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Koduru T, Hantman N, Peters EV, Jaworek MW, Wang J, Zhang S, McCallum SA, Gillilan RE, Fossat MJ, Roumestand C, Sagar A, Winter R, Bernadó P, Cherfils J, Royer CA. A molten globule ensemble primes Arf1-GDP for the nucleotide switch. Proc Natl Acad Sci U S A 2024; 121:e2413100121. [PMID: 39292747 PMCID: PMC11441498 DOI: 10.1073/pnas.2413100121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 07/31/2024] [Indexed: 09/20/2024] Open
Abstract
The adenosine di-phosphate (ADP) ribosylation factor (Arf) small guanosine tri-phosphate (GTP)ases function as molecular switches to activate signaling cascades that control membrane organization in eukaryotic cells. In Arf1, the GDP/GTP switch does not occur spontaneously but requires guanine nucleotide exchange factors (GEFs) and membranes. Exchange involves massive conformational changes, including disruption of the core β-sheet. The mechanisms by which this energetically costly switch occurs remain to be elucidated. To probe the switch mechanism, we coupled pressure perturbation with nuclear magnetic resonance (NMR), Fourier Transform infra-red spectroscopy (FTIR), small-angle X-ray scattering (SAXS), fluorescence, and computation. Pressure induced the formation of a classical molten globule (MG) ensemble. Pressure also favored the GDP to GTP transition, providing strong support for the notion that the MG ensemble plays a functional role in the nucleotide switch. We propose that the MG ensemble allows for switching without the requirement for complete unfolding and may be recognized by GEFs. An MG-based switching mechanism could constitute a pervasive feature in Arfs and Arf-like GTPases, and more generally, the evolutionarily related (Ras-like small GTPases) Rags and Gα GTPases.
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Affiliation(s)
- Tejaswi Koduru
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Noam Hantman
- Graduate Program in Biochemistry and Biophysics, School of Science, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Edgar V. Peters
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Michel W. Jaworek
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, Technical University of Dortmund University, DortmundD-44227, Germany
| | - Jinqiu Wang
- Graduate Program in Biochemistry and Biophysics, School of Science, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Siwen Zhang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Scott A. McCallum
- Shirley Ann Jackson, PhD. Center for Biotechnology and Interdisciplinary Science, Rensselaer Polytechnic Institute, Troy, NY12180
| | | | - Martin J. Fossat
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetic, FreiburgD-79108, Germany
| | - Christian Roumestand
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier34090, France
| | - Amin Sagar
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier34090, France
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, Technical University of Dortmund University, DortmundD-44227, Germany
| | - Pau Bernadó
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier34090, France
| | - Jacqueline Cherfils
- Université Paris-Saclay, Ecole Normale Supérieure Paris-Saclay, CNRS, Gif-sur-Yvette91190, France
| | - Catherine A. Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY12180
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2
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Wang L, Cao C, Zuo S. Protein secondary structure assignment using pc-polyline and convolutional neural network. Proteins 2021; 89:1017-1029. [PMID: 33780034 DOI: 10.1002/prot.26079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/22/2021] [Accepted: 03/15/2021] [Indexed: 01/17/2023]
Abstract
MOTIVATION The assignment of protein secondary structure elements (SSEs) underpins structural analysis and prediction. The backbone of a protein could be adequately represented using a pc-polyline that passes through the centers of its peptide planes. One salient feature of pc-polyline representation is that the secondary structure of a protein becomes recognizable in a matrix whose elements are the pairwise distances between two peptide plane centers. Thus, a pc-polyline could in turn be used to assign SSEs. RESULTS Using convolutional neural network (CNN) here we confirm that a pc-polyline indeed contains enough information for it to be used for the accurate assignments of the six SSE types: α-helix, β-sheet, β-bulge, 310 -helix, turn and loop. The applications to three large data sets show that the assignments by our CNN-based p2psse program agree very well with those by dssp, stride and quite well with those by five other programs. The analyses of their SSE assignments raise some general questions about the characterizations of protein secondary structure. In particular the analyses illustrate the difficulty with giving a quantitative and consistent definition for each of the six SSE types especially for 310 -helix, β-bulge, turn or loop in terms of either backbone H-bond patterns, or backbone dihedral angles, or Cα -polyline or pc-polyline. The difficulty suggests that the SSE space though being dominated by the regions for the six SSE types is to a certain degree continuous. AVAILABILITY The program is available at https://github.com/wlincong/p2pSSE.
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Affiliation(s)
- Lincong Wang
- The College of Computer Science and Technology, Jilin University, Changchun, China
| | - Chen Cao
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Shuxue Zuo
- The College of Computer Science and Technology, Jilin University, Changchun, China
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3
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Abstract
Structural biology often focuses primarily on three-dimensional structures of biological macromolecules, deposited in the Protein Data Bank (PDB). This resource is a remarkable entity for the world-wide scientific and medical communities, as well as the general public, as it is a growing translation into three-dimensional space of the vast information in genomic databases, e.g. GENBANK. There is, however, significantly more to understanding biological function than the three-dimensional coordinate space for ground-state structures of biomolecules. The vast array of biomolecules experiences natural dynamics, interconversion between multiple conformational states, and molecular recognition and allosteric events that play out on timescales ranging from picoseconds to seconds. This wide range of timescales demands ingenious and sophisticated experimental tools to sample and interpret these motions, thus enabling clearer insight into functional annotation of the PDB. NMR spectroscopy is unique in its ability to sample this range of timescales at atomic resolution and in physiologically relevant conditions using spin relaxation methods. The field is constantly expanding to provide new creative experiments, to yield more detailed coverage of timescales, and to broaden the power of interpretation and analysis methods. This review highlights the current state of the methodology and examines the extension of analysis tools for more complex experiments and dynamic models. The future for understanding protein dynamics is bright, and these extended tools bring greater compatibility with developments in computational molecular dynamics, all of which will further our understanding of biological molecular functions. These facets place NMR as a key component in integrated structural biology.
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4
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Katti S, Nyenhuis SB, Her B, Cafiso DS, Igumenova TI. Partial Metal Ion Saturation of C2 Domains Primes Synaptotagmin 1-Membrane Interactions. Biophys J 2020; 118:1409-1423. [PMID: 32075747 DOI: 10.1016/j.bpj.2020.01.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/15/2020] [Accepted: 01/27/2020] [Indexed: 12/29/2022] Open
Abstract
Synaptotagmin 1 (Syt1) is an integral membrane protein whose phospholipid-binding tandem C2 domains, C2A and C2B, act as Ca2+ sensors of neurotransmitter release. Our objective was to understand the role of individual metal-ion binding sites of these domains in the membrane association process. We used Pb2+, a structural and functional surrogate of Ca2+, to generate the protein states with well-defined protein-metal ion stoichiometry. NMR experiments revealed that binding of one divalent metal ion per C2 domain results in loss of conformational plasticity of the loop regions, potentially pre-organizing them for additional metal-ion and membrane-binding events. In C2A, a divalent metal ion in site 1 is sufficient to drive its weak association with phosphatidylserine-containing membranes, whereas in C2B, it enhances the interactions with the signaling lipid phosphatidylinositol-4,5-bisphosphate. In full-length Syt1, both Pb2+-complexed C2 domains associate with phosphatidylserine-containing membranes. Electron paramagnetic resonance experiments show that the extent of membrane insertion correlates with the occupancy of the C2 metal ion sites. Together, our results indicate that upon partial metal ion saturation of the intra-loop region, Syt1 adopts a dynamic, partially membrane-bound state. The properties of this state, such as conformationally restricted loop regions and positioning of C2 domains in close proximity to anionic lipid headgroups, "prime" Syt1 for cooperative binding of a full complement of metal ions and deeper membrane insertion.
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Affiliation(s)
- Sachin Katti
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Sarah B Nyenhuis
- Department of Chemistry and Biophysics Program, University of Virginia, Charlottesville, Virginia
| | - Bin Her
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - David S Cafiso
- Department of Chemistry and Biophysics Program, University of Virginia, Charlottesville, Virginia
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
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5
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Doynikova AN, Vekshin NL. Detection of RNA Hydrolysis with Binase by Acridine Orange Fluorescence. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819050028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Pandya MJ, Schiffers S, Hounslow AM, Baxter NJ, Williamson MP. Why the Energy Landscape of Barnase Is Hierarchical. Front Mol Biosci 2018; 5:115. [PMID: 30619881 PMCID: PMC6306431 DOI: 10.3389/fmolb.2018.00115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/07/2018] [Indexed: 01/29/2023] Open
Abstract
We have used NMR and computational methods to characterize the dynamics of the ribonuclease barnase over a wide range of timescales in free and inhibitor-bound states. Using temperature- and denaturant-dependent measurements of chemical shift, we show that barnase undergoes frequent and highly populated hinge bending. Using relaxation dispersion, we characterize a slower and less populated motion with a rate of 750 ± 200 s−1, involving residues around the lip of the active site, which occurs in both free and bound states and therefore suggests conformational selection. Normal mode calculations characterize correlated hinge bending motions on a very rapid timescale. These three measurements are combined with previous measurements and molecular dynamics calculations on barnase to characterize its dynamic landscape on timescales from picoseconds to milliseconds and length scales from 0.1 to 2.5 nm. We show that barnase has two different large-scale fluctuations: one on a timescale of 10−9−10−6 s that has no free energy barrier and is a hinge bending that is determined by the architecture of the protein; and one on a timescale of milliseconds (i.e., 750 s−1) that has a significant free energy barrier and starts from a partially hinge-bent conformation. These two motions can be described as hierarchical, in that the more highly populated faster motion provides a platform for the slower (less probable) motion. The implications are discussed. The use of temperature and denaturant is suggested as a simple and general way to characterize motions on the intermediate ns-μs timescale.
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Affiliation(s)
- Maya J Pandya
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Stefanie Schiffers
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
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7
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Ikeya T, Ban D, Lee D, Ito Y, Kato K, Griesinger C. Solution NMR views of dynamical ordering of biomacromolecules. Biochim Biophys Acta Gen Subj 2017; 1862:287-306. [PMID: 28847507 DOI: 10.1016/j.bbagen.2017.08.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. SCOPE OF REVIEW In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. MAJOR CONCLUSIONS Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. GENERAL SIGNIFICANCE For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Teppei Ikeya
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabe-dori 3-1, Mizuho-ku, Nagoya 467-8603, Japan
| | - Christian Griesinger
- Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
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8
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Morales KA, Yang Y, Cole TR, Igumenova TI. Dynamic Response of the C2 Domain of Protein Kinase Cα to Ca 2+ Binding. Biophys J 2017; 111:1655-1667. [PMID: 27760353 DOI: 10.1016/j.bpj.2016.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/04/2016] [Accepted: 09/07/2016] [Indexed: 11/28/2022] Open
Abstract
Ca2+-dependent conserved-region 2 (C2) domains target their host signaling proteins to anionic membranes. The Ca2+-binding event is a prerequisite for membrane association. Here, we investigate multiscale metal-ion-dependent dynamics of the C2 domain of protein kinase Cα (C2α) using NMR spectroscopy. Interactions with metal ions attenuate microsecond-timescale motions of the loop regions, indicating that preorganization of the metal-binding loops occurs before membrane insertion. Binding of a full complement of Ca2+ ions has a profound effect on the millisecond-timescale dynamics of the N- and C-terminal regions of C2α. We propose that Ca2+ binding allosterically destabilizes the terminal regions of C2α and thereby facilitates the conformational rearrangement necessary for full membrane insertion and activation of protein kinase Cα.
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Affiliation(s)
- Krystal A Morales
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Yuan Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Taylor R Cole
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
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9
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Ravera E, Sgheri L, Parigi G, Luchinat C. A critical assessment of methods to recover information from averaged data. Phys Chem Chem Phys 2017; 18:5686-701. [PMID: 26565805 DOI: 10.1039/c5cp04077a] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Conformational heterogeneity is key to the function of many biomacromolecules, but only a few groups have tried to characterize it until recently. Now, thanks to the increased throughput of experimental data and the increased computational power, the problem of the characterization of protein structural variability has become more and more popular. Several groups have devoted their efforts in trying to create quantitative, reliable and accurate protocols for extracting such information from averaged data. We analyze here different approaches, discussing strengths and weaknesses of each. All approaches can roughly be clustered into two groups: those satisfying the maximum entropy principle and those recovering ensembles composed of a restricted number of molecular conformations. In the first case, the solution focuses on the features that are common to all the infinite solutions satisfying the experimental data; in the second case, the reconstructed ensemble shows the conformational regions where a large probability can be placed. The upper limits for conformational probabilities (MaxOcc) can also be calculated. We also give an overview of the mainstream experimental observables, with considerations on the assumptions underlying their usage.
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Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
| | - Luca Sgheri
- Istituto per le Applicazioni del Calcolo, Sezione di Firenze, CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
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10
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Abstract
![]()
We review how major cell behaviors,
such as bacterial growth laws,
are derived from the physical chemistry of the cell’s proteins.
On one hand, cell actions depend on the individual biological functionalities
of their many genes and proteins. On the other hand, the common physics
among proteins can be as important as the unique biology that distinguishes
them. For example, bacterial growth rates depend strongly on temperature.
This dependence can be explained by the folding stabilities across
a cell’s proteome. Such modeling explains how thermophilic
and mesophilic organisms differ, and how oxidative damage of highly
charged proteins can lead to unfolding and aggregation in aging cells.
Cells have characteristic time scales. For example, E. coli can duplicate as fast as 2–3 times per hour. These time scales
can be explained by protein dynamics (the rates of synthesis and degradation,
folding, and diffusional transport). It rationalizes how bacterial
growth is slowed down by added salt. In the same way that the behaviors
of inanimate materials can be expressed in terms of the statistical
distributions of atoms and molecules, some cell behaviors can be expressed
in terms of distributions of protein properties, giving insights into
the microscopic basis of growth laws in simple cells.
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Affiliation(s)
- Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver , Denver, Colorado 80209, United States
| | - Adam M R de Graff
- Laufer Center for Physical and Quantitative Biology and Departments of Chemistry and Physics and Astronomy, Stony Brook University , Stony Brook, New York 11794, United States
| | - Lucas Sawle
- Department of Physics and Astronomy, University of Denver , Denver, Colorado 80209, United States
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology and Departments of Chemistry and Physics and Astronomy, Stony Brook University , Stony Brook, New York 11794, United States
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11
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Lisi GP, Loria JP. Using NMR spectroscopy to elucidate the role of molecular motions in enzyme function. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 92-93:1-17. [PMID: 26952190 PMCID: PMC4785347 DOI: 10.1016/j.pnmrs.2015.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 05/04/2023]
Abstract
Conformational motions play an essential role in enzyme function, often facilitating the formation of enzyme-substrate complexes and/or product release. Although considerable debate remains regarding the role of molecular motions in the conversion of enzymatic substrates to products, numerous examples have found motions to be crucial for optimization of enzyme scaffolds, effective substrate binding, and product dissociation. Conformational fluctuations are often rate-limiting to enzyme catalysis, primarily through product release, with the chemical reaction occurring much more quickly. As a result, the direct involvement of motions at various stages along the enzyme reaction coordinate remains largely unknown and untested. In the following review, we describe the use of solution NMR techniques designed to probe various timescales of molecular motions and detail examples in which motions play a role in propagating catalytic effects from the active site and directly participate in essential aspects of enzyme function.
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Affiliation(s)
- George P Lisi
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - J Patrick Loria
- Department of Chemistry, Yale University, New Haven, CT 06520, United States; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, United States.
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12
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Sokurenko JV, Zelenikhin PV, Ulyanova VV, Kolpakov AI, Muler D, Ilinskaya ON. [Identification of 2',3'-cGMP as an intermediate of RNA catalytic cleavage by binase and evaluation of its biological action]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2015; 41:37-43. [PMID: 26050470 DOI: 10.1134/s1068162015010136] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Binase--Bacillus pumilus RNase--endonuclease cleaves the phosphodiester bond between the 3'-guanylic residue and the 5'-OH residue of adjacent nucleotides with the formation of corresponding intermediate 2',3'-cGMP. Subsequent hydrolysis of 2',3'-cGMP into 3'-phosphate is highly specific and occurs slowly So the question arises about the existing time of that positional isomer during RNA catalytic cleavage by binase and about 2',3'-cGMP role in antitumor activity of the enzyme: In present work by means of enzyme-linked immunosorbent assay we established that during catalytic cleavage of RNA by binase 2',3'-cGMP is preserved in reaction mixture for an hour, at the same time phosphodiesterases activation doesn't lead to the total elimination of 2',3'-cGMP. The highest amount of 2',3'-cGMP was observed under the pH 8.5, it reaches nanomolar concentration at initial RNA concentration of 100-1000 μg/mL. Exogenous 2',3'-cGMP, like its positional isomer 3',5'-cGMP, doesn't trigger an apoptosis of human lung adenocarcinoma A549 cells, which are sensitive to binase apoptogenic action. Taking into account data about binase internalization and activation of mitochondrial pores opening by 2',3'-cyclic guanosine phosphates we may consider that 2',3'-cGMP can contribute to the apoptosis initiated by binase only when 2',3'-cGMP is generated intracellularly.
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13
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Schumann FH, Varadan R, Tayakuniyil PP, Grossman JH, Camarero JA, Fushman D. Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain. Front Chem 2015; 3:26. [PMID: 25905098 PMCID: PMC4389572 DOI: 10.3389/fchem.2015.00026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/23/2015] [Indexed: 12/02/2022] Open
Abstract
Understanding of the effects of the backbone cyclization on the structure and dynamics of a protein is essential for using protein topology engineering to alter protein stability and function. Here we have determined, for the first time, the structure and dynamics of the linear and various circular constructs of the N-SH3 domain from protein c-Crk. These constructs differ in the length and amino acid composition of the cyclization region. The backbone cyclization was carried out using intein-mediated intramolecular chemical ligation between the juxtaposed N- and the C-termini. The structure and backbone dynamics studies were performed using solution NMR. Our data suggest that the backbone cyclization has little effect on the overall three-dimensional structure of the SH3 domain: besides the termini, only minor structural changes were found in the proximity of the cyclization region. In contrast to the structure, backbone dynamics are significantly affected by the cyclization. On the subnanosecond time scale, the backbone of all circular constructs on average appears more rigid than that of the linear SH3 domain; this effect is observed over the entire backbone and is not limited to the cyclization site. The backbone mobility of the circular constructs becomes less restricted with increasing length of the circularization loop. In addition, significant conformational exchange motions (on the sub-millisecond time scale) were found in the N-Src loop and in the adjacent β-strands in all circular constructs studied in this work. These effects of backbone cyclization on protein dynamics have potential implications for the stability of the protein fold and for ligand binding.
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Affiliation(s)
- Frank H Schumann
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Ranjani Varadan
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Praveen P Tayakuniyil
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Jennifer H Grossman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Los Angeles, CA, USA ; Department of Chemistry, University of Southern California Los Angeles, CA, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
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14
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Dutta S, Nandi N. Dynamics of the Active Sites of Dimeric Seryl tRNA Synthetase from Methanopyrus kandleri. J Phys Chem B 2015; 119:10832-48. [PMID: 25794108 DOI: 10.1021/jp511585w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Saheb Dutta
- Department
of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal 741235, India
| | - Nilashis Nandi
- Department
of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal 741235, India
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15
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Palmer AG. Chemical exchange in biomacromolecules: past, present, and future. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:3-17. [PMID: 24656076 PMCID: PMC4049312 DOI: 10.1016/j.jmr.2014.01.008] [Citation(s) in RCA: 194] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/09/2014] [Accepted: 01/10/2014] [Indexed: 05/08/2023]
Abstract
The perspective reviews quantitative investigations of chemical exchange phenomena in proteins and other biological macromolecules using NMR spectroscopy, particularly relaxation dispersion methods. The emphasis is on techniques and applications that quantify the populations, interconversion kinetics, and structural features of sparsely populated conformational states in equilibrium with a highly populated ground state. Applications to folding, molecular recognition, catalysis, and allostery by proteins and nucleic acids are highlighted.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States.
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16
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Fragai M, Luchinat C, Parigi G, Ravera E. Conformational freedom of metalloproteins revealed by paramagnetism-assisted NMR. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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17
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Measuring dynamic and kinetic information in the previously inaccessible supra-τ(c) window of nanoseconds to microseconds by solution NMR spectroscopy. Molecules 2013; 18:11904-37. [PMID: 24077173 PMCID: PMC6270068 DOI: 10.3390/molecules181011904] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/28/2013] [Accepted: 09/17/2013] [Indexed: 11/16/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool that has enabled experimentalists to characterize molecular dynamics and kinetics spanning a wide range of time-scales from picoseconds to days. This review focuses on addressing the previously inaccessible supra-tc window (defined as τ(c) < supra-τ(c) < 40 μs; in which tc is the overall tumbling time of a molecule) from the perspective of local inter-nuclear vector dynamics extracted from residual dipolar couplings (RDCs) and from the perspective of conformational exchange captured by relaxation dispersion measurements (RD). The goal of the first section is to present a detailed analysis of how to extract protein dynamics encoded in RDCs and how to relate this information to protein functionality within the previously inaccessible supra-τ(c) window. In the second section, the current state of the art for RD is analyzed, as well as the considerable progress toward pushing the sensitivity of RD further into the supra-τ(c) scale by up to a factor of two (motion up to 25 μs). From the data obtained with these techniques and methodology, the importance of the supra-τ(c) scale for protein function and molecular recognition is becoming increasingly clearer as the connection between motion on the supra-τ(c) scale and protein functionality from the experimental side is further strengthened with results from molecular dynamics simulations.
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18
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NMR spectroscopy on domain dynamics in biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:58-117. [DOI: 10.1016/j.pbiomolbio.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
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19
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Ramakrishnan V, Jagannathan S, Shaikh AR, Rajagopalan R. Dynamic and Structural Changes in the Minimally Restructuring EcoRI Bound to a Minimally Mutated DNA Chain. J Biomol Struct Dyn 2012; 29:743-56. [DOI: 10.1080/073911012010525020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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20
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Abstract
Nitrogen-15 relaxation is the most ubiquitous source of information about protein (backbone) dynamics used by NMR spectroscopists. It provides the general characteristics of hydrodynamics as well as internal motions on subnanosecond, micro- and millisecond timescales of a biomolecule. Here, we present a full protocol to perform and analyze a series of experiments to measure the (15)N longitudinal relaxation rate, the (15)N transverse relaxation rate under an echo train or a single echo, the (15)N-(1)H dipolar cross-relaxation rate, as well as the longitudinal and transverse cross-relaxation rates due to the cross-correlation of the nitrogen-15 chemical shift anisotropy and the dipolar coupling with the adjacent proton. These rates can be employed to carry out model-free analyses and can be used to quantify accurately the contribution of chemical exchange to transverse relaxation.
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Affiliation(s)
- Fabien Ferrage
- Département de chimie, Ecole normale supérieure et Laboratoire des Biomolécules, CNRS UMR 7203, Paris, Cedex, France.
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21
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Bianconi A, Ciasca G, Tenenbaum A, Battisti A, Campi G. Temperature and solvent dependence of the dynamical landscape of tau protein conformations. J Biol Phys 2012; 38:169-79. [PMID: 23277677 PMCID: PMC3285732 DOI: 10.1007/s10867-011-9244-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 10/18/2011] [Indexed: 02/05/2023] Open
Abstract
We report the variation with temperature of the ensemble distribution of conformations spanned by the tau protein in its dynamical states measured by small-angle X-ray scattering (SAXS) using synchrotron radiation. The SAXS data show a clear temperature variation of the distribution of occupied protein conformations from 293 to 318 K. More conformations with a smaller radius of gyration are occupied at higher temperature. The protein-solvent interactions are shown by computer simulation to be essential for controlling the dynamics of protein conformations, providing evidence for the key role of water solvent in the protein dynamics, as proposed by Giorgio Careri.
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Affiliation(s)
- Antonio Bianconi
- Physics Department, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Roma, Italy
| | - Gabriele Ciasca
- Physics Department, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Roma, Italy
| | - Alexander Tenenbaum
- Physics Department, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Roma, Italy
| | - Anna Battisti
- Physics Department, University of Trento, Via Sommarive 14, 38123 Povo (Trento), Italy
- LISC, FBK-CMM and University of Trento, Via Sommarive 18, 38123 Povo (Trento), Italy
| | - Gaetano Campi
- CNR, Institute of Crystallography, Via Salaria Km 29.300, 00016 Monterotondo (Roma), Italy
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22
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Ban D, Funk M, Gulich R, Egger D, Sabo TM, Walter KFA, Fenwick RB, Giller K, Pichierri F, de Groot BL, Lange OF, Grubmüller H, Salvatella X, Wolf M, Loidl A, Kree R, Becker S, Lakomek NA, Lee D, Lunkenheimer P, Griesinger C. Kinetics of Conformational Sampling in Ubiquitin. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201105086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Ban D, Funk M, Gulich R, Egger D, Sabo TM, Walter KFA, Fenwick RB, Giller K, Pichierri F, de Groot BL, Lange OF, Grubmüller H, Salvatella X, Wolf M, Loidl A, Kree R, Becker S, Lakomek NA, Lee D, Lunkenheimer P, Griesinger C. Kinetics of conformational sampling in ubiquitin. Angew Chem Int Ed Engl 2011; 50:11437-40. [PMID: 22113802 DOI: 10.1002/anie.201105086] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Indexed: 11/09/2022]
Affiliation(s)
- David Ban
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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24
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Serrano P, Pedrini B, Geralt M, Jaudzems K, Mohanty B, Horst R, Herrmann T, Elsliger MA, Wilson IA, Wüthrich K. Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1393-405. [PMID: 20944236 PMCID: PMC2954230 DOI: 10.1107/s1744309110033658] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 08/20/2010] [Indexed: 05/12/2023]
Abstract
The JCSG has recently developed a protocol for systematic comparisons of high-quality crystal and NMR structures of proteins. In this paper, the extent to which this approach can provide function-related information on the two functionally annotated proteins TM1081, a Thermotoga maritima anti-σ factor antagonist, and A2LD1 (gi:13879369), a mouse γ-glutamylamine cyclotransferase, is explored. The NMR structures of the two proteins have been determined in solution at 313 and 298 K, respectively, using the current JCSG protocol based on the software package UNIO for extensive automation. The corresponding crystal structures were solved by the JCSG at 100 K and 1.6 Å resolution and at 100 K and 1.9 Å resolution, respectively. The NMR and crystal structures of the two proteins share the same overall molecular architectures. However, the precision of the structure determination along the amino-acid sequence varies over a significantly wider range in the NMR structures than in the crystal structures. Thereby, in each of the two NMR structures about 65% of the residues have displacements below the average and in both proteins the less well ordered residues include large parts of the active sites, in addition to some highly solvent-exposed surface areas. Whereas the latter show increased disorder in the crystal and in solution, the active-site regions display increased displacements only in the NMR structures, where they undergo local conformational exchange on the millisecond time scale that appears to be frozen in the crystals. These observations suggest that a search for molecular regions showing increased structural disorder and slow dynamic processes in solution while being well ordered in the corresponding crystal structure might be a valid initial step in the challenge of identifying putative active sites in functionally unannotated proteins with known three-dimensional structure.
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Affiliation(s)
- Pedro Serrano
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Bill Pedrini
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Michael Geralt
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kristaps Jaudzems
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Biswaranjan Mohanty
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Reto Horst
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Torsten Herrmann
- Centre Européen de RMN à Très Hauts Champs, Université de Lyon FRE 3008 CNRS, F-69100 Villeurbanne, France
| | - Marc-André Elsliger
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Ian A. Wilson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kurt Wüthrich
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
- Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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25
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Kamerlin SCL, Warshel A. The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions. Faraday Discuss 2010; 145:71-106. [PMID: 25285029 PMCID: PMC4184467 DOI: 10.1039/b907354j] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent years have seen dramatic improvements in computer power, allowing ever more challenging problems to be approached. In light of this, it is imperative to have a quantitative model for examining chemical reactivity, both in the condensed phase and in solution, as well as to accurately quantify physical organic chemistry (particularly as experimental approaches can often be inconclusive). Similarly, computational approaches allow for great progress in studying enzyme catalysis, as they allow for the separation of the relevant energy contributions to catalysis. Due to the complexity of the problems that need addressing, there is a need for an approach that can combine reliability with an ability to capture complex systems in order to resolve long-standing controversies in a unique way. Herein, we will demonstrate that the empirical valence bond (EVB) approach provides a powerful way to connect the classical concepts of physical organic chemistry to the actual energies of enzymatic reactions by means of computation. Additionally, we will discuss the proliferation of this approach, as well as attempts to capture its basic chemistry and repackage it under different names. We believe that the EVB approach is the most powerful tool that is currently available for studies of chemical processes in the condensed phase in general and enzymes in particular, particularly when trying to explore the different proposals about the origin of the catalytic power of enzymes.
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Affiliation(s)
- Shina C. L. Kamerlin
- Department of Chemistry SGM418, University of Southern California, 3620 McClintock Ave., Los Angeles, CA-90089, USA
| | - Arieh Warshel
- Department of Chemistry SGM418, University of Southern California, 3620 McClintock Ave., Los Angeles, CA-90089, USA
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26
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Hansen DF, Feng H, Zhou Z, Bai Y, Kay LE. Selective characterization of microsecond motions in proteins by NMR relaxation. J Am Chem Soc 2009; 131:16257-65. [PMID: 19842628 PMCID: PMC7386800 DOI: 10.1021/ja906842s] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The three-dimensional structures of macromolecules fluctuate over a wide range of time-scales. Separating the individual dynamic processes according to frequency is of importance in relating protein motions to biological function and stability. We present here a general NMR method for the specific characterization of microsecond motions at backbone positions in proteins even in the presence of other dynamics such as large-amplitude nanosecond motions and millisecond chemical exchange processes. The method is based on measurement of relaxation rates of four bilinear coherences and relies on the ability of strong continuous radio frequency fields to quench millisecond chemical exchange. The utility of the methodology is demonstrated and validated through two specific examples focusing on the thermo-stable proteins, ubiquitin and protein L, where it is found that small-amplitude microsecond dynamics are more pervasive than previously thought. Specifically, these motions are localized to alpha helices, loop regions, and regions along the rim of beta sheets in both of the proteins examined. A third example focuses on a 28 kDa ternary complex of the chaperone Chz1 and the histones H2A.Z/H2B, where it is established that pervasive microsecond motions are localized to a region of the chaperone that is important for stabilizing the complex. It is further shown that these motions can be well separated from extensive millisecond dynamics that are also present and that derive from exchange of Chz1 between bound and free states. The methodology is straightforward to implement, and data recorded at only a single static magnetic field are required.
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Affiliation(s)
- D Flemming Hansen
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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27
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Borsi V, Luchinat C, Parigi G. Global and local mobility of apocalmodulin monitored through fast-field cycling relaxometry. Biophys J 2009; 97:1765-71. [PMID: 19751682 PMCID: PMC2749786 DOI: 10.1016/j.bpj.2009.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 06/27/2009] [Accepted: 07/08/2009] [Indexed: 02/03/2023] Open
Abstract
Calmodulin (CaM) is a ubiquitous eukaryotic protein with two conformationally independent domains that can bind up to two calcium ions each. In the calcium-bound state, CaM is able to regulate a vast number of cellular activities by binding to a multiplicity of target proteins in different modes. Its versatility has been ascribed to its anomalously high flexibility. The calcium-free form (apoCaM), which is the resting state of CaM in cells, is also able to functionally bind a number of protein targets, but its dynamics has received less attention. At variance with the calcium-bound form, the crystal structure of apoCaM shows a compact organization of the two domains, but NMR measurements could not detect any contact between them, thus indicating the presence of mobility in solution. The mobility of apoCaM is here investigated through protein proton relaxation rate measurements performed with a high-sensitivity fast-field cycling relaxometer. Such measurements provide direct access to the spectral density function and show that 1), the reorientation time is in agreement with a closed form of the protein; but 2), the collective order parameter is much smaller than for other well folded compact proteins, indicating that a remarkably large side-chain mobility must be present.
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Affiliation(s)
- Valentina Borsi
- Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
- Department of Agricultural Biotechnology, University of Florence, Florence, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
- Department of Agricultural Biotechnology, University of Florence, Florence, Italy
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28
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Weaver DS, Zuiderweg ERP. Protein proton-proton dynamics from amide proton spin flip rates. JOURNAL OF BIOMOLECULAR NMR 2009; 45:99-119. [PMID: 19636797 DOI: 10.1007/s10858-009-9351-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 06/29/2009] [Indexed: 05/28/2023]
Abstract
Residue-specific amide proton spin-flip rates K were measured for peptide-free and peptide-bound calmodulin. K approximates the sum of NOE build-up rates between the amide proton and all other protons. This work outlines the theory of multi-proton relaxation, cross relaxation and cross correlation, and how to approximate it with a simple model based on a variable number of equidistant protons. This model is used to extract the sums of K-rates from the experimental data. Error in K is estimated using bootstrap methodology. We define a parameter Q as the ratio of experimental K-rates to theoretical K-rates, where the theoretical K-rates are computed from atomic coordinates. Q is 1 in the case of no local motion, but decreases to values as low as 0.5 with increasing domination of sidechain protons of the same residue to the amide proton flips. This establishes Q as a monotonous measure of local dynamics of the proton network surrounding the amide protons. The method is applied to the study of proton dynamics in Ca(2+)-saturated calmodulin, both free in solution and bound to smMLCK peptide. The mean Q is 0.81 +/- 0.02 for free calmodulin and 0.88 +/- 0.02 for peptide-bound calmodulin. This novel methodology thus reveals the presence of significant interproton disorder in this protein, while the increase in Q indicates rigidification of the proton network upon peptide binding, confirming the known high entropic cost of this process.
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Affiliation(s)
- Daniel S Weaver
- Biophysics, The University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA.
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29
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Farès C, Lakomek NA, Walter KFA, Frank BTC, Meiler J, Becker S, Griesinger C. Accessing ns-micros side chain dynamics in ubiquitin with methyl RDCs. JOURNAL OF BIOMOLECULAR NMR 2009; 45:23-44. [PMID: 19652920 PMCID: PMC2728246 DOI: 10.1007/s10858-009-9354-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 06/27/2009] [Indexed: 05/19/2023]
Abstract
This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098-6107, 2001; Lakomek in J Biomol NMR 34:101-115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-tau (c) dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time tau (c). In fact, the average amplitude of motion expressed in terms of order parameters S (2) associated with the supra-tau (c) window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959-8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471-1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains.
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Affiliation(s)
- Christophe Farès
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
- University Health Network, Max Bell Research Center, University of Toronto, Toronto, ON Canada
| | - Nils-Alexander Lakomek
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD USA
| | - Korvin F. A. Walter
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Benedikt T. C. Frank
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jens Meiler
- Department of Chemistry, Center of Structural Biology, Vanderbilt University, Nashville, TN USA
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
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30
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Fisher CK, Al-Hashimi HM. Approximate reconstruction of continuous spatially complex domain motions by multialignment NMR residual dipolar couplings. J Phys Chem B 2009; 113:6173-6. [PMID: 19358547 DOI: 10.1021/jp900411z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
NMR spectroscopy is one of the most powerful techniques for studying the internal dynamics of biomolecules. Current formalisms approximate the dynamics using simple continuous motional models or models involving discrete jumps between a small number of states. However, no approach currently exists for interpreting NMR data in terms of continuous spatially complex motional paths that may feature more than one distinct maneuver. Here, we present an approach for approximately reconstructing spatially complex continuous motions of chiral domains using NMR anisotropic interactions. The key is to express Wigner matrix elements, which can be determined experimentally using residual dipolar couplings, as a line integral over a curve in configuration space containing an ensemble of conformations and to approximate the curve using a series of geodesic segments. Using this approach and five sets of synthetic residual dipolar couplings computed for five linearly independent alignment conditions, we show that it is theoretically possible to reconstruct salient features of a multisegment interhelical motional trajectory obtained from a 65 ns molecular dynamics simulation of a stem-loop RNA. Our study shows that the 3-D atomic reconstruction of complex motions in biomolecules is within experimental reach.
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31
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Wang Y, Berlow RB, Loria JP. Role of loop-loop interactions in coordinating motions and enzymatic function in triosephosphate isomerase. Biochemistry 2009; 48:4548-56. [PMID: 19348462 PMCID: PMC2713366 DOI: 10.1021/bi9002887] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The enzyme triosephosphate isomerase (TIM) has been used as a model system for understanding the relationship between protein sequence, structure, and biological function. The sequence of the active site loop (loop 6) in TIM is directly correlated with a conserved motif in loop 7. Replacement of loop 7 of chicken TIM with the corresponding loop 7 sequence from an archaeal homologue caused a 10(2)-fold loss in enzymatic activity, a decrease in substrate binding affinity, and a decrease in thermal stability. Isotope exchange studies performed by one-dimensional (1)H NMR showed that the substrate-derived proton in the enzyme is more susceptible to solvent exchange for DHAP formation in the loop 7 mutant than for WT TIM. TROSY-Hahn Echo and TROSY-selected R(1rho) experiments indicate that upon mutation of loop 7, the chemical exchange rate for active site loop motion is nearly doubled and that the coordinated motion of loop 6 is reduced relative to that of the WT. Temperature dependent NMR experiments show differing activation energies for the N- and C-terminal hinges in this mutant enzyme. Together, these data suggest that interactions between loop 6 and loop 7 are necessary to provide the proper chemical context for the enzymatic reaction to occur and that the interactions play a significant role in modulating the chemical dynamics near the active site.
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Affiliation(s)
- Yan Wang
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
| | - Rebecca B. Berlow
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - J. Patrick Loria
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
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32
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Residual dipolar couplings as a tool to study molecular recognition of ubiquitin. Biochem Soc Trans 2009; 36:1433-7. [PMID: 19021570 DOI: 10.1042/bst0361433] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RDCs (residual dipolar couplings) in NMR spectroscopy provide information about protein dynamics complementary to NMR relaxation methods, especially in the previously inaccessible time window between the protein correlation time tau(c) and 50 micros. For ubiquitin, new modes of motion of the protein backbone could be detected using RDC-based techniques. An ensemble of ubiquitin based on these RDC values is found to comprise all different conformations that ubiquitin adopts upon binding to different recognition proteins. These conformations in protein-protein complexes had been derived from 46 X-ray structures. Thus, for ubiquitin recognition by other proteins, conformational selection rather than induced fit seems to be the dominant mechanism.
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33
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Berthoumieux H, Antoine C, Jullien L, Lemarchand A. Resonant response to temperature modulation for enzymatic dynamics characterization. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 79:021906. [PMID: 19391777 DOI: 10.1103/physreve.79.021906] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Indexed: 05/27/2023]
Abstract
We consider enzymes involved in a three-state Michaelis-Menten kinetics and submitted to well-chosen temperature modulations of small amplitude. From the first-order amplitudes of concentration oscillations, we design a response function that is maximum for targeted values of the chemical relaxation times. This resonant function can be used to screen a large set of enzymes and identify the one governed by the desired kinetics. The method gives access to all the dynamical parameters of the targeted enzyme without resorting to a fit. We show how to estimate the precision of this parameter determination and give some hints for experimental validation.
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Affiliation(s)
- H Berthoumieux
- Ecole Normale Supérieure, Département de Chimie, UMR 8640 CNRS ENS UPMC-Paris 6 PASTEUR, 24, rue Lhomond, 75231 Paris Cedex 05, France
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Abstract
The function of bio-macromolecules is determined by both their 3D structure and conformational dynamics. These molecules are inherently flexible systems displaying a broad range of dynamics on time-scales from picoseconds to seconds. Nuclear Magnetic Resonance (NMR) spectroscopy has emerged as the method of choice for studying both protein structure and dynamics in solution. Typically, NMR experiments are sensitive both to structural features and to dynamics, and hence the measured data contain information on both. Despite major progress in both experimental approaches and computational methods, obtaining a consistent view of structure and dynamics from experimental NMR data remains a challenge. Molecular dynamics simulations have emerged as an indispensable tool in the analysis of NMR data.
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Affiliation(s)
- Phineus R. L. Markwick
- Institut Pasteur, Département de Biologie Structurale et Chimie, Unité de Bio-Informatique Structurale, CNRS URA 2185, Paris, France
| | - Thérèse Malliavin
- Institut Pasteur, Département de Biologie Structurale et Chimie, Unité de Bio-Informatique Structurale, CNRS URA 2185, Paris, France
| | - Michael Nilges
- Institut Pasteur, Département de Biologie Structurale et Chimie, Unité de Bio-Informatique Structurale, CNRS URA 2185, Paris, France
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35
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Weaver DS, Zuiderweg ERP. Eta(z)/kappa: a transverse relaxation optimized spectroscopy NMR experiment measuring longitudinal relaxation interference. J Chem Phys 2008; 128:155103. [PMID: 18433284 DOI: 10.1063/1.2889923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
NMR spin relaxation experiments provide a powerful tool for the measurement of global and local biomolecular rotational dynamics at subnanosecond time scales. Technical limitations restrict most spin relaxation studies to biomolecules weighing less than 10 kDa, considerably smaller than the average protein molecular weight of 30 kDa. In particular, experiments measuring eta(z), the longitudinal (1)H(N)-(15)N dipole-dipole (DD)/(15)N chemical shift anisotropy (CSA) cross-correlated relaxation rate, are among those least suitable for use with larger biosystems. This is unfortunate because these experiments yield valuable insight into the variability of the (15)N CSA tensor over the polypeptide backbone, and this knowledge is critical to the correct interpretation of most (15)N-NMR backbone relaxation experiments, including R(2) and R(1). In order to remedy this situation, we present a new (1)H(N)-(15)N transverse relaxation optimized spectroscopy experiment measuring eta(z) suitable for applications with larger proteins (up to at least 30 kDa). The presented experiment also yields kappa, the site-specific rate of longitudinal (1)H(N)-(1)H(') DD cross relaxation. We describe the eta(z)/kappa experiment's performance in protonated human ubiquitin at 30.0 degrees C and in protonated calcium-saturated calmodulin/peptide complex at 20.0 degrees C, and demonstrate preliminary experimental results for a deuterated E. coli DnaK ATPase domain construct at 34 degrees C.
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Affiliation(s)
- Daniel S Weaver
- Biophysics and Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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36
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Edelweiss E, Balandin TG, Ivanova JL, Lutsenko GV, Leonova OG, Popenko VI, Sapozhnikov AM, Deyev SM. Barnase as a new therapeutic agent triggering apoptosis in human cancer cells. PLoS One 2008; 3:e2434. [PMID: 18560598 PMCID: PMC2413406 DOI: 10.1371/journal.pone.0002434] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 05/13/2008] [Indexed: 02/05/2023] Open
Abstract
Background RNases are currently studied as non-mutagenic alternatives to the harmful DNA-damaging anticancer drugs commonly used in clinical practice. Many mammalian RNases are not potent toxins due to the strong inhibition by ribonuclease inhibitor (RI) presented in the cytoplasm of mammalian cells. Methodology/Principal Findings In search of new effective anticancer RNases we studied the effects of barnase, a ribonuclease from Bacillus amyloliquefaciens, on human cancer cells. We found that barnase is resistant to RI. In MTT cell viability assay, barnase was cytotoxic to human carcinoma cell lines with half-inhibitory concentrations (IC50) ranging from 0.2 to 13 µM and to leukemia cell lines with IC50 values ranging from 2.4 to 82 µM. Also, we characterized the cytotoxic effects of barnase-based immunoRNase scFv 4D5-dibarnase, which consists of two barnase molecules serially fused to the single-chain variable fragment (scFv) of humanized antibody 4D5 that recognizes the extracellular domain of cancer marker HER2. The scFv 4D5-dibarnase specifically bound to HER2-positive cells and was internalized via receptor-mediated endocytosis. The intracellular localization of internalized scFv 4D5-dibarnase was determined by electronic microscopy. The cytotoxic effect of scFv 4D5-dibarnase on HER2-positive human ovarian carcinoma SKOV-3 cells (IC50 = 1.8 nM) was three orders of magnitude greater than that of barnase alone. Both barnase and scFv 4D5-dibarnase induced apoptosis in SKOV-3 cells accompanied by internucleosomal chromatin fragmentation, membrane blebbing, the appearance of phosphatidylserine on the outer leaflet of the plasma membrane, and the activation of caspase-3. Conclusions/Significance These results demonstrate that barnase is a potent toxic agent for targeting to cancer cells.
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Affiliation(s)
- Evelina Edelweiss
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (EE); (SMD)
| | - Taras G. Balandin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Julia L. Ivanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Gennady V. Lutsenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olga G. Leonova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir I. Popenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander M. Sapozhnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey M. Deyev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (EE); (SMD)
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37
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Lange OF, Lakomek NA, Fares C, Schroder GF, Walter KFA, Becker S, Meiler J, Grubmuller H, Griesinger C, de Groot BL. Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution. Science 2008; 320:1471-5. [DOI: 10.1126/science.1157092] [Citation(s) in RCA: 865] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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38
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Zasedateleva OA, Mikheikin AL, Turygin AY, Prokopenko DV, Chudinov AV, Belobritskaya EE, Chechetkin VR, Zasedatelev AS. Gel-based oligonucleotide microarray approach to analyze protein-ssDNA binding specificity. Nucleic Acids Res 2008; 36:e61. [PMID: 18474529 PMCID: PMC2425478 DOI: 10.1093/nar/gkn246] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Gel-based oligonucleotide microarray approach was developed for quantitative profiling of binding affinity of a protein to single-stranded DNA (ssDNA). To demonstrate additional capabilities of this method, we analyzed the binding specificity of ribonuclease (RNase) binase from Bacillus intermedius (EC 3.1.27.3) to ssDNA using generic hexamer oligodeoxyribonucleotide microchip. Single-stranded octamer oligonucleotides were immobilized within 3D hemispherical gel pads. The octanucleotides in individual pads 5'-{N}N(1)N(2)N(3)N(4)N(5)N(6){N}-3' consisted of a fixed hexamer motif N(1)N(2)N(3)N(4)N(5)N(6) in the middle and variable parts {N} at the ends, where {N} represent A, C, G and T in equal proportions. The chip has 4096 pads with a complete set of hexamer sequences. The affinity was determined by measuring dissociation of the RNase-ssDNA complexes with the temperature increasing from 0 degrees C to 50 degrees C in quasi-equilibrium conditions. RNase binase showed the highest sequence-specificity of binding to motifs 5'-NNG(A/T/C)GNN-3' with the order of preference: GAG > GTG > GCG. High specificity towards G(A/T/C)G triplets was also confirmed by measuring fluorescent anisotropy of complexes of binase with selected oligodeoxyribonucleotides in solution. The affinity of RNase binase to other 3-nt sequences was also ranked. These results demonstrate the applicability of the method and provide the ground for further investigations of nonenzymatic functions of RNases.
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Affiliation(s)
- Olga A Zasedateleva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russian Federation.
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39
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Affiliation(s)
- Joel R Tolman
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA.
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40
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Olsson MHM, Parson WW, Warshel A. Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. Chem Rev 2007; 106:1737-56. [PMID: 16683752 DOI: 10.1021/cr040427e] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mats H M Olsson
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA.
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41
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Igumenova TI, Brath U, Akke M, Palmer AG. Characterization of chemical exchange using residual dipolar coupling. J Am Chem Soc 2007; 129:13396-7. [PMID: 17929930 DOI: 10.1021/ja0761636] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tatyana I Igumenova
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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42
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Affiliation(s)
- David D Boehr
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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43
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Labeikovsky W, Eisenmesser EZ, Bosco DA, Kern D. Structure and dynamics of pin1 during catalysis by NMR. J Mol Biol 2007; 367:1370-81. [PMID: 17316687 PMCID: PMC2975599 DOI: 10.1016/j.jmb.2007.01.049] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Revised: 01/16/2007] [Accepted: 01/19/2007] [Indexed: 11/21/2022]
Abstract
The link between internal enzyme motions and catalysis is poorly understood. Correlated motions in the microsecond-to-millisecond timescale may be critical for enzyme function. We have characterized the backbone dynamics of the peptidylprolyl isomerase (Pin1) catalytic domain in the free state and during catalysis. Pin1 is a prolyl isomerase of the parvulin family and specifically catalyzes the isomerization of phosphorylated Ser/Thr-Pro peptide bonds. Pin1 has been shown to be essential for cell-cycle progression and to interact with the neuronal tau protein inhibiting its aggregation into fibrillar tangles as found in Alzheimer's disease. (15)N relaxation dispersion measurements performed on Pin1 during catalysis reveal conformational exchange processes in the microsecond timescale. A subset of active site residues undergo kinetically similar exchange processes even in the absence of a substrate, suggesting that this area is already "primed" for catalysis. Furthermore, structural data of the turning-over enzyme were obtained through inter- and intramolecular nuclear Overhauser enhancements. This analysis together with a characterization of the substrate concentration dependence of the conformational exchange allowed the distinguishing of regions of the enzyme active site that are affected primarily by substrate binding versus substrate isomerization. Together these data suggest a model for the reaction trajectory of Pin1 catalysis.
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Affiliation(s)
| | | | | | - Dorothee Kern
- To whom correspondence should be directed. (Dorothee Kern)
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44
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Olsson MH, Mavri J, Warshel A. Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems. Philos Trans R Soc Lond B Biol Sci 2006; 361:1417-32. [PMID: 16873128 PMCID: PMC1647313 DOI: 10.1098/rstb.2006.1880] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The idea that enzyme catalysis involves special factors such as coherent fluctuations, quantum mechanical tunnelling and non-equilibrium solvation (NES) effects has gained popularity in recent years. It has also been suggested that transition state theory (TST) cannot be used in studies of enzyme catalysis. The present work uses reliable state of the art simulation approaches to examine the above ideas. We start by demonstrating that we are able to simulate any of the present catalytic proposals using the empirical valence bond (EVB) potential energy surfaces, the dispersed polaron model and the quantized classical path (QCP) approach, as well as the approximate vibronic method. These approaches do not treat the catalytic effects by phenomenological treatments and thus can be considered as first principles approaches (at least their ability to compare enzymatic reaction to the corresponding solution reactions). This work will consider the lipoxygenase reaction, and to lesser extent other enzymes, for specific demonstration. It will be pointed out that our study of the lipoxygenase reaction reproduces the very large observed isotope effect and the observed rate constant while obtaining no catalytic contribution from nuclear quantum mechanical (NQM) effects. Furthermore, it will be clarified that our studies established that the NQM effect decreases rather than increases when the donor-acceptor distance is compressed. The consequences of these findings in terms of the temperature dependence of the kinetic isotope effect and in terms of different catalytic proposals will be discussed. This paper will also consider briefly the dynamical effects and conclude that such effects do not contribute in a significant way to enzyme catalysis. Furthermore, it will be pointed out that, in contrast to recent suggestions, NES effects are not dynamical effects and should therefore be part of the activation free energy rather than the transmission factor. In view of findings of the present work and our earlier works, it seems that TST provides a quantitative tool for studies of enzyme catalysis and that the key open questions are related to the nature of the factors that lead to transition state stabilization.
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Affiliation(s)
- Mats H.M Olsson
- Department of Chemistry, University of Southern California3620 South McClintock Avenue, Los Angeles, CA 90089-1062, USA
| | - Janez Mavri
- National Institute of Chemistry, Hajdrihova 19S1-1001 Ljubljana, Stovenia
| | - Arieh Warshel
- Department of Chemistry, University of Southern California3620 South McClintock Avenue, Los Angeles, CA 90089-1062, USA
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45
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Kovrigin EL, Kempf JG, Grey MJ, Loria JP. Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 180:93-104. [PMID: 16458551 DOI: 10.1016/j.jmr.2006.01.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 01/12/2006] [Accepted: 01/17/2006] [Indexed: 05/06/2023]
Abstract
This work examines the robustness of fitting of parameters describing conformational exchange (k(ex), p(a/b), and Deltaomega) processes from CPMG relaxation dispersion data. We have analyzed the equations describing conformational exchange processes for the intrinsic inter-dependence of their parameters that leads to the existence of multiple equivalent solutions, which equally satisfy the experimental data. We have used Monte-Carlo simulations and fitting to the synthetic data sets as well as the direct 3-D mapping of the parameter space of k(ex), p(a/b), and Deltaomega to quantitatively assess the degree of the parameter inter-dependence. The demonstrated high correlation between parameters can preclude accurate dynamics parameter estimation from NMR spin-relaxation data obtained at a single static magnetic field. The strong parameter inter-dependence can readily be overcome through acquisition of spin-relaxation data at more than one static magnetic field thereby allowing accurate assessment of conformational exchange properties.
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Affiliation(s)
- Evgenii L Kovrigin
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
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46
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Grey MJ, Tang Y, Alexov E, McKnight CJ, Raleigh DP, Palmer AG. Characterizing a Partially Folded Intermediate of the Villin Headpiece Domain Under Non-denaturing Conditions: Contribution of His41 to the pH-dependent Stability of the N-terminal Subdomain. J Mol Biol 2006; 355:1078-94. [PMID: 16332376 DOI: 10.1016/j.jmb.2005.11.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Revised: 11/01/2005] [Accepted: 11/02/2005] [Indexed: 12/29/2022]
Abstract
The contribution of interactions involving the imidazole ring of His41 to the pH-dependent stability of the villin headpiece (HP67) N-terminal subdomain has been investigated by nuclear magnetic resonance (NMR) spin relaxation. NMR-derived backbone N-H order parameters (S2) for wild-type (WT) HP67 and H41Y HP67 indicate that reduced conformational flexibility of the N-terminal subdomain in WT HP67 is due to intramolecular interactions with the His41 imidazole ring. These interactions, together with desolvation effects, contribute to significantly depress the pKa of the buried imidazole ring in the native state. 15N R1rho relaxation dispersion data indicate that WT HP67 populates a partially folded intermediate state that is 10.9 kJ mol(-1) higher in free energy than the native state under non-denaturing conditions at neutral pH. The partially folded intermediate is characterized as having an unfolded N-terminal subdomain while the C-terminal subdomain retains a native-like fold. Although the majority of the residues in the N-terminal subdomain sample a random-coil distribution of conformations, deviations of backbone amide 1H and 15N chemical shifts from canonical random-coil values for residues within 5A of the His41 imidazole ring indicate that a significant degree of residual structure is maintained in the partially folded ensemble. The pH-dependence of exchange broadening is consistent with a linear three-state exchange model whereby unfolding of the N-terminal subdomain is coupled to titration of His41 in the partially folded intermediate with a pKa,I=5.69+/-0.07. Although maintenance of residual interactions with the imidazole ring in the unfolded N-terminal subdomain appears to reduce pKa,I compared to model histidine compounds, protonation of His41 disrupts these interactions and reduces the difference in free energy between the native state and partially folded intermediate under acidic conditions. In addition, chemical shift changes for residues Lys70-Phe76 in the C-terminal subdomain suggest that the HP67 actin binding site is disrupted upon unfolding of the N-terminal subdomain, providing a potential mechanism for regulating the villin-dependent bundling of actin filaments.
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Affiliation(s)
- Michael J Grey
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
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47
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Ding Z, Lee GI, Liang X, Gallazzi F, Arunima A, Van Doren SR. PhosphoThr peptide binding globally rigidifies much of the FHA domain from Arabidopsis receptor kinase-associated protein phosphatase. Biochemistry 2005; 44:10119-34. [PMID: 16042389 PMCID: PMC2813517 DOI: 10.1021/bi050414a] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A net increase in the backbone rigidity of the kinase-interacting FHA domain (KI-FHA) from the Arabidopsis receptor kinase-associated protein phosphatase (KAPP) accompanies the binding of a phosphoThr peptide from its CLV1 receptor-like kinase partner, according to (15)N NMR relaxation at 11.7 and 14.1 T. All of the loops of free KI-FHA display evidence of nanosecond-scale motions. Many of these same residues have residual dipolar couplings that deviate from structural predictions. Binding of the CLV1 pT868 peptide seems to reduce nanosecond-scale fluctuations of all loops, including half of the residues of recognition loops. Residues important for affinity are found to be rigid, i.e., conserved residues and residues of the subsite for the key pT+3 peptide position. This behavior parallels SH2 and PTB domain recognition of pTyr peptides. PhosphoThr peptide binding increases KI-FHA backbone rigidity (S(2)) of three recognition loops, a loop nearby, seven strands from the beta-sandwich, and a distal loop. Compensating the trend of increased rigidity, binding enhances fast mobility at a few sites in four loops on the periphery of the recognition surface and in two loops on the far side of the beta-sandwich. Line broadening evidence of microsecond- to millisecond-scale fluctuations occurs across the six-stranded beta-sheet and nearby edges of the beta-sandwich; this forms a network connected by packing of interior side chains and H-bonding. A patch of the slowly fluctuating residues coincides with the site of segment-swapped dimerization in crystals of the FHA domain of human Chfr. Phosphopeptide binding introduces microsecond- to millisecond-scale fluctuations to more residues of the long 8/9 recognition loop of KI-FHA. The rigidity of this FHA domain appears to couple as a whole to pThr peptide binding.
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Affiliation(s)
| | | | - Xiangyang Liang
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri, 65211
| | - Fabio Gallazzi
- Molecular Biology Program, 125 Chemistry, 601 S. College Ave., University of Missouri, Columbia, Missouri, 65211 USA
| | - A. Arunima
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri, 65211
| | - Steven R. Van Doren
- To whom correspondence should be addressed, E-mail: , Phone: 1 (573) 882-5113, FAX: 1 (573) 884-4812
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48
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Naik MT, Suree N, Ilangovan U, Liew CK, Thieu W, Campbell DO, Clemens JJ, Jung ME, Clubb RT. Staphylococcus aureus Sortase A transpeptidase. Calcium promotes sorting signal binding by altering the mobility and structure of an active site loop. J Biol Chem 2005; 281:1817-26. [PMID: 16269411 DOI: 10.1074/jbc.m506123200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Many virulence factors in gram-positive bacteria are covalently anchored to the cell-wall peptidoglycan by sortase enzymes, a group of widely distributed cysteine transpeptidases. The Staphylococcus aureus Sortase A protein (SrtA) is the archetypal member of the Sortase family and is activated by Ca2+, an adaptation that may facilitate host colonization as elevated concentrations of this ion are encountered in human tissue. Here we show that a single Ca2+ ion bound to an ordered pocket on SrtA allosterically activates catalysis by modulating both the structure and dynamics of a large active site loop. Detailed nitrogen-15 relaxation measurements indicate that Ca2+ may facilitate the adaptive recognition of the substrate by inducing slow micro- to millisecond time-scale dynamics in the active site. Interestingly, relaxation compensated Carr-Purcell-Meiboom-Gill experiments suggest that the time scale of these motions is directly correlated with ion binding. The results of site-directed mutagenesis indicate that this motional coupling is mediated by the side chain of Glu-171, which is positioned within the beta6/beta7 loop and shown to contribute to Ca2+ binding. The available structural and dynamics data are compatible with a loop closure model of Ca2+ activation, in which the beta6/beta7 loop fluctuates between a binding competent closed form that is stabilized by Ca2+, and an open, highly flexible state that removes key substrate contacting residues from the active site.
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Affiliation(s)
- Mandar T Naik
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California 90095-1570, USA
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49
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Simon K, Xu J, Kim C, Skrynnikov NR. Estimating the accuracy of protein structures using residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2005; 33:83-93. [PMID: 16258827 DOI: 10.1007/s10858-005-2601-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Accepted: 08/05/2005] [Indexed: 05/05/2023]
Abstract
It has been commonly recognized that residual dipolar coupling data provide a measure of quality for protein structures. To quantify this observation, a database of 100 single-domain proteins has been compiled where each protein was represented by two independently solved structures. Backbone 1H-15N dipolar couplings were simulated for the target structures and then fitted to the model structures. The fits were characterized by an R-factor which was corrected for the effects of non-uniform distribution of dipolar vectors on a unit sphere. The analyses show that favorable R values virtually guarantee high accuracy of the model structure (where accuracy is defined as the backbone coordinate rms deviation). On the other hand, unfavorable R values do not necessarily suggest low accuracy. Based on the simulated data, a simple empirical formula is proposed to estimate the accuracy of protein structures. The method is illustrated with a number of examples, including PDZ2 domain of human phosphatase hPTP1E.
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Affiliation(s)
- Katya Simon
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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50
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Yip GNB, Zuiderweg ERP. Improvement of duty-cycle heating compensation in NMR spin relaxation experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2005; 176:171-8. [PMID: 16009587 DOI: 10.1016/j.jmr.2005.06.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Revised: 05/27/2005] [Accepted: 06/03/2005] [Indexed: 05/03/2023]
Abstract
To reliably measure NMR relaxation properties of macromolecules is a prerequisite for precise experiments that identify subtle variations in relaxation rates, as required for the determination of rotational diffusion anisotropy, CSA tensor determination, advanced motional modeling or entropy difference estimations. An underlying problem with current NMR relaxation measurement protocols is maintaining constant sample temperature throughout the execution of the relaxation series especially when rapid data acquisition is required. Here, it is proposed to use a combination of a heating compensation and a proton saturation sequence at the beginning of the NMR relaxation pulse scheme. This simple extension allows reproducible, robust and rapid acquisition of NMR spin relaxation data sets. The method is verified with (15)N spin relaxation measurements for human ubiquitin.
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Affiliation(s)
- Grover N B Yip
- Department of Chemistry, University of Michigan, 930 N. University Ave., MI 48109-1055, USA
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