordered proteins (IDPs) do not adopt stable three-dimensional structures in physiological conditions, yet these proteins play crucial roles in biological phenomena. In most cases, intrinsic disorder manifests itself in segments or domains of an IDP, called intrinsically disordered regions (IDRs), but fully disordered IDPs also exist. Although IDRs can be detected as missing residues in protein structures determined by X-ray crystallography, no protocol has been developed to identify IDRs from structures obtained by Nuclear Magnetic Resonance (NMR). Here, we propose a computational method to assign IDRs based on NMR structures. We compared missing residues of X-ray structures with residue-wise deviations of NMR structures for identical proteins, and derived a threshold deviation that gives the best correlation of ordered and disordered regions of both structures. The obtained threshold of 3.2Å was applied to proteins whose structures were only determined by NMR, and the resulting IDRs were analyzed and compared to those of X-ray structures with no NMR counterpart in terms of sequence length, IDR fraction, protein function, cellular location, and amino acid composition, all of which suggest distinct characteristics. The structural knowledge of IDPs is still inadequate compared with that of structured proteins. Our method can collect and utilize IDRs from structures determined by NMR, potentially enhancing the understanding of IDPs.
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Affiliation(s)
- Motonori Ota
- Graduate School of Information Sciences, Nagoya University, Nagoya 464-8601, Japan.
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Vögeli B. How uniform is the peptide plane geometry? A high-accuracy NMR study of dipolar Cα-C'/H N-N cross-correlated relaxation. JOURNAL OF BIOMOLECULAR NMR 2011; 50:315-329. [PMID: 21638015 DOI: 10.1007/s10858-011-9519-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 05/17/2011] [Indexed: 05/30/2023]
Abstract
Highly precise and accurate measurements of very small NMR cross-correlated relaxation rates, namely those between protein H (i) (N) -N(i) and C (i-1) (α) -C(i-1)' dipoles, are demonstrated with an error of 0.03 s(-1) for GB3. Because the projection angles between the two dipole vectors are very close to the magic angle the rates range only from -0.2 to +0.2 s(-1). Small changes of the average vector orientations have a dramatic impact on the relative values. The rates suggest deviation from idealized peptide plane geometry caused by twists around the C'-N bonds and/or pyramidalization of the nitrogen atoms. A clear alternating pattern along the sequence is observed in β strands 1, 3 and 4 of GB3, where the side chains of almost all residues with large positive rates are solvent exposed. In the α helix all rates are relatively large and positive. Some of the currently most accurate structures of GB3 determined by both high resolution X-ray crystallography and NMR are in satisfactory agreement with the experimental rates in the helix and β strand 3, but not in the loops and the two central strands of the sheet for which no alternating pattern is predicted.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093, Zürich, Switzerland.
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Vögeli B, Yao L. Correlated dynamics between protein HN and HC bonds observed by NMR cross relaxation. J Am Chem Soc 2009; 131:3668-78. [PMID: 19235934 DOI: 10.1021/ja808616v] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although collective dynamics of atom groups steer many biologically relevant processes in biomacromolecules, most atomic resolution motional studies focus on isolated bonds. In this study, a new method is introduced to assess correlated dynamics between bond vectors by cross relaxation nuclear magnetic resonance (NMR). Dipole-dipole cross correlated relaxation rates between intra- and inter-residual H(N)-N and H(alpha)-C(alpha) in the 56 residue protein GB3 are measured with high accuracy. It is demonstrated that the assumption of anisotropic molecular tumbling is necessary to evaluate rates accurately and predictions from the static structure using effective bond lengths of 1.041 and 1.117 A for H(N)-N and H(alpha)-C(alpha) are within 3% of both experimental intra- and inter-residual rates. Deviations are matched to models of different degrees of motional correlation. These models are based on previously determined orientations and motional amplitudes from residual dipolar couplings with high accuracy and precision. Clear evidence of correlated motion in the loops comprising residues 10-14, 20-22, and 47-50 and anticorrelated motion in the alpha helix comprising 23-38 is presented. Somewhat weaker correlation is observed in the beta strands 2-4, which have previously been shown to exhibit slow correlated motional modes.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Honggerberg, CH-8093 Zurich, Switzerland.
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Takahashi H, Shimada I. Pairwise NMR experiments for the determination of protein backbone dihedral angle Phi based on cross-correlated spin relaxation. JOURNAL OF BIOMOLECULAR NMR 2007; 37:179-85. [PMID: 17237977 DOI: 10.1007/s10858-006-9108-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 10/05/2006] [Accepted: 10/16/2006] [Indexed: 05/13/2023]
Abstract
Novel cross-correlated spin relaxation (CCR) experiments are described, which measure pairwise CCR rates for obtaining peptide dihedral angles Phi. The experiments utilize intra-HNCA type coherence transfer to refocus 2-bond JNCalpha coupling evolution and generate the N(i)-Calpha(i) or C'(i-1)-Calpha(i) multiple quantum coherences which are required for measuring the desired CCR rates. The contribution from other coherences is also discussed and an appropriate setting of the evolution delays is presented. These CCR experiments were applied to 15N- and 13C-labeled human ubiquitin. The relevant CCR rates showed a high degree of correlation with the Phi angles observed in the X-ray structure. By utilizing these CCR experiments in combination with those previously established for obtaining dihedral angle Psi, we can determine high resolution structures of peptides that bind weakly to large target molecules.
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Affiliation(s)
- Hideo Takahashi
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo, 135-0064, Japan.
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Markwick PRL, Sprangers R, Sattler M. Local structure and anisotropic backbone dynamics from cross-correlated NMR relaxation in proteins. Angew Chem Int Ed Engl 2006; 44:3232-7. [PMID: 15844105 DOI: 10.1002/anie.200462495] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Phineus R L Markwick
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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Loth K, Abergel D, Pelupessy P, Delarue M, Lopes P, Ouazzani J, Duclert-Savatier N, Nilges M, Bodenhausen G, Stoven V. Determination of dihedral Ψ angles in large proteins by combining NHN/CαHα dipole/dipole cross-correlation and chemical shifts. Proteins 2006; 64:931-9. [PMID: 16786593 DOI: 10.1002/prot.21063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We propose a strategy based on the combination of experimental NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlated relaxation rates and chemical shift analysis for the determination of Psi torsion angles in proteins. The method allows the determination of a dihedral angle that is not easily accessible by nuclear magnetic resonance (NMR). The measurement of dihedral angle restraints can be used for structure calculation, which is known to improve the quality of NMR structures. The method is of particular interest in the case of large proteins, for which spectral assignment of the nuclear Overhauser effect spectra, and therefore straightforward structural determination, is out of reach. One advantage of the method is that it is reasonably simple to implement, and could be used in association with other methods aiming at obtaining structural information on complex systems, such as residual dipolar coupling measurements. An illustrative example is analyzed in the case of the 30-kDa protein 6-phosphogluconolactonase.
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Affiliation(s)
- Karine Loth
- Département de Chimie, Ecole Normale Supérieure, Paris, France
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Markwick PRL, Sprangers R, Sattler M. Local Structure and Anisotropic Backbone Dynamics from Cross-Correlated NMR Relaxation in Proteins. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200462495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Hartl M, Matt T, Schüler W, Siemeister G, Kontaxis G, Kloiber K, Konrat R, Bister K. Cell Transformation by the v-myc Oncogene Abrogates c-Myc/Max-mediated Suppression of a C/EBPβ-dependent Lipocalin Gene. J Mol Biol 2003; 333:33-46. [PMID: 14516741 DOI: 10.1016/j.jmb.2003.08.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Using differential hybridization techniques, a cDNA clone (Q83) was isolated that corresponds to a highly abundant mRNA in quail embryo fibroblasts transformed by the v-myc oncogene. The deduced 178 amino acid protein product of Q83 contains an N-terminal signal sequence and a lipocalin sequence motif, the hallmark of a family of secretory proteins binding and transporting small hydrophobic molecules of diverse biological function, including retinoids and steroids. The quail Q83 protein displays 87% sequence identity with a developmentally regulated chicken protein, termed p20K or Ch21. Cell transformation specifically by v-myc, but not by other oncogenic agents, induces high-level expression of Q83 mRNA and of the Q83 protein. Nucleotide sequence analysis and transcriptional mapping revealed that the Q83 gene encompasses seven exons with the coding region confined to exons 1 through 6. The promoter region contains consensus binding sites for the transcriptional regulators Myc and C/EBP beta. Transcriptional activation of Q83 is principally dependent on C/EBP beta, but is blocked in normal cells by the endogenous c-Myc/Max/Mad transcription factor network. In v-myc-transformed cells, high-level expression of the v-Myc protein and formation of highly stable v-Myc/Max heterodimers leads to abrogation of Q83 gene suppression and activation by C/EBP beta. A 157 amino acid residue recombinant protein representing the secreted form of Q83 was used for structure determination by nuclear magnetic resonance spectroscopy. Q83 folds into a single globular domain of the lipocalin-type. The central part consists of an eight-stranded up-and-down beta-barrel core flanked by an N-terminal 3(10)-like helix and a C-terminal alpha-helix. The orientation of the C-terminal alpha-helix is partially determined by a disulfide bridge between Cys59 and Cys152. The three-dimensional structure determination of the Q83 protein will facilitate the identification of its authentic ligand and the assessment of its biological function, including the putative role in myc-induced cell transformation.
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Affiliation(s)
- Markus Hartl
- Institute of Biochemistry, University of Innsbruck, A-6020 Innsbruck, Austria
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Deschamps M. Cross-Correlated Relaxation with Anisotropic Reorientation and Small Amplitude Local Motions. J Phys Chem A 2002. [DOI: 10.1021/jp013407e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michaël Deschamps
- Département de Chimie, Associé au CNRS, École Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France
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Schwalbe H, Carlomagno T, Hennig M, Junker J, Reif B, Richter C, Griesinger C. Cross-correlated relaxation for measurement of angles between tensorial interactions. Methods Enzymol 2002; 338:35-81. [PMID: 11460558 DOI: 10.1016/s0076-6879(02)38215-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- H Schwalbe
- Center for Magnetic Resonance, Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Lipid-peptide interaction investigated by NMR. CURRENT TOPICS IN MEMBRANES 2002. [DOI: 10.1016/s1063-5823(02)52008-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Linge JP, O'Donoghue SI, Nilges M. Automated assignment of ambiguous nuclear overhauser effects with ARIA. Methods Enzymol 2001; 339:71-90. [PMID: 11462826 DOI: 10.1016/s0076-6879(01)39310-2] [Citation(s) in RCA: 286] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- J P Linge
- Structural Biology Programme, European Molecular Biology Laboratory, Heidelberg D-69117, Germany
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Schüler W, Kloiber K, Matt T, Bister K, Konrat R. Application of cross-correlated NMR spin relaxation to the zinc-finger protein CRP2(LIM2): evidence for collective motions in LIM domains. Biochemistry 2001; 40:9596-604. [PMID: 11583159 DOI: 10.1021/bi010509m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solution structure of quail CRP2(LIM2) was significantly improved by using an increased number of NOE constraints obtained from a 13C,15N-labeled protein sample and by applying a recently developed triple-resonance cross-correlated relaxation experiment for the determination of the backbone dihedral angle psi. Additionally, the relative orientation of the 15N(i)-1HN(i) dipole and the 13CO(i) CSA tensor, which is related to both backbone angles phi and psi, was probed by nitrogen-carbonyl multiple-quantum relaxation and used as an additional constraint for the refinement of the local geometry of the metal-coordination sites in CRP2(LIM2). The backbone dynamics of residues located in the folded part of CRP2(LIM2) have been characterized by proton-detected 13C'(i-1)-15N(i) and 15N(i)-1HN(i) multiple-quantum relaxation, respectively. We show that regions having cross-correlated time modulation of backbone isotropic chemical shifts on the millisecond to microsecond time scale correlate with residues that are structurally altered in the mutant protein CRP2(LIM2)R122A (disruption of the CCHC zinc-finger stabilizing side-chain hydrogen bond) and that these residues are part of an extended hydrogen-bonding network connecting the two zinc-binding sites. This indicates the presence of long-range collective motions in the two zinc-binding subdomains. The conformational plasticity of the LIM domain may be of functional relevance for this important protein recognition motif.
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Affiliation(s)
- W Schüler
- Institute of Organic Chemistry and Institute of Biochemistry, University of Innsbruck, Austria
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Skrynnikov NR, Konrat R, Muhandiram DR, Kay LE. Relative Orientation of Peptide Planes in Proteins Is Reflected in Carbonyl−Carbonyl Chemical Shift Anisotropy Cross-Correlated Spin Relaxation. J Am Chem Soc 2000. [DOI: 10.1021/ja0000201] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nikolai R. Skrynnikov
- Contribution from the Protein Engineering Network Centers of Excellence and Departments of Medical Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 1A8, and The Institute of Organic Chemistry, University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Robert Konrat
- Contribution from the Protein Engineering Network Centers of Excellence and Departments of Medical Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 1A8, and The Institute of Organic Chemistry, University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - D. R. Muhandiram
- Contribution from the Protein Engineering Network Centers of Excellence and Departments of Medical Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 1A8, and The Institute of Organic Chemistry, University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Lewis E. Kay
- Contribution from the Protein Engineering Network Centers of Excellence and Departments of Medical Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 1A8, and The Institute of Organic Chemistry, University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
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