1
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Maiti S, Singh A, Maji T, Saibo NV, De S. Experimental methods to study the structure and dynamics of intrinsically disordered regions in proteins. Curr Res Struct Biol 2024; 7:100138. [PMID: 38707546 PMCID: PMC11068507 DOI: 10.1016/j.crstbi.2024.100138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 05/07/2024] Open
Abstract
Eukaryotic proteins often feature long stretches of amino acids that lack a well-defined three-dimensional structure and are referred to as intrinsically disordered proteins (IDPs) or regions (IDRs). Although these proteins challenge conventional structure-function paradigms, they play vital roles in cellular processes. Recent progress in experimental techniques, such as NMR spectroscopy, single molecule FRET, high speed AFM and SAXS, have provided valuable insights into the biophysical basis of IDP function. This review discusses the advancements made in these techniques particularly for the study of disordered regions in proteins. In NMR spectroscopy new strategies such as 13C detection, non-uniform sampling, segmental isotope labeling, and rapid data acquisition methods address the challenges posed by spectral overcrowding and low stability of IDPs. The importance of various NMR parameters, including chemical shifts, hydrogen exchange rates, and relaxation measurements, to reveal transient secondary structures within IDRs and IDPs are presented. Given the high flexibility of IDPs, the review outlines NMR methods for assessing their dynamics at both fast (ps-ns) and slow (μs-ms) timescales. IDPs exert their functions through interactions with other molecules such as proteins, DNA, or RNA. NMR-based titration experiments yield insights into the thermodynamics and kinetics of these interactions. Detailed study of IDPs requires multiple experimental techniques, and thus, several methods are described for studying disordered proteins, highlighting their respective advantages and limitations. The potential for integrating these complementary techniques, each offering unique perspectives, is explored to achieve a comprehensive understanding of IDPs.
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Affiliation(s)
| | - Aakanksha Singh
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Tanisha Maji
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Nikita V. Saibo
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
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2
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Bhuvaneshwari RA, Shivamani A, Sengupta I. Line Shape Analysis of 19F NMR-Monitored Chemical Denaturation of a Fold-Switching Protein RfaH Reveals Its Slow Folding Dynamics. J Phys Chem B 2024; 128:465-471. [PMID: 37991741 DOI: 10.1021/acs.jpcb.3c06550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
The recent discovery of metamorphic proteins, which can switch between multiple conformations under native conditions, has challenged the well-established one sequence-one structure paradigm of protein folding. This is exemplified in the C-terminal domain of the multidomain transcription factor RfaH, which converts from an α-helical coiled-coil conformation in its autoinhibited state to a β-barrel conformation upon activation. Here, we use multisite line shape analysis of 19F NMR-monitored equilibrium chemical denaturation measurements of two 19F-labeled variants of full-length RfaH, to show that it folds/unfolds slowly on the NMR time scale, in an apparent all-or-none fashion at physiological pH and room temperature in the 3.3-4.8 M urea concentration range. The significant thermodynamic stability and slow unfolding rate (kinetic stability) are likely responsible for maintaining the closed autoinhibited state of RfaH, preventing spurious interactions with RNA polymerase (RNAP) when not functional. Our results provide a quantitative understanding of the folding-function relationship in the model fold-switching protein RfaH.
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Affiliation(s)
| | - Anish Shivamani
- Department of Chemistry, IIT Bombay, Powai, Mumbai 400076, India
| | - Ishita Sengupta
- Department of Chemistry, IIT Bombay, Powai, Mumbai 400076, India
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3
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Ono J, Matsumura Y, Mori T, Saito S. Conformational Dynamics in Proteins: Entangled Slow Fluctuations and Nonequilibrium Reaction Events. J Phys Chem B 2024; 128:20-32. [PMID: 38133567 DOI: 10.1021/acs.jpcb.3c05307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Proteins exhibit conformational fluctuations and changes over various time scales, ranging from rapid picosecond-scale local atomic motions to slower microsecond-scale global conformational transformations. In the presence of these intricate fluctuations, chemical reactions occur and functions emerge. These conformational fluctuations of proteins are not merely stochastic random motions but possess distinct spatiotemporal characteristics. Moreover, chemical reactions do not always proceed along a single reaction coordinate in a quasi-equilibrium manner. Therefore, it is essential to understand spatiotemporal conformational fluctuations of proteins and the conformational change processes associated with reactions. In this Perspective, we shed light on the complex dynamics of proteins and their role in enzyme catalysis by presenting recent results regarding dynamic couplings and disorder in the conformational dynamics of proteins and rare but rapid enzymatic reaction events obtained from molecular dynamics simulations.
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Affiliation(s)
- Junichi Ono
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Yoshihiro Matsumura
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Toshifumi Mori
- Institute for Materials Chemistry and Engineering, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
| | - Shinji Saito
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8585, Japan
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4
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Kanna M, Nakatsu Y, Yamamotoya T, Encinas J, Ito H, Okabe T, Asano T, Sakaguchi T. Roles of peptidyl prolyl isomerase Pin1 in viral propagation. Front Cell Dev Biol 2022; 10:1005325. [PMID: 36393854 PMCID: PMC9642847 DOI: 10.3389/fcell.2022.1005325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/13/2022] [Indexed: 07/30/2023] Open
Abstract
Peptidyl-prolyl isomerase (PPIase) is a unique enzyme that promotes cis-trans isomerization of a proline residue of a target protein. Peptidyl-prolyl cis-trans isomerase NIMA (never in mitosis A)-interacting 1 (Pin1) is a PPIase that binds to the pSer/pThr-Pro motif of target proteins and isomerizes their prolines. Pin1 has been reported to be involved in cancer development, obesity, aging, and Alzheimer's disease and has been shown to promote the growth of several viruses including SARS-CoV-2. Pin1 enhances the efficiency of viral infection by promoting uncoating and integration of the human immunodeficiency virus. It has also been shown that Pin1 interacts with hepatitis B virus proteins and participates in viral replication. Furthermore, Pin1 promotes not only viral proliferation but also the progression of virus-induced tumorigenesis. In this review, we focus on the effects of Pin1 on the proliferation of various viruses and discuss the underlying molecular mechanisms.
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Affiliation(s)
- Machi Kanna
- Department of Biomedical Chemistry, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima City, Japan
| | - Yusuke Nakatsu
- Department of Biomedical Chemistry, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima City, Japan
| | - Takeshi Yamamotoya
- Department of Biomedical Chemistry, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima City, Japan
| | | | - Hisanaka Ito
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Takayoshi Okabe
- Drug Discovery Initiative, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Tomoichiro Asano
- Department of Biomedical Chemistry, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima City, Japan
| | - Takemasa Sakaguchi
- Department of Virology, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima City, Japan
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5
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Mori T, Saito S. Molecular Insights into the Intrinsic Dynamics and Their Roles During Catalysis in Pin1 Peptidyl-prolyl Isomerase. J Phys Chem B 2022; 126:5185-5193. [PMID: 35795989 DOI: 10.1021/acs.jpcb.2c02095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins are intrinsically dynamic and change conformations over a wide range of time scales. While the conformational dynamics have been realized to be important for protein functions, e.g., in activity-stability trade-offs, how they play a role during enzyme catalysis has been of debate over decades. By studying Pin1 peptidyl-prolyl isomerase using extensive molecular dynamics simulations, here we discuss how the slow intrinsic dynamics of Pin1 observed in the NMR relaxation dispersion experiment occur and couple to isomerization reactions in molecular detail. In particular, we analyze the angular correlation functions of the backbone N-H bonds and find that slow conformational transitions occur at about the 310 helix in the apo state. These events at the helical region further affect the residues at about the ligand binding site. Unfolding of this helix leads to a tight hydrogen bond between the helical region and the ligand binding loop, thus forming a stable coiled structure. The helical and coiled structures are found to be characteristic of the Pin1-ligand complex with the ligand in the trans and cis states, respectively. These results indicate that the changes in the slow dynamics of Pin1 by the isomerization reaction occur via the shift in populations of the helical and coiled states, where the balance is dependent on the ligand isomerization states.
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Affiliation(s)
- Toshifumi Mori
- Institute for Materials Chemistry and Engineering, Kyushu University, Kasuga, Fukuoka 816-8580, Japan.,Department of Interdisciplinary Engineering Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
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6
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Pazicky S, Werle ALA, Lei J, Löw C, Weininger U. Impact of distant peptide substrate residues on enzymatic activity of SlyD. Cell Mol Life Sci 2022; 79:138. [PMID: 35184231 PMCID: PMC8858294 DOI: 10.1007/s00018-022-04179-4] [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: 10/29/2021] [Revised: 01/18/2022] [Accepted: 01/28/2022] [Indexed: 11/05/2022]
Abstract
Peptidyl-prolyl isomerases (PPIases) catalyze intrinsically slow and often rate-limiting isomerization of prolyl-peptide bonds in unfolded or partially folded proteins, thereby speeding up the folding process and preventing misfolding. They often possess binding and chaperone domains in addition to the domain carrying the isomerization activity. Although generally, their substrates display no identity in their amino acid sequence upstream and downstream of the proline with 20 possibilities for each residue, PPIases are efficient enzymes. SlyD is a highly efficient PPIase consisting of an isomerase domain and an additional chaperone domain. The binding of peptide substrates to SlyD and its enzymatic activity depend to some extend on the proline-proximal residues, however, the impact of proline-distant residues has not been investigated so far. Here, we introduce a label-free NMR-based method to measure SlyD activity on different peptide substrates and analysed the data in the context of obtained binding affinities and several co-crystal structures. We show that especially charged and aromatic residues up to eight positions downstream and three positions upstream of the proline and outside the canonical region of similar conformations affect the activity and binding, although they rarely display distinct conformations in our crystal structures. We hypothesize that these positions primarily influence the association reaction. In the absence of the chaperone domain the isomerase activity strongly correlates with substrate affinity, whereas additional factors play a role in its presence. The mutual orientation of isomerase and chaperone domains depends on the presence of substrates in both binding sites, implying allosteric regulation of enzymatic activity.
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7
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Ban D, Rice CT, McCoy MA. Quantification of natural abundance NMR data differentiates the solution behavior of monoclonal antibodies and their fragments. MAbs 2021; 13:1978132. [PMID: 34612804 PMCID: PMC8496538 DOI: 10.1080/19420862.2021.1978132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Biotherapeutics are an important class of molecules for the treatment of a wide range of diseases. They include low molecular weight peptides, highly engineered protein scaffolds and monoclonal antibodies. During their discovery and development, assessments of the biophysical attributes is critical to understanding the solution behavior of therapeutic proteins and for de-risking liabilities. Thus, methods that can quantify, characterize, and provide a basis to inform risks and drive the selection of more optimal antibody and alternative scaffolds are needed. Nuclear Magnetic Resonance (NMR) spectroscopy is a technique that provides a means to probe antibody and antibody-like molecules in solution, at atomic resolution, under any formulated conditions. Here, all samples were profiled at natural abundance requiring no isotope enrichment. We present a numerical approach that quantitates two-dimensional methyl spectra. The approach was tested with a reference dataset that contained different types of antibody and antibody-like molecules. This dataset was processed through a procedure we call a Random Sampling of NMR Peaks for Covariance Analysis. This analysis revealed that the first two components were well correlated with the hydrodynamic radius of the molecules included in the reference set. Higher-order principal components were also linked to dynamic features between different tethered antibody-like molecules and contributed to decisions around candidate selection. The reference set provides a basis to characterize molecules with unknown solution behavior and is sensitive to the behavior of a molecule formulated under different conditions. The approach is independent of protein design, scaffold, formulation and provides a facile method to quantify solution behavior.
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Affiliation(s)
- David Ban
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Cory T Rice
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Mark A McCoy
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
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8
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Kancherla AK, Marincin KA, Mishra SH, Frueh DP. Minimizing Pervasive Artifacts in 4D Covariance Maps for Protein Side Chain NMR Assignments. J Phys Chem A 2021; 125:8313-8323. [PMID: 34510900 PMCID: PMC8480538 DOI: 10.1021/acs.jpca.1c05507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/24/2021] [Indexed: 01/23/2023]
Abstract
Nuclear magnetic resonance (NMR) is a mainstay of biophysical studies that provides atomic level readouts to formulate molecular mechanisms. Side chains are particularly important to derive mechanisms involving proteins as they carry functional groups, but NMR studies of side chains are often limited by challenges in assigning their signals. Here, we designed a novel computational method that combines spectral derivatives and matrix square-rooting to produce reliable 4D covariance maps from routinely acquired 3D spectra and facilitates side chain resonance assignments. Thus, we generate two 4D maps from 3D-HcccoNH and 3D-HCcH-TOCSY spectra that each help overcome signal overlap or sensitivity losses. These 4D maps feature HC-HSQCs of individual side chains that can be paired to assigned backbone amide resonances of individual aliphatic signals, and both are obtained from a single modified covariance calculation. Further, we present 4D maps produced using conventional triple resonance experiments to easily assign asparagine side chain amide resonances. The 4D covariance maps encapsulate the lengthy manual pattern recognition used in traditional assignment methods and distill the information as correlations that can be easily visualized. We showcase the utility of the 4D covariance maps with a 10 kDa peptidyl carrier protein and a 52 kDa cyclization domain from a nonribosomal peptide synthetase.
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Affiliation(s)
- Aswani K. Kancherla
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Room 701 Hunterian, Baltimore, Maryland 21205, United States
| | - Kenneth A. Marincin
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Room 701 Hunterian, Baltimore, Maryland 21205, United States
| | - Subrata H. Mishra
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Room 701 Hunterian, Baltimore, Maryland 21205, United States
| | - Dominique P. Frueh
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Room 701 Hunterian, Baltimore, Maryland 21205, United States
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9
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Mori T, Saito S. Dissecting the Dynamics during Enzyme Catalysis: A Case Study of Pin1 Peptidyl-Prolyl Isomerase. J Chem Theory Comput 2020; 16:3396-3407. [PMID: 32268066 DOI: 10.1021/acs.jctc.9b01279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Free energy surfaces have played a central role in studying protein conformational changes and enzymatic reactions over decades. Yet, free energy barriers and kinetics are highly dependent on the coordinates chosen to define the surface, and furthermore, the dynamics during the reactions are often overlooked. Our recent study on the Pin1-catalyzed isomerization reaction has indicated that the isomerization transition events remarkably deviate from the free energy path, highlighting the need to understand the reaction dynamics in more detail. To this end, here we investigate the reaction coordinates that describe the transition states of the free energy and transition pathways by minimizing the cross-entropy function. We show that the isomerization transition events can be expressed by the concerted changes in the improper torsion angle ζ and nearby backbone torsional angles of the ligand, whereas the transition state of the free energy surface involves changes in a broad range of coordinates including multiple protein-ligand interactions. The current result supports the previous finding that the isomerization transitions occur quickly from the conformational excited states, which is in sharp contrast to the slow and collective changes suggested from the free energy path. Our results further indicate that the coordinates derived from the transition trajectories are not sufficient for finding the transition states on the free energy surfaces due to the lack of information from conformational excited states.
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Affiliation(s)
- Toshifumi Mori
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
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10
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Stadmiller SS, Aguilar JS, Waudby CA, Pielak GJ. Rapid Quantification of Protein-Ligand Binding via 19F NMR Lineshape Analysis. Biophys J 2020; 118:2537-2548. [PMID: 32348722 DOI: 10.1016/j.bpj.2020.03.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
Fluorine incorporation is ideally suited to many NMR techniques, and incorporation of fluorine into proteins and fragment libraries for drug discovery has become increasingly common. Here, we use one-dimensional 19F NMR lineshape analysis to quantify the kinetics and equilibrium thermodynamics for the binding of a fluorine-labeled Src homology 3 (SH3) protein domain to four proline-rich peptides. SH3 domains are one of the largest and most well-characterized families of protein recognition domains and have a multitude of functions in eukaryotic cell signaling. First, we showe that fluorine incorporation into SH3 causes only minor structural changes to both the free and bound states using amide proton temperature coefficients. We then compare the results from lineshape analysis of one-dimensional 19F spectra to those from two-dimensional 1H-15N heteronuclear single quantum coherence spectra. Their agreement demonstrates that one-dimensional 19F lineshape analysis is a robust, low-cost, and fast alternative to traditional heteronuclear single quantum coherence-based experiments. The data show that binding is diffusion limited and indicate that the transition state is highly similar to the free state. We also measured binding as a function of temperature. At equilibrium, binding is enthalpically driven and arises from a highly positive activation enthalpy for association with small entropic contributions. Our results agree with those from studies using different techniques, providing additional evidence for the utility of 19F NMR lineshape analysis, and we anticipate that this analysis will be an effective tool for rapidly characterizing the energetics of protein interactions.
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Affiliation(s)
| | - Jhoan S Aguilar
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Christopher A Waudby
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina.
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11
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Abstract
Interactions of intrinsically disordered proteins are central to their cellular functions, and solution-state NMR spectroscopy provides a powerful tool for characterizing both structural and mechanistic aspects of such interactions. Here we focus on the analysis of IDP interactions using NMR titration measurements. Changes in resonance lineshapes in two-dimensional NMR spectra upon titration with a ligand contain rich information on structural changes in the protein and the thermodynamics and kinetics of the interaction, as well as on the microscopic association mechanism. Here we present protocols for the optimal design of titration experiments, data acquisition, and data analysis by two-dimensional lineshape fitting using the TITAN software package.
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12
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Waudby CA, Ouvry M, Davis B, Christodoulou J. Two-dimensional NMR lineshape analysis of single, multiple, zero and double quantum correlation experiments. JOURNAL OF BIOMOLECULAR NMR 2020; 74:95-109. [PMID: 31915980 PMCID: PMC7015968 DOI: 10.1007/s10858-019-00297-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 12/31/2019] [Indexed: 05/05/2023]
Abstract
NMR spectroscopy provides a powerful approach for the characterisation of chemical exchange and molecular interactions by analysis of series of experiments acquired over the course of a titration measurement. The appearance of NMR resonances undergoing chemical exchange depends on the frequency difference relative to the rate of exchange, and in the case of one-dimensional experiments chemical exchange regimes are well established and well known. However, two-dimensional experiments present additional complexity, as at least one additional frequency difference must be considered. Here we provide a systematic classification of chemical exchange regimes in two-dimensional NMR spectra. We highlight important differences between exchange in HSQC and HMQC experiments, that on a practical level result in more severe exchange broadening in HMQC spectra, but show that complementary alternatives to the HMQC are available in the form of HZQC and HDQC experiments. We present the longitudinal relaxation optimised SOFAST-H(Z/D)QC experiment for the simultaneous acquisition of sensitivity-enhanced HZQC and HDQC spectra, and the longitudinal and transverse relaxation optimised BEST-ZQ-TROSY for analysis of large molecular weight systems. We describe the application of these experiments to the characterisation of the interaction between the Hsp90 N-terminal domain and a small molecule ligand, and show that the independent analysis of HSQC, HMQC, HZQC and HDQC experiments provides improved confidence in the fitted dissociation constant and dissociation rate. Joint analysis of such data may provide improved sensitivity to detect and analyse more complex multi-state interaction mechanisms such as induced fit or conformational selection.
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Affiliation(s)
- Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK.
| | - Margaux Ouvry
- Biotechnologie, Sanofi, Route d'Avignon, 30390, Aramon, France
| | - Ben Davis
- Vernalis (R&D) Limited, Granta Park, Great Abington, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK
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13
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NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models. Sci Rep 2019; 9:16023. [PMID: 31690758 PMCID: PMC6831641 DOI: 10.1038/s41598-019-52451-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/14/2019] [Indexed: 11/08/2022] Open
Abstract
The ability of high-resolution NMR spectroscopy to readout the response of molecular interactions at multiple atomic sites presents a unique capability to define thermodynamic equilibrium constants and kinetic rate constants for complex, multiple-step biological interactions. Nonetheless, the extraction of the relevant equilibrium binding and rate constants requires the appropriate analysis of not only a readout that follows the equilibrium concentrations of typical binding titration curves, but also the lineshapes of NMR spectra. To best take advantage of NMR data for characterizing molecular interactions, we developed NmrLineGuru, a software tool with a user-friendly graphical user interface (GUI) to model two-state, three-state, and four-state binding processes. Application of NmrLineGuru is through stand-alone GUIs, with no dependency on other software and no scripted input. NMR spectra can be fitted or simulated starting with user-specified input parameters and a chosen kinetic model. The ability to both simulate and fit NMR spectra provides the user the opportunity to not only determine the binding parameters that best reproduce the measured NMR spectra for the selected kinetic model, but to also query the possibility that alternative models agree with the data. NmrLineGuru is shown to provide an accurate, quantitative analysis of complex molecular interactions.
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14
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Acevedo LA, Korson NE, Williams JM, Nicholson LK. Tuning a timing device that regulates lateral root development in rice. JOURNAL OF BIOMOLECULAR NMR 2019; 73:493-507. [PMID: 31407206 PMCID: PMC7141409 DOI: 10.1007/s10858-019-00258-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
Peptidyl Prolyl Isomerases (PPIases) accelerate cis-trans isomerization of prolyl peptide bonds. In rice, the PPIase LRT2 is essential for lateral root initiation. LRT2 displays in vitro isomerization of a highly conserved W-P peptide bond (104W-P105) in the natural substrate OsIAA11. OsIAA11 is a transcription repressor that, in response to the plant hormone auxin, is targeted to ubiquitin-mediated proteasomal degradation via specific recognition of the cis isomer of its 104W-P105 peptide bond. OsIAA11 controls transcription of specific genes, including its own, that are required for lateral root development. This auxin-responsive negative feedback circuit governs patterning and development of lateral roots along the primary root. The ability to tune LRT2 activity via mutagenesis is crucial for understanding and modeling the role of this bimodal switch in the auxin circuit and lateral root development. We present characterization of the thermal stability and isomerization rates of several LRT2 mutants acting on the OsIAA11 substrate. The thermally stable mutants display activities lower than that of wild-type (WT) LRT2. These include binding diminished but catalytically active P125K, binding incompetent W128A, and binding capable but catalytically incompetent H133Q mutations. Additionally, LRT2 homologs hCypA from human, TaCypA from Triticum aestivum (wheat) and PPIB from E. coli were shown to have 110, 50 and 60% of WT LRT2 activity on the OsIAA11 substrate. These studies identify several thermally stable LRT2 mutants with altered activities that will be useful for establishing relationships between cis-trans isomerization, auxin circuit dynamics, and lateral root development in rice.
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Affiliation(s)
- Lucila Andrea Acevedo
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA
- Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nathan E Korson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Justin M Williams
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Linda K Nicholson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA.
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15
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Boulton S, Selvaratnam R, Ahmed R, Van K, Cheng X, Melacini G. Mechanisms of Specific versus Nonspecific Interactions of Aggregation-Prone Inhibitors and Attenuators. J Med Chem 2019; 62:5063-5079. [PMID: 31074269 PMCID: PMC7255057 DOI: 10.1021/acs.jmedchem.9b00258] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A common source of false positives in drug discovery is ligand self-association into large colloidal assemblies that nonspecifically inhibit target proteins. However, the mechanisms of aggregation-based inhibition (ABI) and ABI-attenuation by additives, such as Triton X-100 (TX) and human serum albumin (HSA), are not fully understood. Here, we investigate the molecular basis of ABI and ABI-attenuation through the lens of NMR and coupled thermodynamic cycles. We unexpectedly discover a new class of aggregating ligands that exhibit negligible interactions with proteins but act as competitive sinks for the free inhibitor, resulting in bell-shaped dose-response curves. TX attenuates ABI by converting inhibitory, protein-binding aggregates into nonbinding coaggregates, whereas HSA minimizes nonspecific ligand interactions by functioning as a reservoir for free inhibitor and preventing self-association. Hence, both TX and HSA are useful tools to minimize false positives arising from nonspecific binding but at the cost of potentially introducing false negatives due to suppression of specific interactions.
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Affiliation(s)
- Stephen Boulton
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Rajeevan Selvaratnam
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
- Department of Laboratory Medicine, University Health Network, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 2C4, Canada
| | - Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Katherine Van
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Xiaodong Cheng
- Department of Integrative Biology and Pharmacology and Texas Therapeutics Institute, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
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16
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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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17
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Mori T, Saito S. Conformational Excitation and Nonequilibrium Transition Facilitate Enzymatic Reactions: Application to Pin1 Peptidyl-Prolyl Isomerase. J Phys Chem Lett 2019; 10:474-480. [PMID: 30607953 DOI: 10.1021/acs.jpclett.8b03607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Conformational flexibility of protein is essential for enzyme catalysis. Yet, how protein's conformational rearrangements and dynamics contribute to catalysis remains highly controversial. To unravel protein's role in catalysis, it is inevitable to understand the static and dynamic mechanisms simultaneously. To this end, here the Pin1-catalyzed isomerization reaction is studied from the two perspectives. The static view indicates that the hydrogen bonds involving Pin1 rearrange in a tightly coupled manner with isomerization. In sharp contrast, the isomerization dynamics are found to be very rapid; protein's slow conformational rearrangements thus cannot occur simultaneously with isomerization, and the reaction proceeds in a nonequilibrium manner. The distinctive protein conformations necessary to stabilize the transition state are prepared a priori, i.e., as conformational excited states. The present result suggests that enzymatic reaction is not a simple thermal activation from equilibrium directly to the transition state, thus adding a novel perspective to Pauling's view.
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Affiliation(s)
- Toshifumi Mori
- Institute for Molecular Science, Myodaiji , Okazaki , Aichi 444-8585 , Japan
- School of Physical Sciences , The Graduate University for Advanced Studies , Okazaki , Aichi 444-8585 , Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji , Okazaki , Aichi 444-8585 , Japan
- School of Physical Sciences , The Graduate University for Advanced Studies , Okazaki , Aichi 444-8585 , Japan
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18
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Quantification of reaction cycle parameters for an essential molecular switch in an auxin-responsive transcription circuit in rice. Proc Natl Acad Sci U S A 2019; 116:2589-2594. [PMID: 30696765 DOI: 10.1073/pnas.1817038116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Protein-based molecular switches play critical roles in biological processes. The importance of the prolyl cis-trans switch is underscored by the ubiquitous presence of peptidyl prolyl isomerases such as cyclophilins that accelerate the intrinsically slow isomerization rate. In rice, a tryptophan-proline (W-P) cis-trans switch in transcription repressor protein OsIAA11 along with its associated cyclophilin LRT2 are essential components in a negative feedback gene regulation circuit that controls lateral root initiation in response to the plant hormone auxin. Importantly, no quantitative characterizations of the individual (microscopic) thermodynamic and kinetic parameters for any cyclophilin-catalyzed W-P isomerization have been reported. Here we present NMR studies that determine and independently validate these parameters for LRT2 catalysis of the W-P motif in OsIAA11, providing predictive power for understanding the role of this switch in the auxin-responsive circuit and the resulting lateral rootless phenotype in rice. We show that the observed isomerization rate is linearly dependent on LRT2 concentration but is independent of OsIAA11 concentration over a wide range, and LRT2 is optimally tuned to maintain OsIAA11 at its cis-trans equilibrium to supply the slower downstream cis-specific proteasomal degradation with maximal OsIAA11 substrate. This indicates that accelerating the LRT2-catalyzed isomerization would not accelerate OsIAA degradation, whereas decreasing this rate via targeted mutation could reveal relationships between circuit dynamics and lateral root development. Moreover, we show that sequences flanking the highly conserved Aux/IAA W-P motif do not impact LRT2 catalysis, suggesting that the parameters determined here are broadly applicable across highly conserved cyclophilins and their Aux/IAA targets.
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19
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Matena A, Rehic E, Hönig D, Kamba B, Bayer P. Structure and function of the human parvulins Pin1 and Par14/17. Biol Chem 2018; 399:101-125. [PMID: 29040060 DOI: 10.1515/hsz-2017-0137] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Parvulins belong to the family of peptidyl-prolyl cis/trans isomerases (PPIases) assisting in protein folding and in regulating the function of a broad variety of proteins in all branches of life. The human representatives Pin1 and Par14/17 are directly involved in processes influencing cellular maintenance and cell fate decisions such as cell-cycle progression, metabolic pathways and ribosome biogenesis. This review on human parvulins summarizes the current knowledge of these enzymes and intends to oppose the well-studied Pin1 to its less well-examined homolog human Par14/17 with respect to structure, catalytic and cellular function.
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Affiliation(s)
- Anja Matena
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Edisa Rehic
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Dana Hönig
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Bianca Kamba
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
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20
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Fisher CL, Resnick RJ, De S, Acevedo LA, Lu KP, Schroeder FC, Nicholson LK. Cyclic cis-Locked Phospho-Dipeptides Reduce Entry of AβPP into Amyloidogenic Processing Pathway. J Alzheimers Dis 2018; 55:391-410. [PMID: 27662285 DOI: 10.3233/jad-160051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cis/trans isomerization of X-Pro peptide bonds in proteins in some instances acts as a molecular switch in biological pathways. Our prior work suggests that the cis isomer of the phospho-Thr668-Pro669 motif, located in the cytoplasmic domain of the amyloid-β protein precursor (AβPP), is correlated with an increase in amyloidogenic processing of AβPP and production of amyloid-beta (Aβ), the neurotoxic peptide fragment in Alzheimer's disease (AD). We designed a 100% cis-locked cyclic dipeptide composed of cyclized phospho-Thr-Pro (pCDP) as a mimic for this putative pathological conformation, and three phosphate-blocked derivatives (pCDP-diBzl, pCDP-Bzl, and pCDP-diPOM). Two H4 neuroglioma cell lines were established as AD cell models for use in testing these compounds: H4-AβPP695 for stable overexpression of wild-type AβPP695, and H4-BACE1 for stable overexpression of β-site AβPP cleaving enzyme-1 (BACE1). The level of the secreted AβPP fragment resulting from BACE1 activity, sAβPPβ, served as a key proxy for amyloidogenic processing, since cleavage of AβPP by BACE1 is a requisite first step in Aβ production. Of the compounds tested, pCDP-diBzl decreased sAβPPβ levels in both cell lines, while pCDP-diPOM decreased sAβPPβ levels in only H4-BACE1 cells, all with similar dose-dependences and patterns of proteolytic AβPP fragments. Enzymatic assays showed that none of the pCDP derivatives directly inhibit BACE1 catalytic activity. These results suggest a model in which pCDP-diBzl and pCDP-diPOM act at a common point to inhibit entry of AβPP into the amyloidogenic AβPP processing pathway but through different targets, and provide important insights for the development of novel AD therapeutics.
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Affiliation(s)
- Carolyn L Fisher
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Ross J Resnick
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Soumya De
- School of Bio Science, Indian Institute of Technology, Kharagpur, WB, India
| | - Lucila A Acevedo
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Kun Ping Lu
- Department of Medicine, Division of Translational Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Linda K Nicholson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
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21
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Boulton S, Akimoto M, Akbarizadeh S, Melacini G. Free energy landscape remodeling of the cardiac pacemaker channel explains the molecular basis of familial sinus bradycardia. J Biol Chem 2017; 292:6414-6428. [PMID: 28174302 DOI: 10.1074/jbc.m116.773697] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/28/2017] [Indexed: 12/21/2022] Open
Abstract
The hyperpolarization-activated and cyclic nucleotide-modulated ion channel (HCN) drives the pacemaker activity in the heart, and its malfunction can result in heart disorders. One such disorder, familial sinus bradycardia, is caused by the S672R mutation in HCN, whose electrophysiological phenotypes include a negative shift in the channel activation voltage and an accelerated HCN deactivation. The outcomes of these changes are abnormally low resting heart rates. However, the molecular mechanism underlying these electrophysiological changes is currently not fully understood. Crystallographic investigations indicate that the S672R mutation causes limited changes in the structure of the HCN intracellular gating tetramer, but its effects on protein dynamics are unknown. Here, we utilize comparative S672R versus WT NMR analyses to show that the S672R mutation results in extensive perturbations of the dynamics in both apo- and holo-forms of the HCN4 isoform, reflecting how S672R remodels the free energy landscape for the modulation of HCN4 by cAMP, i.e. the primary cyclic nucleotide modulator of HCN channels. We show that the S672R mutation results in a constitutive shift of the dynamic auto-inhibitory equilibrium toward inactive states of HCN4 and broadens the free-energy well of the apo-form, enhancing the millisecond to microsecond dynamics of the holo-form at sites critical for gating cAMP binding. These S672R-induced variations in dynamics provide a molecular basis for the electrophysiological phenotypes of this mutation and demonstrate that the pathogenic effects of the S672R mutation can be rationalized primarily in terms of modulations of protein dynamics.
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Affiliation(s)
- Stephen Boulton
- From the Departments of Biochemistry and Biomedical Sciences and
| | - Madoka Akimoto
- Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Sam Akbarizadeh
- Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Giuseppe Melacini
- From the Departments of Biochemistry and Biomedical Sciences and .,Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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22
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Holliday MJ, Camilloni C, Armstrong GS, Vendruscolo M, Eisenmesser EZ. Networks of Dynamic Allostery Regulate Enzyme Function. Structure 2017; 25:276-286. [PMID: 28089447 DOI: 10.1016/j.str.2016.12.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/28/2016] [Accepted: 12/12/2016] [Indexed: 11/16/2022]
Abstract
Many protein systems rely on coupled dynamic networks to allosterically regulate function. However, the broad conformational space sampled by non-coherently dynamic systems has precluded detailed analysis of their communication mechanisms. Here, we have developed a methodology that combines the high sensitivity afforded by nuclear magnetic resonance relaxation techniques and single-site multiple mutations, termed RASSMM, to identify two allosterically coupled dynamic networks within the non-coherently dynamic enzyme cyclophilin A. Using this methodology, we discovered two key hotspot residues, Val6 and Val29, that communicate through these networks, the mutation of which altered active-site dynamics, modulating enzymatic turnover of multiple substrates. Finally, we utilized molecular dynamics simulations to identify the mechanism by which one of these hotspots is coupled to the larger dynamic networks. These studies confirm a link between enzyme dynamics and the catalytic cycle of cyclophilin A and demonstrate how dynamic allostery may be engineered to tune enzyme function.
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Affiliation(s)
- Michael Joseph Holliday
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, 12801 East 17th Avenue, MS 8101, Aurora, CO 80045, USA
| | - Carlo Camilloni
- Department of Chemistry, Institute for Advanced Study, Technische Universität München, 85748 Garching, Germany
| | | | | | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, 12801 East 17th Avenue, MS 8101, Aurora, CO 80045, USA.
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23
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Rogals MJ, Greenwood AI, Kwon J, Lu KP, Nicholson LK. Neighboring phosphoSer-Pro motifs in the undefined domain of IRAK1 impart bivalent advantage for Pin1 binding. FEBS J 2016; 283:4528-4548. [PMID: 27790836 DOI: 10.1111/febs.13943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/20/2016] [Accepted: 10/25/2016] [Indexed: 01/01/2023]
Abstract
The peptidyl prolyl isomerase Pin1 has two domains that are considered to be its binding (WW) and catalytic (PPIase) domains, both of which interact with phosphorylated Ser/Thr-Pro motifs. This shared specificity might influence substrate selection, as many known Pin1 substrates have multiple sequentially close phosphoSer/Thr-Pro motifs, including the protein interleukin-1 receptor-associated kinase-1 (IRAK1). The IRAK1 undefined domain (UD) contains two sets of such neighboring motifs (Ser131/Ser144 and Ser163/Ser173), suggesting possible bivalent interactions with Pin1. Using a series of NMR titrations with 15N-labeled full-length Pin1 (Pin1-FL), PPIase, or WW domain and phosphopeptides representing the Ser131/Ser144 and Ser163/Ser173 regions of IRAK1-UD, bivalent interactions were investigated. Binding studies using singly phosphorylated peptides showed that individual motifs displayed weak affinities (> 100 μm) for Pin1-FL and each isolated domain. Analysis of dually phosphorylated peptides binding to Pin1-FL showed that inclusion of bivalent states was necessary to fit the data. The resulting complex model and fitted parameters were applied to predict the impact of bivalent states at low micromolar concentrations, demonstrating significant affinity enhancement for both dually phosphorylated peptides (3.5 and 24 μm for peptides based on the Ser131/Ser144 and Ser163/Ser173 regions, respectively). The complementary technique biolayer interferometry confirmed the predicted affinity enhancement for a representative set of singly and dually phosphorylated Ser131/Ser144 peptides at low micromolar concentrations, validating model predictions. These studies provide novel insights regarding the complexity of interactions between Pin1 and activated IRAK1, and more broadly suggest that phosphorylation of neighboring Ser/Thr-Pro motifs in proteins might provide competitive advantage at cellular concentrations for engaging with Pin1.
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Affiliation(s)
- Monique J Rogals
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Alexander I Greenwood
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, IL, USA
| | - Jeahoo Kwon
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Kun Ping Lu
- Division of Translational Therapeutics, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Linda K Nicholson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
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24
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Chang S, Kong R, Wang LQ, Shi H, Piao LH. Molecular dynamics simulations of wild type and mutant of Pin1 peptidyl-prolyl isomerase. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1185791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Shan Chang
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, P.R. China
| | - Ren Kong
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, P.R. China
| | - Li-qin Wang
- Changzhou College of Information Technology, Changzhou, P.R. China
| | - Hang Shi
- School of Computer Science & Engineering, Jiangsu University of Technology, Changzhou, P.R. China
| | - Lian-hua Piao
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, P.R. China
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25
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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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26
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Barman A, Hamelberg D. Coupled Dynamics and Entropic Contribution to the Allosteric Mechanism of Pin1. J Phys Chem B 2016; 120:8405-15. [DOI: 10.1021/acs.jpcb.6b02123] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Arghya Barman
- Department
of Chemistry and
the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department
of Chemistry and
the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
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27
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Waudby CA, Ramos A, Cabrita LD, Christodoulou J. Two-Dimensional NMR Lineshape Analysis. Sci Rep 2016; 6:24826. [PMID: 27109776 PMCID: PMC4843008 DOI: 10.1038/srep24826] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/31/2016] [Indexed: 12/18/2022] Open
Abstract
NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of two-dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire two-dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions.
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Affiliation(s)
- Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
| | - Andres Ramos
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
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28
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Barman A, Smitherman C, Souffrant M, Gadda G, Hamelberg D. Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. J Chem Inf Model 2015; 56:139-47. [DOI: 10.1021/acs.jcim.5b00560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Arghya Barman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Crystal Smitherman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Michael Souffrant
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Giovanni Gadda
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
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29
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Wang X, Mahoney BJ, Zhang M, Zintsmaster JS, Peng JW. Negative Regulation of Peptidyl-Prolyl Isomerase Activity by Interdomain Contact in Human Pin1. Structure 2015; 23:2224-2233. [PMID: 26602185 DOI: 10.1016/j.str.2015.08.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 08/22/2015] [Accepted: 08/24/2015] [Indexed: 01/10/2023]
Abstract
Pin1 is a modular peptidyl-prolyl isomerase specific for phosphorylated Ser/Thr-Pro (pS/T-P) motifs, typically within intrinsically disordered regions of signaling proteins. Pin1 consists of two flexibly linked domains: an N-terminal WW domain for substrate binding and a larger C-terminal peptidyl-prolyl isomerase (PPIase) domain. Previous studies showed that binding of phosphopeptide substrates to Pin1 could alter Pin1 interdomain contact, strengthening or weakening it depending on the substrate sequence. Thus, substrate-induced changes in interdomain contact may act as a trigger within the Pin1 mechanism. Here, we investigate this possibility via nuclear magnetic resonance studies of several Pin1 mutants. Our findings provide new mechanistic insights for those substrates that reduce interdomain contact. Specifically, the reduced interdomain contact can allosterically enhance PPIase activity relative to that when the contact is sustained. These findings suggest Pin1 interdomain contact can negatively regulate its activity.
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Affiliation(s)
- Xingsheng Wang
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Brendan J Mahoney
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Meiling Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - John S Zintsmaster
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Jeffrey W Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA.
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30
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Holliday MJ, Armstrong GS, Eisenmesser EZ. Determination of the Full Catalytic Cycle among Multiple Cyclophilin Family Members and Limitations on the Application of CPMG-RD in Reversible Catalytic Systems. Biochemistry 2015; 54:5815-27. [PMID: 26335054 DOI: 10.1021/acs.biochem.5b00746] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Cyclophilins catalyze cis ↔ trans isomerization of peptidyl-prolyl bonds, influencing protein folding along with a breadth of other biological functions such as signal transduction. Here, we have determined the microscopic rate constants defining the full enzymatic cycle for three human cyclophilins and a more distantly related thermophilic bacterial cyclophilin when catalyzing interconversion of a biologically representative peptide substrate. The cyclophilins studied here exhibit variability in on-enzyme interconversion as well as an up to 2-fold range in rates of substrate binding and release. However, among the human cyclophilins, the microscopic rate constants appear to have been tuned to maintain remarkably similar isomerization rates without a concurrent conservation of apparent binding affinities. While the structures and active site compositions of the human cyclophilins studied here are highly conserved, we find that the enzymes exhibit significant variability in microsecond to millisecond time scale mobility, suggesting a role for the inherent conformational fluctuations that exist within the cyclophilin family as being functionally relevant in regulating substrate interactions. We have additionally modeled the relaxation dispersion profile given by the commonly employed Carr-Purcell-Meiboom-Gill relaxation dispersion (CPMG-RD) experiment when applied to a reversible enzymatic system such as cyclophilin isomerization and identified a significant limitation in the applicability of this approach for monitoring on-enzyme turnover. Specifically, we show both computationally and experimentally that the CPMG-RD experiment is sensitive to noncatalyzed substrate binding and release in reversible systems even at saturating substrate concentrations unless the on-enzyme interconversion rate is much faster than the substrate release rate.
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Affiliation(s)
- Michael J Holliday
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver , 12801 East 17th Avenue, Aurora, Colorado 80045, United States
| | - Geoffrey S Armstrong
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309, United States
| | - Elan Z Eisenmesser
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver , 12801 East 17th Avenue, Aurora, Colorado 80045, United States
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31
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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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32
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Barman A, Hamelberg D. Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self-association ofcis-tau peptide. Proteins 2015; 83:436-44. [DOI: 10.1002/prot.24740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/07/2014] [Accepted: 11/26/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Arghya Barman
- Department of Chemistry and the Center for Biotechnology and Drug Design; Georgia State University; Atlanta Georgia 30302-4098
| | - Donald Hamelberg
- Department of Chemistry and the Center for Biotechnology and Drug Design; Georgia State University; Atlanta Georgia 30302-4098
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33
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Ladani ST, Souffrant MG, Barman A, Hamelberg D. Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl cis-trans isomerases. Biochim Biophys Acta Gen Subj 2015; 1850:1994-2004. [PMID: 25585011 DOI: 10.1016/j.bbagen.2014.12.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/23/2014] [Accepted: 12/29/2014] [Indexed: 01/16/2023]
Abstract
BACKGROUND Peptidyl prolyl cis-trans isomerization of the protein backbone is involved in the regulation of many biological processes. Cis-trans isomerization is notoriously slow and is catalyzed by a family of cis-trans peptidyl prolyl isomerases (PPIases) that have been implicated in many diseases. A general consensus on how these enzymes speed up prolyl isomerization has not been reached after decades of both experimental and computational studies. SCOPE OF REVIEW Computational studies carried out to understand the catalytic mechanism of the prototypical FK506 binding protein 12, Cyclophilin A and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) are reviewed. A summary and an evaluation of the implications of the proposed mechanisms from computational studies are presented. MAJOR CONCLUSIONS The analysis of computational studies and evaluation of the proposed mechanisms provide a general consensus and a better understanding of PPIase catalysis. The speedup of the rate of peptidyl-prolyl isomerization by PPIases can be best described by a catalytic mechanism in which the substrate in transition state configuration is stabilized. The enzymes preferentially bind the transition state configuration of the substrate relative to the cis conformation, which in most cases is bound better than the trans conformation of the substrate. Stabilization of the transition state configuration of the substrate leads to a lower free energy barrier and a faster rate of isomerization when compared to the uncatalyzed isomerization reaction. GENERAL SIGNIFICANCE Fully understanding the catalytic mechanism of PPIases has broad implications for drug design, elucidation of the molecular basis of many diseases, protein engineering, and enzyme catalysis in general. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Safieh Tork Ladani
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA
| | - Michael G Souffrant
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA
| | - Arghya Barman
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA
| | - Donald Hamelberg
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA.
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34
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Di Martino GP, Masetti M, Cavalli A, Recanatini M. Mechanistic insights into Pin1 peptidyl-prolyl cis-trans isomerization from umbrella sampling simulations. Proteins 2014; 82:2943-56. [PMID: 25066180 DOI: 10.1002/prot.24650] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 06/25/2014] [Accepted: 07/15/2014] [Indexed: 12/22/2022]
Abstract
The peptidyl-proyl isomerase Pin1 plays a key role in the regulation of phospho(p)-Ser/Thr-Pro proteins, acting as a molecular timer of the cell cycle. After recognition of these motifs, Pin1 catalyzes the rapid cis-trans isomerization of proline amide bonds of substrates, contributing to maintain the equilibrium between the two conformations. Although a great interest has arisen on this enzyme, its catalytic mechanism has long been debated. Here, the cis-trans isomerization of a model peptide system was investigated by means of umbrella sampling simulations in the Pin1-bound and unbound states. We obtained free energy barriers consistent with experimental data, and identified several enzymatic features directly linked to the acceleration of the prolyl bond isomerization. In particular, an enhanced autocatalysis, the stabilization of perturbed ground state conformations, and the substrate binding in a procatalytic conformation were found as main contributions to explain the lowering of the isomerization free energy barrier.
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Affiliation(s)
- Giovanni Paolo Di Martino
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Università di Bologna, Via Belmeloro 6, 40126, Bologna, Italy
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35
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Barman A, Hamelberg D. Cysteine-mediated dynamic hydrogen-bonding network in the active site of Pin1. Biochemistry 2014; 53:3839-50. [PMID: 24840168 DOI: 10.1021/bi5000977] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Enzymes catalyze a plethora of chemical reactions that are tightly regulated and intricately coupled in biology. Catalysis of phosphorylation-dependent cis-trans isomerization of peptidyl-prolyl bonds, which act as conformational switches in regulating many post-phosphorylation processes, is considered to be one of the most critical. Pin1 is a cis-trans isomerase of peptidyl-prolyl(ω-) bonds of phosphorylated-Ser/Thr-Pro motifs and has been implicated in many diseases. Structural and experimental studies are still unable to resolve the mechanistic role and protonation states of two adjacent histidines (His59 and His157) and a cysteine (Cys113) in the active site of Pin1. Here, we show that the protonation state of Cys113 mediates a dynamic hydrogen-bonding network in the active site of Pin1, involving the two adjacent histidines and several other residues that are highly conserved and necessary for catalysis. We have used detailed free energy calculations and molecular dynamics simulations, complementing previous experiments, to resolve the ambiguities in the orientations of the histidines and protonation states of these key active site residues, details that are critical for fully understanding the mechanism of Pin1 and necessary for developing potent inhibitors. Importantly, Cys113 is shown to alternate between the unprotonated and neutral states, unprotonated in free Pin1 and neutral in substrate-bound Pin1. Our results are consistent with experiments and provide an explanation for the chemical reactivity of free Pin1 that is suggested to be necessary for the regulation of the enzyme.
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Affiliation(s)
- Arghya Barman
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University , Atlanta, Georgia 30302-4098, United States
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36
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Hawse WF, De S, Greenwood AI, Nicholson LK, Zajicek J, Kovrigin EL, Kranz DM, Garcia KC, Baker BM. TCR scanning of peptide/MHC through complementary matching of receptor and ligand molecular flexibility. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 192:2885-91. [PMID: 24523505 PMCID: PMC3992338 DOI: 10.4049/jimmunol.1302953] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Although conformational changes in TCRs and peptide Ags presented by MHC protein (pMHC) molecules often occur upon binding, their relationship to intrinsic flexibility and role in ligand selectivity are poorly understood. In this study, we used nuclear magnetic resonance to study TCR-pMHC binding, examining recognition of the QL9/H-2L(d) complex by the 2C TCR. Although the majority of the CDR loops of the 2C TCR rigidify upon binding, the CDR3β loop remains mobile within the TCR-pMHC interface. Remarkably, the region of the QL9 peptide that interfaces with CDR3β is also mobile in the free pMHC and in the TCR-pMHC complex. Determination of conformational exchange kinetics revealed that the motions of CDR3β and QL9 are closely matched. The matching of conformational exchange in the free proteins and its persistence in the complex enhances the thermodynamic and kinetic stability of the TCR-pMHC complex and provides a mechanism for facile binding. We thus propose that matching of structural fluctuations is a component of how TCRs scan among potential ligands for those that can bind with sufficient stability to enable T cell signaling.
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Affiliation(s)
- William F. Hawse
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46530, USA
| | - Soumya De
- Department of Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Alex I. Greenwood
- Department of Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Linda K. Nicholson
- Department of Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jaroslav Zajicek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46530, USA
| | | | - David M. Kranz
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana IL 61801, USA
| | - K. Christopher Garcia
- Departments of Molecular & Cellular Physiology and Structural Biology, Program in Immunology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46530, USA
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37
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Mercedes-Camacho AY, Mullins AB, Mason MD, Xu GG, Mahoney BJ, Wang X, Peng JW, Etzkorn FA. Kinetic isotope effects support the twisted amide mechanism of Pin1 peptidyl-prolyl isomerase. Biochemistry 2013; 52:7707-13. [PMID: 24116866 DOI: 10.1021/bi400700b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Pin1 peptidyl-prolyl isomerase catalyzes isomerization of pSer/pThr-Pro motifs in regulating the cell cycle. Peptide substrates, Ac-Phe-Phe-phosphoSer-Pro-Arg-p-nitroaniline, were synthesized in unlabeled form, and with deuterium-labeled Ser-d3 and Pro-d7 amino acids. Kinetic data were collected as a function of Pin1 concentration to measure kinetic isotope effects (KIEs) on catalytic efficiency (kcat/Km). The normal secondary (2°) KIE value measured for the Ser-d3 substrate (kH/kD = 1.6 ± 0.2) indicates that the serine carbonyl does not rehybridize from sp(2) to sp(3) in the rate-determining step, ruling out a nucleophilic addition mechanism. The normal 2° KIE can be explained by hyperconjugation between Ser α-C-H/D and C═O and release of steric strain upon rotation of the amide bond from cis to syn-exo. The inverse 2° KIE value (kH/kD = 0.86 ± 0.08) measured for the Pro-d7 substrate indicates rehybridization of the prolyl nitrogen from sp(2) to sp(3) during the rate-limiting step of isomerization. No solvent kinetic isotope was measured by NMR exchange spectroscopy (kH2O/kD2O = 0.92 ± 0.12), indicating little or no involvement of exchangeable protons in the mechanism. These results support the formation of a simple twisted amide transition state as the mechanism for peptidyl prolyl isomerization catalyzed by Pin1. A model of the reaction mechanism is presented using crystal structures of Pin1 with ground state analogues and an inhibitor that resembles a twisted amide transition state.
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38
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Velazquez HA, Hamelberg D. Conformation-Directed Catalysis and Coupled Enzyme–Substrate Dynamics in Pin1 Phosphorylation-Dependent Cis–Trans Isomerase. J Phys Chem B 2013; 117:11509-17. [DOI: 10.1021/jp405271s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hector A. Velazquez
- Department
of Chemistry and
the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Donald Hamelberg
- Department
of Chemistry and
the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
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39
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Monneau YR, Soufari H, Nelson CJ, Mackereth CD. Structure and activity of the peptidyl-prolyl isomerase domain from the histone chaperone Fpr4 toward histone H3 proline isomerization. J Biol Chem 2013; 288:25826-25837. [PMID: 23888048 DOI: 10.1074/jbc.m113.479964] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The FK506-binding protein (FKBP) family of peptidyl-prolyl isomerases (PPIases) is characterized by a common catalytic domain that binds to the inhibitors FK506 and rapamycin. As one of four FKBPs within the yeast Saccharomyces cerevisiae, Fpr4 has been described as a histone chaperone, and is in addition implicated in epigenetic function in part due to its mediation of cis-trans conversion of proline residues within histone tails. To better understand the molecular details of this activity, we have determined the solution structure of the Fpr4 C-terminal PPIase domain by using NMR spectroscopy. This canonical FKBP domain actively increases the rate of isomerization of three decapeptides derived from the N terminus of yeast histone H3, whereas maintaining intrinsic cis and trans populations. Observation of the uncatalyzed and Fpr4-catalyzed isomerization rates at equilibrium demonstrate Pro(16) and Pro(30) of histone H3 as the major proline targets of Fpr4, with little activity shown against Pro(38). This alternate ranking of the three target prolines, as compared with affinity determination or the classical chymotrypsin-based fluorescent assay, reveals the mechanistic importance of substrate residues C-terminal to the peptidyl-prolyl bond.
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Affiliation(s)
- Yoan R Monneau
- From the Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Heddy Soufari
- From the Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France,; the INSERM U869, University of Bordeaux, 33076 Bordeaux, France, and
| | - Christopher J Nelson
- the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - Cameron D Mackereth
- From the Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France,; the INSERM U869, University of Bordeaux, 33076 Bordeaux, France, and.
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40
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Markin CJ, Spyracopoulos L. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations. JOURNAL OF BIOMOLECULAR NMR 2012; 54:355-376. [PMID: 23086713 DOI: 10.1007/s10858-012-9678-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 10/10/2012] [Indexed: 06/01/2023]
Abstract
NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements from NMR-monitored chemical shift titrations, for which the dependence of K ( D ) on the chemical shift difference (Δω) between free and bound states is extrapolated to Δω = 0. The demonstrated accuracy and precision for k ( off ) will be valuable for the interpretation of biological kinetics in weakly interacting protein-protein networks, where a small change in the magnitude of the underlying kinetics of a given pathway may lead to large changes in the associated downstream signaling cascade.
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Affiliation(s)
- Craig J Markin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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41
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O'Connor C, Kovrigin EL. Characterization of the second ion-binding site in the G domain of H-Ras. Biochemistry 2012; 51:9638-46. [PMID: 23148511 DOI: 10.1021/bi301304g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ras is a small monomeric GTPase acting as molecular switch in multiple cellular processes. The N-terminal G domain of Ras binds GTP or GDP accompanied by a magnesium ion, which is strictly required for GTPase activity and performs a structural role. Another ion-binding site on the opposite face of the G domain has been recently observed to specifically associate with calcium acetate in the crystal [Buhrman, G., et al. (2010) Proc. Natl. Aacd. Sci. U.S.A. 107, 4931-4936]. In this article, we report thermodynamic measurements of the affinity and specificity of the remote ion-binding site in H-Ras as observed in solution. Using (15)N-(1)H nuclear magnetic resonance spectroscopy, we determined that, in contrast to the crystalline state, the remote site in solution is specific for a divalent cation, binding both calcium and magnesium with anions playing a minimal role. The affinity of the remote site for divalent cations is in the low millimolar range and remarkably different for GDP- and GppNHp-bound forms of the G domain, indicating that the GTP-binding pocket and the remote site are allosterically coupled through the distance of more than 25 Å. Considering that the remote site is oriented toward the membrane surface in vivo, we hypothesize that its cognate biological ligand might be a positively charged group extending from a lipid or an integral membrane protein.
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Affiliation(s)
- Casey O'Connor
- Biochemistry Department, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
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42
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Krishnan N, Lam TT, Fritz A, Rempinski D, O'Loughlin K, Minderman H, Berezney R, Marzluff WF, Thapar R. The prolyl isomerase Pin1 targets stem-loop binding protein (SLBP) to dissociate the SLBP-histone mRNA complex linking histone mRNA decay with SLBP ubiquitination. Mol Cell Biol 2012; 32:4306-22. [PMID: 22907757 PMCID: PMC3486140 DOI: 10.1128/mcb.00382-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 08/13/2012] [Indexed: 01/04/2023] Open
Abstract
Histone mRNAs are rapidly degraded at the end of S phase, and a 26-nucleotide stem-loop in the 3' untranslated region is a key determinant of histone mRNA stability. This sequence is the binding site for stem-loop binding protein (SLBP), which helps to recruit components of the RNA degradation machinery to the histone mRNA 3' end. SLBP is the only protein whose expression is cell cycle regulated during S phase and whose degradation is temporally correlated with histone mRNA degradation. Here we report that chemical inhibition of the prolyl isomerase Pin1 or downregulation of Pin1 by small interfering RNA (siRNA) increases the mRNA stability of all five core histone mRNAs and the stability of SLBP. Pin1 regulates SLBP polyubiquitination via the Ser20/Ser23 phosphodegron in the N terminus. siRNA knockdown of Pin1 results in accumulation of SLBP in the nucleus. We show that Pin1 can act along with protein phosphatase 2A (PP2A) in vitro to dephosphorylate a phosphothreonine in a conserved TPNK sequence in the SLBP RNA binding domain, thereby dissociating SLBP from the histone mRNA hairpin. Our data suggest that Pin1 and PP2A act to coordinate the degradation of SLBP by the ubiquitin proteasome system and the exosome-mediated degradation of the histone mRNA by regulating complex dissociation.
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Affiliation(s)
| | - TuKiet T. Lam
- W. M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut, USA
| | - Andrew Fritz
- Department of Biological Sciences, SUNY at Buffalo, Buffalo, New York, USA
| | | | - Kieran O'Loughlin
- Department of Flow and Image Cytometry, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Hans Minderman
- Department of Flow and Image Cytometry, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Ronald Berezney
- Department of Biological Sciences, SUNY at Buffalo, Buffalo, New York, USA
| | - William F. Marzluff
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Roopa Thapar
- Hauptman Woodward Medical Research Institute
- Department of Structural Biology, SUNY at Buffalo, Buffalo, New York, USA
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43
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Vöhringer-Martinez E, Duarte F, Toro-Labbé A. How Does Pin1 Catalyze the Cis–Trans Prolyl Peptide Bond Isomerization? A QM/MM and Mean Reaction Force Study. J Phys Chem B 2012; 116:12972-9. [DOI: 10.1021/jp307946h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Fernanda Duarte
- Laboratorio de Química
Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Santiago,
Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química
Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Santiago,
Chile
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44
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De S, Greenwood AI, Rogals MJ, Kovrigin EL, Lu KP, Nicholson LK. Complete thermodynamic and kinetic characterization of the isomer-specific interaction between Pin1-WW domain and the amyloid precursor protein cytoplasmic tail phosphorylated at Thr668. Biochemistry 2012; 51:8583-96. [PMID: 23025283 DOI: 10.1021/bi3008214] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Peptidyl prolyl cis-trans isomerization acts as an effective molecular timer that plays significant roles in biological and pathological processes. Enzymes such as Pin1 catalyze cis-trans isomerization, accelerating the otherwise slow isomerization rate into time scales relevant for cellular signaling. Here we have combined NMR line shape analysis, fluorescence spectroscopy, and isothermal titration calorimetry to determine the kinetic and thermodynamic parameters describing the trans-specific interaction between the binding domain of Pin1 (WW domain) and a key cis-trans molecular switch in the amyloid precursor protein cytoplasmic tail. A three-state model, in which the cis-trans isomerization equilibrium is coupled to the binding equilibrium through the trans isomer, was found to fit the data well. The trans isomer binds the WW domain with ∼22 μM affinity via very fast association (approaching the diffusion limit) and dissociation rates. The common structural and electrostatic characteristics of Pin1 substrates, which contain a phosphorylated serine/threonine-proline motif, suggest that very rapid binding kinetics are a general feature of Pin1 interactions with other substrates. The fast binding kinetics of the WW domain allows rapid response of Pin1 to the dynamic events of phosphorylation and dephosphorylation in the cell that alter the relative populations of diverse Pin1 substrates. Furthermore, our results also highlight the vastly different rates at which slow uncatalyzed cis-trans isomerization and fast isomer-specific binding events occur. These results, along with the experimental methods presented herein, should guide future experiments aimed at the thermodynamic and kinetic characterization of cis-trans molecular switches and isomer-specific interactions involved in various biological processes.
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Affiliation(s)
- Soumya De
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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45
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Kovrigin EL. NMR line shapes and multi-state binding equilibria. JOURNAL OF BIOMOLECULAR NMR 2012; 53:257-70. [PMID: 22610542 DOI: 10.1007/s10858-012-9636-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 05/01/2012] [Indexed: 05/21/2023]
Abstract
Biological function of proteins relies on conformational transitions and binding of specific ligands. Protein-ligand interactions are thermodynamically and kinetically coupled to conformational changes in protein structures as conceptualized by the models of pre-existing equilibria and induced fit. NMR spectroscopy is particularly sensitive to complex ligand-binding modes-NMR line-shape analysis can provide for thermodynamic and kinetic constants of ligand-binding equilibria with the site-specific resolution. However, broad use of line shape analysis is hampered by complexity of NMR line shapes in multi-state systems. To facilitate interpretation of such spectral patterns, I computationally explored systems where isomerization or dimerization of a protein (receptor) molecule is coupled to binding of a ligand. Through an extensive analysis of multiple exchange regimes for a family of three-state models, I identified signature features to guide an NMR experimentalist in recognizing specific interaction mechanisms. Results show that distinct multi-state models may produce very similar spectral patterns. I also discussed aggregation of a receptor as a possible source of spurious three-state line shapes and provided specific suggestions for complementary experiments that can ensure reliable mechanistic insight.
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Affiliation(s)
- Evgenii L Kovrigin
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI 53201, USA.
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