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Kobayakawa T, Tsuji K, Tamamura H. Design, synthesis and evaluation of bioactivity of peptidomimetics based on chloroalkene dipeptide isosteres. Bioorg Med Chem 2024; 110:117811. [PMID: 38959684 DOI: 10.1016/j.bmc.2024.117811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 07/05/2024]
Abstract
Ample biologically active peptides have been found, identified and modified for use in drug discovery to date. However, several factors, such as low metabolic stability due to proteolysis and non-specific interactions with multiple off-target molecules, might limit the therapeutic use of peptides. To enhance the stability and/or bioactivity of peptides, the development of "peptidomimetics," which mimick peptide molecules, is considered to be idealistic. Hence, chloroalkene dipeptide isosteres (CADIs) was designed, and their synthetic methods have been developed by us. Briefly, in a CADI an amide bond in peptides is replaced with a chloroalkene structure. CADIs might be superior mimetics of amide bonds because the Van der Waals radii (VDR) and the electronegativity value of a chlorine atom are close to those of the replaced oxygen atom. By a developed method of the "liner synthesis", N-tert-butylsulfonyl protected CADIs can be synthesized via a key reaction involving diastereoselective allylic alkylation using organocopper reagents. On the other hand, by a developed method of the "convergent synthesis", N-fluorenylmethoxycarbonyl (Fmoc)-protected carboxylic acids can be also constructed based on N- and C-terminal analogues from corresponding amino acid starting materials via an Evans syn aldol reaction and the Ichikawa allylcyanate rearrangement reaction involving a [3.3] sigmatropic rearrangement. Notably, CADIs can also be applied for Fmoc-based solid-phase peptide synthesis and therefore introduced into bioactive peptides including as the Arg-Gly-Asp (RGD) peptide and the amyloid β fragment Lys-Leu-Val-Phe-Phe (KLVFF) peptide, which are correlated with cell attachment and Alzheimer's disease (AD), respectively. These CADI-containing peptidomimetics stabilized the conformation and enhanced the potency of the cyclic RGD peptide and the cyclic KLVFF peptide.
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Affiliation(s)
- Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Kohei Tsuji
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hirokazu Tamamura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
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2
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Born A, Soetbeer J, Henen MA, Breitgoff F, Polyhach Y, Jeschke G, Vögeli B. Ligand-specific conformational change drives interdomain allostery in Pin1. Nat Commun 2022; 13:4546. [PMID: 35927276 PMCID: PMC9352728 DOI: 10.1038/s41467-022-32340-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Pin1 is a two-domain cell regulator that isomerizes peptidyl-prolines. The catalytic domain (PPIase) and the other ligand-binding domain (WW) sample extended and compact conformations. Ligand binding changes the equilibrium of the interdomain conformations, but the conformational changes that lead to the altered domain sampling were unknown. Prior evidence has supported an interdomain allosteric mechanism. We recently introduced a magnetic resonance-based protocol that allowed us to determine the coupling of intra- and interdomain structural sampling in apo Pin1. Here, we describe ligand-specific conformational changes that occur upon binding of pCDC25c and FFpSPR. pCDC25c binding doubles the population of the extended states compared to the virtually identical populations of the apo and FFpSPR-bound forms. pCDC25c binding to the WW domain triggers conformational changes to propagate via the interdomain interface to the catalytic site, while FFpSPR binding displaces a helix in the PPIase that leads to repositioning of the PPIase catalytic loop.
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Affiliation(s)
- Alexandra Born
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO, USA
| | - Janne Soetbeer
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Morkos A Henen
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO, USA.,Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Frauke Breitgoff
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Beat Vögeli
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO, USA.
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3
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Dubey A, Takeuchi K, Reibarkh M, Arthanari H. The role of NMR in leveraging dynamics and entropy in drug design. JOURNAL OF BIOMOLECULAR NMR 2020; 74:479-498. [PMID: 32720098 PMCID: PMC7686249 DOI: 10.1007/s10858-020-00335-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/11/2020] [Indexed: 05/03/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has contributed to structure-based drug development (SBDD) in a unique way compared to the other biophysical methods. The potency of a ligand binding to a protein is dictated by the binding free energy, which is an intricate interplay between entropy and enthalpy. In addition to providing the atomic resolution structural information, NMR can help to identify protein-ligand interactions that potentially contribute to the enthalpic component of the free energy. NMR can also illuminate dynamic aspects of the interaction, which correspond to the entropic term of the free energy. The ability of NMR to access both terms in the free energy equation stems from the suite of experiments developed to shed light on various aspects that contribute to both entropy and enthalpy, deepening our understanding of the biological function of macromolecules and assisting to target them in physiological conditions. Here we provide a brief account of the contribution of NMR to SBDD, highlighting hallmark examples and discussing the challenges that demand further method development. In the era of integrated biology, the unique ability of NMR to directly ascertain structural and dynamical aspects of macromolecule and monitor changes in these properties upon engaging a ligand can be combined with computational and other structural and biophysical methods to provide a more complete picture of the energetics of drug engagement with the target. Such efforts can be used to engineer better drugs.
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Affiliation(s)
- Abhinav Dubey
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute & Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan.
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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4
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Stoffel S, Zhang QW, Li DH, Smith BD, Peng JW. NMR Relaxation Dispersion Reveals Macrocycle Breathing Dynamics in a Cyclodextrin-based Rotaxane. J Am Chem Soc 2020; 142:7413-7424. [PMID: 32212648 DOI: 10.1021/jacs.9b12524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A distinctive feature of mechanically interlocked molecules (MIMs) is the relative motion between the mechanically bonded components, and often it is the functional basis for artificial molecular machines and new functional materials. Optimization of machine or materials performance requires knowledge of the underlying atomic-level mechanisms that control the motion. The field of biomolecular NMR spectroscopy has developed a diverse set of pulse schemes that can characterize molecular dynamics over a broad time scale, but these techniques have not yet been used to characterize the motion within MIMs. This study reports the first observation of NMR relaxation dispersion related to MIM motion. The rotary (pirouette) motion of α-cyclodextrin (αCD) wheels was characterized in a complementary pair of rotaxanes with pirouetting switched ON or OFF. 13C and 1H NMR relaxation dispersion measurements reveal previously unknown exchange dynamics for the αCD wheels in the pirouette-ON rotaxane with a rate constant of 2200 s-1 at 298 K and an activation barrier of ΔF‡ = 43 ± 3 kJ/mol. The exchange dynamics disappear in the pirouette-OFF rotaxane, demonstrating their switchable nature. The 13C and 1H sites exhibiting relaxation dispersion suggest that the exchange involves "macrocycle breathing", in which the αCD wheel fluctuates between a contracted or expanded state, the latter enabling diffusive rotary motion about the axle. The substantial insight from these NMR relaxation dispersion methods suggests similar dynamic NMR methods can illuminate the fast time scale (microsecond to millisecond) mechanisms of intercomponent motion in a wide range of MIMs.
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Affiliation(s)
| | - Qi-Wei Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
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5
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Spotlight on the Ballet of Proteins: The Structural Dynamic Properties of Proteins Illuminated by Solution NMR. Int J Mol Sci 2020; 21:ijms21051829. [PMID: 32155847 PMCID: PMC7084655 DOI: 10.3390/ijms21051829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 12/22/2022] Open
Abstract
Solution NMR spectroscopy is a unique and powerful technique that has the ability to directly connect the structural dynamics of proteins in physiological conditions to their activity and function. Here, we summarize recent studies in which solution NMR contributed to the discovery of relationships between key dynamic properties of proteins and functional mechanisms in important biological systems. The capacity of NMR to quantify the dynamics of proteins over a range of time scales and to detect lowly populated protein conformations plays a critical role in its power to unveil functional protein dynamics. This analysis of dynamics is not only important for the understanding of biological function, but also in the design of specific ligands for pharmacologically important proteins. Thus, the dynamic view of structure provided by NMR is of importance in both basic and applied biology.
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6
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Born A, Henen MA, Vögeli B. Activity and Affinity of Pin1 Variants. MOLECULES (BASEL, SWITZERLAND) 2019; 25:molecules25010036. [PMID: 31861908 PMCID: PMC6983177 DOI: 10.3390/molecules25010036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/07/2019] [Accepted: 12/18/2019] [Indexed: 12/14/2022]
Abstract
Pin1 is a peptidyl-prolyl isomerase responsible for isomerizing phosphorylated S/T-P motifs. Pin1 has two domains that each have a distinct ligand binding site, but only its PPIase domain has catalytic activity. Vast evidence supports interdomain allostery of Pin1, with binding of a ligand to its regulatory WW domain impacting activity in the PPIase domain. Many diverse studies have made mutations in Pin1 in order to elucidate interactions that are responsible for ligand binding, isomerase activity, and interdomain allostery. Here, we summarize these mutations and their impact on Pin1′s structure and function.
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Affiliation(s)
- Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.)
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.)
- Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.)
- Correspondence: ; Tel.: +1-303-724-1627
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7
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Enhanced dynamics of conformationally heterogeneous T7 bacteriophage lysozyme native state attenuates its stability and activity. Biochem J 2019; 476:613-628. [DOI: 10.1042/bcj20180703] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/17/2019] [Accepted: 01/25/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Proteins are dynamic in nature and exist in a set of equilibrium conformations on various timescale motions. The flexibility of proteins governs various biological functions, and therefore elucidation of such functional dynamics is essential. In this context, we have studied the structure–dynamics–stability–activity relationship of bacteriophage T7 lysozyme/endolysin (T7L) native-state ensemble in the pH range of 6–8. Our studies established that T7L native state is conformationally heterogeneous, as several residues of its C-terminal half are present in two conformations (major and minor) in the slow exchange time scale of nuclear magnetic resonance (NMR). Structural and dynamic studies suggested that the residues belonging to minor conformations do exhibit native-like structural and dynamic features. Furthermore, the NMR relaxation experiments unraveled that the native state is highly dynamic and the dynamic behavior is regulated by the pH, as the pH 6 conformation exhibited enhanced dynamics compared with pH 7 and 8. The stability measurements and cell-based activity studies on T7L indicated that the native protein at pH 6 is ∼2 kcal less stable and is ∼50% less active than those of pH 7 and 8. A comprehensive analysis of the T7L active site, unfolding initiation sites and the residues with altered dynamics outlined that the attenuation of stability and activity is a resultant of its enhanced dynamic properties, which, in turn, can be attributed to the protonation/deprotonation of its partially buried His residues. Our study on T7L structure–dynamics–activity paradigm could assist in engineering novel amidase-based endolysins with enhanced activity and stability over a broad pH range.
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Jinasena D, Simmons R, Gyamfi H, Fitzkee NC. Molecular Mechanism of the Pin1-Histone H1 Interaction. Biochemistry 2019; 58:788-798. [PMID: 30507159 DOI: 10.1021/acs.biochem.8b01036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Pin1 is an essential peptidyl-prolyl isomerase (PPIase) that catalyzes cis-trans prolyl isomerization in proteins containing pSer/Thr-Pro motifs. It has an N-terminal WW domain that targets these motifs and a C-terminal PPIase domain that catalyzes isomerization. Recently, Pin1 was shown to modify the conformation of phosphorylated histone H1 and stabilize the chromatin-H1 interaction by increasing its residence time. This Pin1-histone H1 interaction plays a key role in pathogen response, in infection, and in cell cycle control; therefore, anti-Pin1 therapeutics are an important focus for treating infections as well as cancer. Each of the H1 histones (H1.0-H1.5) contains several potential Pin1 recognition pSer/pThr-Pro motifs. To understand the Pin1-histone H1 interaction fully, we investigated how both the isolated WW domain and full-length Pin1 interact with three H1 histone substrate peptide sequences that were previously identified as important binding partners (H1.1, H1.4, and H1.5). NMR spectroscopy was used to measure the binding affinities and the interdomain dynamics upon binding to these sequences. We observed different KD values depending on the histone binding site, suggesting that energetics play a role in guiding the Pin1-histone interaction. While interdomain interactions vary between the peptides, we find no evidence for allosteric activation for the histone H1 substrates.
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Affiliation(s)
- Dinusha Jinasena
- Department of Chemistry , Mississippi State University , Mississippi State , Mississippi 39762 , United States
| | - Robert Simmons
- Department of Chemistry , Mississippi State University , Mississippi State , Mississippi 39762 , United States
| | - Hawa Gyamfi
- Department of Chemistry , University of Waterloo , Waterloo , Ontario , Ontario N2l 3G1 , Canada
| | - Nicholas C Fitzkee
- Department of Chemistry , Mississippi State University , Mississippi State , Mississippi 39762 , United States
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9
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Pernas M, Blanco B, Lence E, Thompson P, Hawkins AR, González-Bello C. Synthesis of rigidified shikimic acid derivatives by ring-closing metathesis to imprint inhibitor efficacy against shikimate kinase enzyme. Org Chem Front 2019. [DOI: 10.1039/c9qo00562e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rigidification of the high-energy conformation of shikimic acid was used to enhance inhibitor efficacy against shikimate kinase enzyme, an attractive target for antibiotic drug discovery.
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Affiliation(s)
- Marina Pernas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Beatriz Blanco
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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10
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Gohda K. Computational conformational analysis of α-thrombin inhibitors possessing distinct scaffolds in aqueous solution and on Ala-sheet. J Mol Graph Model 2018; 87:165-171. [PMID: 30551079 DOI: 10.1016/j.jmgm.2018.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 11/10/2018] [Accepted: 11/29/2018] [Indexed: 11/19/2022]
Abstract
Recent computational simulations on protein-ligand binding/unbinding have precisely been uncovering the ligand-binding process at the atomic level. In the process, the non-specific binding of ligands to the target site is suggested to occur before binding to the target. We in this study analyzed the conformations of ligands under the non-specific binding on a protein surface to figure out the differences in the conformational characteristics in aqueous solution using the 55-ns molecular dynamic simulation. As for the protein surface, we constructed an artificial β-sheet, composed of poly-alanine residues (Ala-sheet). For the ligands, the four α-thrombin inhibitors possessing two scaffolds with distinct hydrophobicity profiles were used. During the simulation, all the inhibitors kept interaction with Ala-sheet and had the limited conformational fluctuations compared with in aqueous solution. The representative conformations obtained from the cluster analysis showed that two of hydrophobic inhibitors adopted the extended conformations in aqueous solution and also on Ala-sheet. For the other two hydrophilic inhibitors, the conformations in aqueous solution adopted the bent conformation with two terminal hydrophobic rings closely packed. On Ala-sheet, contrarily, the two hydrophobic rings were open and took the extended conformations, which were placed on the sheet as a foothold. The charged moieties in the hydrophilic inhibitors were protruded into aqueous environment with the extended conformation. The conformational characteristics of the inhibitors in aqueous solution and Ala-sheet varied likely by chemical features or structures of the inhibitors, but each was considered to be physicochemically reasonable.
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Affiliation(s)
- Keigo Gohda
- Computer-aided Molecular Modeling Research Center, Kansai (CAMM-Kansai), 3-32-302, Tsuto-Otsuka, Nishinomiya, 663-8241, Japan.
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11
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Khirich G, Holliday MJ, Lin JC, Nandy A. Measurement and Characterization of Hydrogen-Deuterium Exchange Chemistry Using Relaxation Dispersion NMR Spectroscopy. J Phys Chem B 2018; 122:2368-2378. [PMID: 29376350 DOI: 10.1021/acs.jpcb.7b10849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One-dimensional heteronuclear relaxation dispersion NMR spectroscopy at 13C natural abundance successfully characterized the dynamics of the hydrogen-deuterium exchange reaction occurring at the Nε position in l-arginine by monitoring Cδ in varying amounts of D2O. A small equilibrium isotope effect was observed and quantified, corresponding to ΔG = -0.14 kcal mol-1. A bimolecular rate constant of kD = 5.1 × 109 s-1 M-1 was determined from the pH*-dependence of kex (where pH* is the direct electrode reading of pH in 10% D2O and kex is the nuclear spin exchange rate constant), consistent with diffusion-controlled kinetics. The measurement of ΔG serves to bridge the millisecond time scale lifetimes of the detectable positively charged arginine species with the nanosecond time scale lifetime of the nonobservable low-populated neutral arginine intermediate species, thus allowing for characterization of the equilibrium lifetimes of the various arginine species in solution as a function of fractional solvent deuterium content. Despite the system being in fast exchange on the chemical shift time scale, the magnitude of the secondary isotope shift due to the exchange reaction at Nε was accurately measured to be 0.12 ppm directly from curve-fitting D2O-dependent dispersion data collected at a single static field strength. These results indicate that relaxation dispersion NMR spectroscopy is a robust and general method for studying base-catalyzed hydrogen-deuterium exchange chemistry at equilibrium.
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Affiliation(s)
- Gennady Khirich
- Protein Analytical Chemistry, ‡Early Discovery Biochemistry, and §Late Stage Pharmaceutical Development, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Michael J Holliday
- Protein Analytical Chemistry, ‡Early Discovery Biochemistry, and §Late Stage Pharmaceutical Development, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Jasper C Lin
- Protein Analytical Chemistry, ‡Early Discovery Biochemistry, and §Late Stage Pharmaceutical Development, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Aditya Nandy
- Protein Analytical Chemistry, ‡Early Discovery Biochemistry, and §Late Stage Pharmaceutical Development, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
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12
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Trigo-Mouriño P, Griesinger C, Lee D. Label-free NMR-based dissociation kinetics determination. JOURNAL OF BIOMOLECULAR NMR 2017; 69:229-235. [PMID: 29143948 DOI: 10.1007/s10858-017-0150-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/03/2017] [Indexed: 06/07/2023]
Abstract
Understanding the dissociation of molecules is the basis to modulate interactions of biomedical interest. Optimizing drugs for dissociation rates is found to be important for their efficacy, selectivity, and safety. Here, we show an application of the high-power relaxation dispersion (RD) method to the determination of the dissociation rates of weak binding ligands from receptors. The experiment probes proton RD on the ligand and, therefore, avoids the need for any isotopic labeling. The large ligand excess eases the detection significantly. Importantly, the use of large spin-lock fields allows the detection of faster dissociation rates than other relaxation approaches. Moreover, this experimental approach allows to access directly the off-rate of the binding process without the need for analyzing a series of samples with increasing ligand saturation. The validity of the method is shown with small molecule interactions using two macromolecules, bovine serum albumin and tubulin heterodimers.
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Affiliation(s)
- Pablo Trigo-Mouriño
- 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
| | - Donghan Lee
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, 40202, USA.
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Kobayakawa T, Tamamura H. Efficient synthesis of Xaa-Gly type (Z)-chloroalkene dipeptide isosteres via organocuprate mediated reduction. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.06.080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Molecular Mechanism of Pin1–Tau Recognition and Catalysis. J Mol Biol 2016; 428:1760-75. [DOI: 10.1016/j.jmb.2016.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 02/06/2023]
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15
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Foloppe N, Chen IJ. Towards understanding the unbound state of drug compounds: Implications for the intramolecular reorganization energy upon binding. Bioorg Med Chem 2016; 24:2159-89. [PMID: 27061672 DOI: 10.1016/j.bmc.2016.03.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 01/24/2023]
Abstract
There has been an explosion of structural information for pharmaceutical compounds bound to biological targets, but the conformations and dynamics of compounds free in solution are poorly characterized, if at all. Yet, knowledge of the unbound state is essential to understand the fundamentals of molecular recognition, including the much debated conformational intramolecular reorganization energy of a compound upon binding (ΔEReorg). Also, dependable observation of the unbound compounds is important for ligand-based drug discovery, e.g. with pharmacophore modelling. Here, these questions are addressed with long (⩾0.5μs) state-of-the-art molecular dynamics (MD) simulations of 26 compounds (including 7 approved drugs) unbound in explicit solvent. These compounds were selected to be chemically diverse, with a range of flexibility, and good quality bioactive X-ray structures. The MD-simulated free compounds are compared to their bioactive structure and conformers generated with ad hoc sampling in vacuo or with implicit generalized Born (GB) aqueous solvation models. The GB conformational models clearly depart from those obtained in explicit solvent, and suffer from conformational collapse almost as severe as in vacuo. Thus, the global energy minima in vacuo or with GB are not suitable representations of the unbound state, which can instead be extensively sampled by MD simulations. Many, but not all, MD-simulated compounds displayed some structural similarity to their bioactive structure, supporting the notion of conformational pre-organization for binding. The ligand-protein complexes were also simulated in explicit solvent, to estimate ΔEReorg as an enthalpic difference ΔHReorg between the intramolecular energies in the bound and unbound states. This fresh approach yielded ΔHReorg values⩽6kcal/mol for 18 out of 26 compounds. For three particularly polar compounds 15⩽ΔHReorg⩽20kcal/mol, supporting the notion that ΔHReorg can be substantial. Those large ΔHReorg values correspond to a redistribution of electrostatic interactions upon binding. Overall, the study illustrates how MD simulations offer a promising avenue to characterize the unbound state of medicinal compounds.
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Affiliation(s)
- Nicolas Foloppe
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, UK.
| | - I-Jen Chen
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, UK.
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16
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Vögeli B, Bibow S, Chi CN. Enzyme Selectivity Fine-Tuned through Dynamic Control of a Loop. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry; ETH Zurich, ETH-Hönggerberg; CH-8093 Zürich Switzerland
| | - Stefan Bibow
- Laboratory of Physical Chemistry; ETH Zurich, ETH-Hönggerberg; CH-8093 Zürich Switzerland
| | - Celestine N. Chi
- Laboratory of Physical Chemistry; ETH Zurich, ETH-Hönggerberg; CH-8093 Zürich Switzerland
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17
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Vögeli B, Bibow S, Chi CN. Enzyme Selectivity Fine-Tuned through Dynamic Control of a Loop. Angew Chem Int Ed Engl 2016; 55:3096-100. [PMID: 26822756 PMCID: PMC4760428 DOI: 10.1002/anie.201511476] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Indexed: 12/14/2022]
Abstract
Allostery has been revealed as an essential property of all proteins. For enzymes, shifting of the structural equilibrium distribution at one site can have substantial impacts on protein dynamics and selectivity. Promising sites of remotely shifting such a distribution by changing the dynamics would be at flexible loops because relatively large changes may be achieved with minimal modification of the protein. A ligand-selective change of binding affinity to the active site of cyclophilin is presented involving tuning of the dynamics of a highly flexible loop. Binding affinity is increased upon substitution of double Gly to Ala at the hinge regions of the loop. Quenching of the motional amplitudes of the loop slightly rearranges the active site. In particular, key residues for binding Phe60 and His126 adopt a more fixed orientation in the bound protein. Our system may serve as a model system for studying the effects of various time scales of loop motion on protein function tuned by mutations.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093, Zürich, Switzerland
| | - Stefan Bibow
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093, Zürich, Switzerland
| | - Celestine N Chi
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, CH-8093, Zürich, Switzerland.
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18
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Namanja AT, Wang J, Buettner R, Colson L, Chen Y. Allosteric Communication across STAT3 Domains Associated with STAT3 Function and Disease-Causing Mutation. J Mol Biol 2016; 428:579-589. [PMID: 26774853 DOI: 10.1016/j.jmb.2016.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 01/03/2016] [Accepted: 01/06/2016] [Indexed: 01/10/2023]
Abstract
STAT3 is a member of STAT (signal transducer and activator of transcription) transcription activators. Aberration in STAT3 activity due to constitutive activation or mutations leads to diseases such as cancer and hyper-immunoglobulin E syndrome (HIES). STAT3 contains several structured domains including the Src homology 2 domain (SH2), linker domain (LD), DNA-binding domain (DBD) and the coiled-coil domain. Here we report the discovery of inter-domain allosteric communications in STAT3 from studies using nuclear magnetic resonance (NMR) and other methods. We found that pTyr-peptide interactions with SH2 cause structural and dynamics changes in LD and DBD. The inter-domain allosteric effect is likely mediated by the flexibility in the hydrophobic core. In addition, a mutation in LD found in HIES (I568F) induces NMR chemical shift perturbation in SH2, DBD and the coiled-coil domain, suggesting conformational changes in these domains. Consistent with conformational changes in SH2, the I568F mutant reduces SH2's binding affinity to a pTyr-containing peptide. This study provides an example of dynamics-dependent allosteric effects, and due to the structural conservation of the STAT family of proteins, the inter-domain allosteric communication observed in STAT3 likely occurs in other STATs.
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Affiliation(s)
- Andrew T Namanja
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Jianghai Wang
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Ralf Buettner
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Loren Colson
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Yuan Chen
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
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19
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Mayfield JE, Fan S, Wei S, Zhang M, Li B, Ellington AD, Etzkorn FA, Zhang YJ. Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II. ACS Chem Biol 2015; 10:2405-14. [PMID: 26332362 DOI: 10.1021/acschembio.5b00296] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Proline isomerization greatly impacts biological signaling but is subtle and difficult to detect in proteins. We characterize this poorly understood regulatory mechanism for RNA polymerase II carboxyl terminal domain (CTD) phosphorylation state using novel, direct, and quantitative chemical tools. We determine the proline isomeric preference of three CTD phosphatases: Ssu72 as cis-proline specific, Scp1 and Fcp1 as strongly trans-preferred. Due to this inherent characteristic, these phosphatases respond differently to enzymes that catalyze the isomerization of proline, like Ess1/Pin1. We demonstrate that this selective regulation of RNA polymerase II phosphorylation state exists within human cells, consistent with in vitro assays. These results support a model in which, instead of a global enhancement of downstream enzymatic activities, proline isomerases selectively boost the activity of a subset of CTD regulatory factors specific for cis-proline. This leads to diversified phosphorylation states of CTD in vitro and in cells. We provide the chemical tools to investigate proline isomerization and its ability to selectively enhance signaling in transcription and other biological contexts.
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Affiliation(s)
- Joshua E. Mayfield
- Department
of Molecular Biosciences and Institute for Cellular and Molecular
Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Shuang Fan
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Shuo Wei
- 1 Cancer
Research Institute, Beth Israel Deaconess Cancer Center, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department
of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Mengmeng Zhang
- Department
of Molecular Biosciences and Institute for Cellular and Molecular
Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Bing Li
- Department
of Molecular Biology, UT Southwestern Medical Center, 5323 Harry Hines
Boulevard, Dallas, Texas 75390, United States
| | - Andrew D. Ellington
- Department
of Molecular Biosciences and Institute for Cellular and Molecular
Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Felicia A. Etzkorn
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Yan Jessie Zhang
- Department
of Molecular Biosciences and Institute for Cellular and Molecular
Biology, University of Texas at Austin, Austin, Texas 78712, United States
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20
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Stereochemical Control in the Still-Wittig Rearrangement Synthesis of Cyclohexyl (Z)-Alkene Inhibitors of Pin1. PLoS One 2015; 10:e0139543. [PMID: 26445009 PMCID: PMC4596862 DOI: 10.1371/journal.pone.0139543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/14/2015] [Indexed: 11/29/2022] Open
Abstract
Three stereoisomeric inhibitors of Pin1: (2R,5S)-, (2S,5R)- and (2S,5S)-Ac–pSer–Ψ[(Z)CH = C]–pipecolyl(Pip)–2-(2-naphthyl)ethylamine 1, that mimic L-pSer–D-Pro, D-pSer–L-Pro, and D-pSer–D-Pro amides respectively, were synthesized by a 13-step route. The newly formed stereogenic centers in the pipecolyl ring were introduced by Luche reduction, followed by stereospecific [2,3]-Still-Wittig rearrangement. The (Z)- to (E)-alkene ratio in the rearrangements were consistently 5.5 to 1. The stereochemistry at the original Ser α-carbon controlled the stereochemistry of the Luche reduction, but it did not affect the stereochemical outcome of the rearrangement, which consistently gave the (Z)-alkene. The epimerized by-product, (2S,5S)-10, resulting from the work-up after Na/NH3 debenzylation of (2S,5R)-9, was carried on to the (2S,5S)-1 isomer. Compound (2S,5S)-10 was resynthesized from the Luche reduction by-product, (2R,3R)-3, and the stereochemistry was confirmed by comparison of the optical rotations. The IC50 values for (2R,5S)-1, (2S,5R)-1 and (2S,5S)-1 Pin1 inhibition were: 52, 85, and 140 μM, respectively.
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21
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Huang KY, Horng JC. Modulating the Affinities of Phosphopeptides for the Human Pin1 WW Domain Using 4-Substituted Proline Derivatives. Biochemistry 2015; 54:6186-94. [DOI: 10.1021/acs.biochem.5b00880] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kuei-Yen Huang
- Department
of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC
- Frontier
Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC
| | - Jia-Cherng Horng
- Department
of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC
- Frontier
Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC
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22
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Kobayakawa T, Narumi T, Tamamura H. Remote Stereoinduction in the Organocuprate-Mediated Allylic Alkylation of Allylic gem-Dichlorides: Highly Diastereoselective Synthesis of (Z)-Chloroalkene Dipeptide Isosteres. Org Lett 2015; 17:2302-5. [DOI: 10.1021/acs.orglett.5b00611] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takuya Kobayakawa
- Institute
of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Tetsuo Narumi
- Institute
of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan
- Department
of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University,
Hamamatsu, Shizuoka, 432-8561, Japan
| | - Hirokazu Tamamura
- Institute
of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan
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23
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Abstract
Signaling proteins often sequester complementary functional sites in separate domains. How do the different domains communicate with one another? An attractive system to address this question is the mitotic regulator, human Pin1 (Lu et al. 1996). Pin-1 consists of two tethered domains: a WW domain for substrate binding, and a catalytic domain for peptidyl-prolyl isomerase (PPIase) activity. Pin1 accelerates the cis-trans isomerization of phospho-Ser/Thr-Pro (pS/T-P) motifs within proteins regulating the cell cycle and neuronal development. The early x-ray (Ranganathan et al. 1997; Verdecia et al. 2000) and solution NMR studies (Bayer et al. 2003; Jacobs et al. 2003) of Pin1 indicated inter- and intradomain motion. We became interested in exploring how such motions might affect interdomain communication, using NMR. Our accumulated results indicate substrate binding to Pin1 WW domain changes the intra/inter domain mobility, thereby altering substrate activity in the distal PPIase domain catalytic site. Thus, Pin1 shows evidence of dynamic allostery, in the sense of Cooper and Dryden (Cooper and Dryden 1984). We highlight our results supporting this conclusion, and summarize them via a simple speculative model of conformational selection.
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24
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Etzkorn FA, Zhao S. Stereospecific phosphorylation by the central mitotic kinase Cdk1-cyclin B. ACS Chem Biol 2015; 10:952-6. [PMID: 25603287 DOI: 10.1021/cb500815b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The cis vs trans conformation, or shape, of phosphoserine-proline (pSer-Pro), a prevalent motif in cell cycle proteins, may play a significant role in regulating mitosis. We demonstrate that Cdk1-cyclin B, the central mitotic kinase, is specific for the trans conformation, not cis, of synthetic, locked Ser-Pro 11-residue peptide substrates, using LC-MSMS detection and sequencing of phosphorylated products. This substrate stereospecificity may contribute an additional level of mitotic regulation.
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Affiliation(s)
- Felicia A. Etzkorn
- Virginia Tech, Department
of Chemistry, Blacksburg, Virginia 24061, United States
| | - Song Zhao
- Virginia Tech, Department
of Chemistry, Blacksburg, Virginia 24061, United States
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25
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Abstract
![]()
Biological activities of enzymes, including
regulation or coordination of mechanistic stages preceding or following
the chemical step, may depend upon kinetic or equilibrium changes
in protein conformations. Exchange of more open or flexible conformational
states with more closed or constrained states can influence inhibition,
allosteric regulation, substrate recognition, formation of the Michaelis
complex, side reactions, and product release. NMR spectroscopy has
long been applied to the study of conformational dynamic processes
in enzymes because these phenomena can be characterized over multiple
time scales with atomic site resolution. Laboratory-frame spin-relaxation
measurements, sensitive to reorientational motions on picosecond–nanosecond
time scales, and rotating-frame relaxation-dispersion measurements,
sensitive to chemical exchange processes on microsecond–millisecond
time scales, provide information on both conformational distributions
and kinetics. This Account reviews NMR spin relaxation studies of
the enzymes ribonuclease HI from mesophilic (Escherichia coli) and thermophilic (Thermus thermophilus) bacteria, E. coli AlkB, and Saccharomyces cerevisiae triosephosphate isomerase to illustrate the contributions of conformational
flexibility and dynamics to diverse steps in enzyme mechanism. Spin relaxation measurements and molecular dynamics (MD) simulations
of the bacterial ribonuclease H enzymes show that the handle region,
one of three loop regions that interact with substrates, interconverts
between two conformations. Comparison of these conformations with
the structure of the complex between Homo sapiens ribonuclease H and a DNA:RNA substrate suggests that the more closed
state is inhibitory to binding. The large population of the closed
conformation in T. thermophilus ribonuclease H contributes
to the increased Michaelis constant compared with the E. coli enzyme. NMR spin relaxation and fluorescence spectroscopy have characterized
a conformational transition in AlkB between an open state, in which
the side chains of methionine residues in the active site are disordered,
and a closed state, in which these residues are ordered. The open
state is highly populated in the AlkB/Zn(II) complex, and the closed
state is highly populated in the AlkB/Zn(II)/2OG/substrate complex,
in which 2OG is the 2-oxoglutarate cosubstrate and the substrate is
a methylated DNA oligonucleotide. The equilibrium is shifted to approximately
equal populations of the two conformations in the AlkB/Zn(II)/2OG
complex. The conformational shift induced by 2OG ensures that 2OG
binds to AlkB/Zn(II) prior to the substrate. In addition, the opening
rate of the closed conformation limits premature release of substrate,
preventing generation of toxic side products by reaction with water.
Closure of active site loop 6 in triosephosphate isomerase is critical
for forming the Michaelis complex, but reopening of the loop after
the reaction is (partially) rate limiting. NMR spin relaxation and
MD simulations of triosephosphate isomerase in complex with glycerol
3-phosphate demonstrate that closure of loop 6 is a highly correlated
rigid-body motion. The MD simulations also indicate that motions of
Gly173 in the most flexible region of loop 6 contribute to opening
of the active site loop for product release. Considered together,
these three enzyme systems illustrate the power of NMR spin relaxation
investigations in providing global insights into the role of conformational
dynamic processes in the mechanisms of enzymes from initial activation
to final product release.
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Affiliation(s)
- Arthur G. Palmer
- Department of Biochemistry and
Molecular Biophysics, Columbia University, 701 West 168th Street, New York, New York 10032, United States
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26
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Moschen T, Wunderlich CH, Spitzer R, Levic J, Micura R, Tollinger M, Kreutz C. Ligand-detected relaxation dispersion NMR spectroscopy: dynamics of preQ1-RNA binding. Angew Chem Int Ed Engl 2015; 54:560-3. [PMID: 25403518 PMCID: PMC4353840 DOI: 10.1002/anie.201409779] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 12/21/2022]
Abstract
An NMR-based approach to characterizing the binding kinetics of ligand molecules to biomolecules, like RNA or proteins, by ligand-detected Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments is described. A (15)N-modified preQ1 ligand is used to acquire relaxation dispersion experiments in the presence of low amounts of the Fsu class I preQ1 aptamer RNA, and increasing ligand concentrations to probe the RNA small molecule interaction. Our experimental data strongly support the conformational selection mechanism postulated. The approach gives direct access to two parameters of a ligand-receptor interaction: the off rate and the population of the small molecule-receptor complex. A detailed description of the kinetics underlying the ligand binding process is of crucial importance to fully understanding a riboswitch's function and to evaluate potential new antibiotics candidates targeting the noncoding RNA species. Ligand-detected NMR relaxation dispersion experiments represent a valuable diagnostic tool for the characterization of binding mechanisms.
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Affiliation(s)
- Thomas Moschen
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Christoph Hermann Wunderlich
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Romana Spitzer
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Jasmin Levic
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Martin Tollinger
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
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27
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Moschen T, Wunderlich CH, Spitzer R, Levic J, Micura R, Tollinger M, Kreutz C. Ligand-Detected Relaxation Dispersion NMR Spectroscopy: Dynamics of preQ1-RNA Binding. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409779] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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28
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Affiliation(s)
- Alan C. Gibbs
- Janssen Pharmaceutical Research and Development, LLC, Welsh and McKean Road, Spring House, Pennsylvania 19477-0776, United States
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29
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Narumi T, Takano H, Ohashi N, Suzuki A, Furuta T, Tamamura H. Isostere-based design of 8-azacoumarin-type photolabile protecting groups: a hydrophilicity-increasing strategy for coumarin-4-ylmethyls. Org Lett 2014; 16:1184-7. [PMID: 24495035 DOI: 10.1021/ol5000583] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Described is the development of 8-azacoumarin-4-ylmethyl groups as aqueous photolabile protecting groups. A key feature of the strategy is the isosteric replacement of the C7-C8 enol double bond of the Bhc derivative with an amide bond, resulting in conversion of the chromophore from coumarin to 8-azacoumarin. This strategy makes dramatically enhanced water solubility and facile photocleavage possible.
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Affiliation(s)
- Tetsuo Narumi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University , Chiyoda-ku, Tokyo 101-0062, Japan
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30
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Park JM, Hu JH, Milshteyn A, Zhang PW, Moore CG, Park S, Datko MC, Domingo RD, Reyes CM, Wang XJ, Etzkorn FA, Xiao B, Szumlinski KK, Kern D, Linden DJ, Worley PF. A prolyl-isomerase mediates dopamine-dependent plasticity and cocaine motor sensitization. Cell 2013; 154:637-50. [PMID: 23911326 DOI: 10.1016/j.cell.2013.07.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 04/14/2013] [Accepted: 07/01/2013] [Indexed: 01/02/2023]
Abstract
Synaptic plasticity induced by cocaine and other drugs underlies addiction. Here we elucidate molecular events at synapses that cause this plasticity and the resulting behavioral response to cocaine in mice. In response to D1-dopamine-receptor signaling that is induced by drug administration, the glutamate-receptor protein metabotropic glutamate receptor 5 (mGluR5) is phosphorylated by microtubule-associated protein kinase (MAPK), which we show potentiates Pin1-mediated prolyl-isomerization of mGluR5 in instances where the product of an activity-dependent gene, Homer1a, is present to enable Pin1-mGluR5 interaction. These biochemical events potentiate N-methyl-D-aspartate receptor (NMDAR)-mediated currents that underlie synaptic plasticity and cocaine-evoked motor sensitization as tested in mice with relevant mutations. The findings elucidate how a coincidence of signals from the nucleus and the synapse can render mGluR5 accessible to activation with consequences for drug-induced dopamine responses and point to depotentiation at corticostriatal synapses as a possible therapeutic target for treating addiction.
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Affiliation(s)
- Joo Min Park
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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31
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Wilson KA, Bouchard JJ, Peng JW. Interdomain interactions support interdomain communication in human Pin1. Biochemistry 2013; 52:6968-81. [PMID: 24020391 PMCID: PMC3794440 DOI: 10.1021/bi401057x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
![]()
Pin1 is an essential mitotic regulator
consisting of a peptidyl–prolyl
isomerase (PPIase) domain flexibly tethered to a smaller Trp–Trp
(WW) binding domain. Communication between these domains is important
for Pin1 in vivo activity; however, the atomic basis for this communication
has remained elusive. Our previous nuclear magnetic resonance (NMR)
studies of Pin1 functional dynamics suggested that weak interdomain
contacts within Pin1 enable allosteric communication between the domain
interface and the distal active site of the PPIase domain.1,2 A necessary condition for this hypothesis is that the intrinsic
properties of the PPIase domain should be sensitive to interdomain
contact. Here, we test this sensitivity by generating a Pin1 mutant,
I28A, which weakens the wild-type interdomain contact while maintaining
the overall folds of the two domains. Using NMR, we show that I28A
leads to altered substrate binding affinity and isomerase activity.
Moreover, I28A causes long-range perturbations to conformational flexibility
in both domains, for both the apo and substrate-complexed states of
the protein. These results show that the distribution of conformations
sampled by the PPIase domain is sensitive to interdomain contact and
strengthen the hypothesis that such contact supports interdomain allosteric
communication in Pin1. Other modular systems may exploit interdomain
interactions in a similar manner.
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Affiliation(s)
- Kimberly A Wilson
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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32
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Kovermann M, Balbach J. Dynamic control of the prolyl isomerase function of the dual-domain SlyD protein. Biophys Chem 2013; 171:16-23. [DOI: 10.1016/j.bpc.2012.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/22/2012] [Accepted: 11/22/2012] [Indexed: 12/13/2022]
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33
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Zhang M, Wang XJ, Chen X, Bowman ME, Luo Y, Noel JP, Ellington AD, Etzkorn FA, Zhang Y. Structural and kinetic analysis of prolyl-isomerization/phosphorylation cross-talk in the CTD code. ACS Chem Biol 2012; 7:1462-70. [PMID: 22670809 DOI: 10.1021/cb3000887] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The C-terminal domain (CTD) of eukaryotic RNA polymerase II is an essential regulator for RNA polymerase II-mediated transcription. It is composed of multiple repeats of a consensus sequence Tyr(1)Ser(2)Pro(3)Thr(4)Ser(5)Pro(6)Ser(7). CTD regulation of transcription is mediated by both phosphorylation of the serines and prolyl isomerization of the two prolines. Interestingly, the phosphorylation sites are typically close to prolines, and thus the conformation of the adjacent proline could impact the specificity of the corresponding kinases and phosphatases. Experimental evidence of cross-talk between these two regulatory mechanisms has been elusive. Pin1 is a highly conserved phosphorylation-specific peptidyl-prolyl isomerase (PPIase) that recognizes the phospho-Ser/Thr (pSer/Thr)-Pro motif with CTD as one of its primary substrates in vivo. In the present study, we provide structural snapshots and kinetic evidence that support the concept of cross-talk between prolyl isomerization and phosphorylation. We determined the structures of Pin1 bound with two substrate isosteres that mimic peptides containing pSer/Thr-Pro motifs in cis or trans conformations. The results unequivocally demonstrate the utility of both cis- and trans-locked alkene isosteres as close geometric mimics of peptides bound to a protein target. Building on this result, we identified a specific case in which Pin1 differentially affects the rate of dephosphorylation catalyzed by two phosphatases (Scp1 and Ssu72) that target the same serine residue in the CTD heptad repeat but have different preferences for the isomerization state of the adjacent proline residue. These data exemplify for the first time how modulation of proline isomerization can kinetically impact signal transduction in transcription regulation.
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Affiliation(s)
- Mengmeng Zhang
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Xiaodong J. Wang
- Department of Chemistry, Virginia Tech, MC 0212, Blacksburg, Virginia 24061,
United States
| | - Xi Chen
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Marianne E. Bowman
- Jack Skirball Chemical Biology
and Protein Laboratory, The Salk Institute, 10010 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Yonghua Luo
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Joseph P. Noel
- Jack Skirball Chemical Biology
and Protein Laboratory, The Salk Institute, 10010 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Andrew D. Ellington
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Felicia A. Etzkorn
- Department of Chemistry, Virginia Tech, MC 0212, Blacksburg, Virginia 24061,
United States
| | - Yan Zhang
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
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Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool for investigating the dynamics of biomolecules since it provides a description of motion that is comprehensive, site-specific, and relatively non-invasive. In particular, the study of protein dynamics has benefited from sustained methodological advances in NMR that have expanded the scope and time scales of accessible motion. Yet, many of these advances may not be well known to the more general physical chemistry community. Accordingly, this Perspective provides a glimpse of some of the more powerful methods in liquid state NMR that are helping reshape our understanding of functional motions of proteins.
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Affiliation(s)
- J W Peng
- Department of Chemistry and Biochemistry & Department of Physics University of Notre Dame, Notre Dame, IN 46556
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35
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Carroll MJ, Mauldin RV, Gromova AV, Singleton SF, Collins EJ, Lee AL. Evidence for dynamics in proteins as a mechanism for ligand dissociation. Nat Chem Biol 2012; 8:246-52. [PMID: 22246400 PMCID: PMC3288659 DOI: 10.1038/nchembio.769] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 11/23/2011] [Indexed: 01/16/2023]
Abstract
Signal transduction, regulatory processes, and pharmaceutical responses are highly dependent upon ligand residence times. Gaining insight into how physical factors influence residence times, or koff, should enhance our ability to manipulate biological interactions. We report experiments that yield structural insight into koff for a series of eight 2,4-diaminopyrimidine inhibitors of dihydrofolate reductase that vary by six orders of magnitude in binding affinity. NMR relaxation dispersion experiments revealed a common set of residues near the binding site that undergo a concerted, millisecond-timescale switching event to a previously unidentified conformation. The rate of switching from ground to excited conformations correlates exponentially with Ki and koff, suggesting that protein dynamics serves as a mechanical initiator of ligand dissociation within this series and potentially for other macromolecule-ligand systems. Although kconf,forward is faster than koff, use of the ligand series allowed for connections to be drawn between kinetic events on different timescales.
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Affiliation(s)
- Mary J Carroll
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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36
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Kleckner IR, Foster MP. GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data. JOURNAL OF BIOMOLECULAR NMR 2012; 52:11-22. [PMID: 22160811 PMCID: PMC3593345 DOI: 10.1007/s10858-011-9589-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 09/25/2011] [Indexed: 05/20/2023]
Abstract
Molecular dynamics are essential for life, and nuclear magnetic resonance (NMR) spectroscopy has been used extensively to characterize these phenomena since the 1950s. For the past 15 years, the Carr-Purcell Meiboom-Gill relaxation dispersion (CPMG RD) NMR experiment has afforded advanced NMR labs access to kinetic, thermodynamic, and structural details of protein and RNA dynamics in the crucial μs-ms time window. However, analysis of RD data is challenging because datasets are often large and require many non-linear fitting parameters, thereby confounding assessment of accuracy. Moreover, novice CPMG experimentalists face an additional barrier because current software options lack an intuitive user interface and extensive documentation. Hence, we present the open-source software package GUARDD (Graphical User-friendly Analysis of Relaxation Dispersion Data), which is designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD data ( http://code.google.com/p/guardd/). This MATLAB-based program includes a graphical user interface, permits global fitting to multi-field, multi-temperature, multi-coherence data, and implements χ (2)-mapping procedures, via grid-search and Monte Carlo methods, to enhance and assess fitting accuracy. The presentation features allow users to seamlessly traverse the large amount of results, and the RD Simulator feature can help design future experiments as well as serve as a teaching tool for those unfamiliar with RD phenomena. Based on these innovative features, we expect that GUARDD will fill a well-defined gap in service of the RD NMR community.
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Affiliation(s)
- Ian R. Kleckner
- Biophysics Program, The Ohio State University, 484 West 12th Ave Room 776, Columbus, OH 43210, USA,
| | - Mark P. Foster
- Biochemistry Department, The Ohio State University, 484 West 12th Ave Room 776, Columbus, OH 43210, USA,
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37
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Xu GG, Zhang Y, Mercedes-Camacho AY, Etzkorn FA. A reduced-amide inhibitor of Pin1 binds in a conformation resembling a twisted-amide transition state. Biochemistry 2011; 50:9545-50. [PMID: 21980916 DOI: 10.1021/bi201055c] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R-pSer-Ψ[CH(2)N]-Pro-2-(indol-3-yl)ethylamine, 1 [R = fluorenylmethoxycarbonyl (Fmoc)] and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC(50) value of 6.3 μM, which is 4.5-fold better for Pin1 than our comparable ground-state analogue, a cis-amide alkene isostere-containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination and resulted in an IC(50) value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1.
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Affiliation(s)
- Guoyan G Xu
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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38
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Namanja AT, Wang XJ, Xu B, Mercedes-Camacho AY, Wilson KA, Etzkorn FA, Peng JW. Stereospecific gating of functional motions in Pin1. Proc Natl Acad Sci U S A 2011; 108:12289-94. [PMID: 21746900 PMCID: PMC3145719 DOI: 10.1073/pnas.1019382108] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pin1 is a modular enzyme that accelerates the cis-trans isomerization of phosphorylated-Ser/Thr-Pro (pS/T-P) motifs found in numerous signaling proteins regulating cell growth and neuronal survival. We have used NMR to investigate the interaction of Pin1 with three related ligands that include a pS-P substrate peptide, and two pS-P substrate analogue inhibitors locked in the cis and trans conformations. Specifically, we compared the ligand binding modes and binding-induced changes in Pin1 side-chain flexibility. The cis and trans binding modes differ, and produce different mobility in Pin1. The cis-locked inhibitor and substrate produced a loss of side-chain flexibility along an internal conduit of conserved hydrophobic residues, connecting the domain interface with the isomerase active site. The trans-locked inhibitor produces a weaker conduit response. Thus, the conduit response is stereoselective. We further show interactions between the peptidyl-prolyl isomerase and Trp-Trp (WW) domains amplify the conduit response, and alter binding properties at the remote peptidyl-prolyl isomerase active site. These results suggest that specific input conformations can gate dynamic changes that support intraprotein communication. Such gating may help control the propagation of chemical signals by Pin1, and other modular signaling proteins.
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Affiliation(s)
- Andrew T. Namanja
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556
| | | | - Bailing Xu
- Department of Chemistry, Virginia Tech, Blacksburg, VA 24061
| | | | - Kimberly A. Wilson
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556
| | | | - Jeffrey W. Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556
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39
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Stelzer AC, Kratz JD, Zhang Q, Al-Hashimi HM. RNA dynamics by design: biasing ensembles towards the ligand-bound state. Angew Chem Int Ed Engl 2011; 49:5731-3. [PMID: 20583015 DOI: 10.1002/anie.201000814] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew C Stelzer
- Department of Chemistry and Biophysics, University of Michigan, 930 North University, Ann Arbor, MI 48109, USA
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40
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Zhang J, Sapienza PJ, Ke H, Chang A, Hengel SR, Wang H, Phillips GN, Lee AL. Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E. Biochemistry 2010; 49:9280-91. [PMID: 20839809 DOI: 10.1021/bi101131f] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PDZ (PSD95/Discs large/ZO-1) domains are ubiquitous protein interaction motifs found in scaffolding proteins involved in signal transduction. Despite the fact that many PDZ domains show a limited tendency to undergo structural change, the PDZ family has been associated with long-range communication and allostery. One of the PDZ domains studied most in terms of structure and biophysical properties is the second PDZ ("PDZ2") domain from protein tyrosine phosphatase 1E (PTP1E, also known as PTPL1). Previously, we showed through NMR relaxation studies that binding of the RA-GEF2 C-terminal peptide substrate results in long-range propagation of side-chain dynamic changes in human PDZ2 [Fuentes, E. J., et al. (2004) J. Mol. Biol. 335, 1105-1115]. Here, we present the first X-ray crystal structures of PDZ2 in the absence and presence of RA-GEF2 ligand, determined to resolutions of 1.65 and 1.3 Å, respectively. These structures deviate somewhat from previously determined NMR structures and indicate that very minor structural changes in PDZ2 accompany peptide binding. NMR residual dipolar couplings confirm the crystal structures to be accurate models of the time-averaged atomic coordinates of PDZ2. The impact on side-chain dynamics was further tested with a C-terminal peptide from APC, which showed results nearly identical to those of RA-GEF2. Thus, allosteric transmission in PDZ2 induced by peptide binding is conveyed purely and robustly by dynamics. (15)N relaxation dispersion measurements did not detect appreciable populations of a kinetic structural intermediate. Collectively, for ligand binding to PDZ2, these data support a lock-and-key binding model from a structural perspective and an allosteric model from a dynamical perspective, which together suggest a complex energy landscape for functional transitions within the ensemble.
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Affiliation(s)
- Jun Zhang
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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41
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Mangia S, Traaseth NJ, Veglia G, Garwood M, Michaeli S. Probing slow protein dynamics by adiabatic R(1rho) and R(2rho) NMR experiments. J Am Chem Soc 2010; 132:9979-81. [PMID: 20590094 DOI: 10.1021/ja1038787] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Slow micros/ms dynamics involved in protein folding, binding, catalysis, and allostery are currently detected using NMR dispersion experiments such as CPMG (Carr-Purcell-Meiboom-Gill) or spin-lock R(1rho). In these methods, protein dynamics are obtained by analyzing relaxation dispersion curves obtained from either changing the time spacing between 180 degree pulses or by changing the effective spin-locking field strength. In this Communication, we introduce a new method to induce a dispersion of relaxation rates. Our approach relies on altering the shape of the adiabatic full passage pulse and is conceptually different from existing approaches. By changing the nature of the adiabatic radiofrequency irradiation, we are able to obtain rotating frame R(1rho) and R(2rho) dispersion curves that are sensitive to slow micros/ms protein dynamics (demonstrated with ubiquitin). The strengths of this method are to (a) extend the dynamic range of the relaxation dispersion analysis, (b) avoid the need for multiple magnetic field strengths to extract dynamic parameters, (c) measure accurate relaxation rates that are independent of frequency offset, and (d) reduce the stress to NMR hardware (e.g., cryoprobes).
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Affiliation(s)
- Silvia Mangia
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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Kleckner IR, Foster MP. An introduction to NMR-based approaches for measuring protein dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:942-68. [PMID: 21059410 DOI: 10.1016/j.bbapap.2010.10.012] [Citation(s) in RCA: 346] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/27/2010] [Accepted: 10/29/2010] [Indexed: 01/15/2023]
Abstract
Proteins are inherently flexible at ambient temperature. At equilibrium, they are characterized by a set of conformations that undergo continuous exchange within a hierarchy of spatial and temporal scales ranging from nanometers to micrometers and femtoseconds to hours. Dynamic properties of proteins are essential for describing the structural bases of their biological functions including catalysis, binding, regulation and cellular structure. Nuclear magnetic resonance (NMR) spectroscopy represents a powerful technique for measuring these essential features of proteins. Here we provide an introduction to NMR-based approaches for studying protein dynamics, highlighting eight distinct methods with recent examples, contextualized within a common experimental and analytical framework. The selected methods are (1) Real-time NMR, (2) Exchange spectroscopy, (3) Lineshape analysis, (4) CPMG relaxation dispersion, (5) Rotating frame relaxation dispersion, (6) Nuclear spin relaxation, (7) Residual dipolar coupling, (8) Paramagnetic relaxation enhancement. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Ian R Kleckner
- The Ohio State University Biophysics Program, 484 West 12th Ave Room 776, Columbus, OH 43210, USA
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43
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Stelzer A, Kratz J, Zhang Q, Al-Hashimi H. RNA Dynamics by Design: Biasing Ensembles Towards the Ligand-Bound State. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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