1
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Masoumzadeh E, Ying J, Baber JL, Anfinrud P, Bax A. Proline Peptide Bond Isomerization in Ubiquitin Under Folding and Denaturing Conditions by Pressure-Jump NMR. J Mol Biol 2024; 436:168587. [PMID: 38663546 PMCID: PMC11166230 DOI: 10.1016/j.jmb.2024.168587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024]
Abstract
Proline isomerization is widely recognized as a kinetic bottleneck in protein folding, amplified for proteins rich in Pro residues. We introduced repeated hydrostatic pressure jumps between native and pressure-denaturing conditions inside an NMR sample cell to study proline isomerization in the pressure-sensitized L50A ubiquitin mutant. Whereas in two unfolded heptapeptides, X-Pro peptide bonds isomerized ca 1.6-fold faster at 1 bar than at 2.5 kbar, for ubiquitin ca eight-fold faster isomerization was observed for Pro-38 and ca two-fold for Pro-19 and Pro-37 relative to rates measured in the pressure-denatured state. Activation energies for isomerization in pressure-denatured ubiquitin were close to literature values of 20 kcal/mole for denatured polypeptides but showed a substantial drop to 12.7 kcal/mole for Pro-38 at atmospheric pressure. For ubiquitin isomers with a cis E18-P19 peptide bond, the 1-bar NMR spectrum showed sharp resonances with near random coil chemical shifts for the C-terminal half of the protein, characteristic of an unfolded chain, while most of the N-terminal residues were invisible due to exchange broadening, pointing to a metastable partially folded state for this previously recognized 'folding nucleus'. For cis-P37 isomers, a drop in pressure resulted in the rapid loss of nearly all unfolded-state NMR resonances, while the recovery of native state intensity revealed a slow component attributed to cis → trans isomerization of P37. This result implies that the NMR-invisible cis-P37 isomer adopts a molten globule state that encompasses the entire length of the ubiquitin chain, suggestive of a structure that mostly resembles the folded state.
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Affiliation(s)
- Elahe Masoumzadeh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - James L Baber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Philip Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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2
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Ferreon JC, Ta HM, Yun H, Choi KJ, Quan MD, Tsoi PS, Kim C, Lee CW, Ferreon ACM. Stereospecific NANOG PEST Stabilization by Pin1. Biochemistry 2024; 63:1067-1074. [PMID: 38619104 DOI: 10.1021/acs.biochem.4c00056] [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: 04/16/2024]
Abstract
NANOG protein levels correlate with stem cell pluripotency. NANOG concentrations fluctuate constantly with low NANOG levels leading to spontaneous cell differentiation. Previous literature implicated Pin1, a phosphorylation-dependent prolyl isomerase, as a key player in NANOG stabilization. Here, using NMR spectroscopy, we investigate the molecular interactions of Pin1 with the NANOG unstructured N-terminal domain that contains a PEST sequence with two phosphorylation sites. Phosphorylation of NANOG PEST peptides increases affinity to Pin1. By systematically increasing the amount of cis PEST conformers, we show that the peptides bind tighter to the prolyl isomerase domain (PPIase) of Pin1. Phosphorylation and cis Pro enhancement at both PEST sites lead to a 5-10-fold increase in NANOG binding to the Pin1 WW domain and PPIase domain, respectively. The cis-populated NANOG PEST peptides can be potential inhibitors for disrupting Pin1-dependent NANOG stabilization in cancer stem cells.
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Affiliation(s)
- Josephine C Ferreon
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Hai Minh Ta
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Hyosuk Yun
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Kyoung-Jae Choi
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - My Diem Quan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Phoebe S Tsoi
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Choel Kim
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Chul Won Lee
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Allan Chris M Ferreon
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
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3
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Bai Y, Yuan Z, Yuan S, He Z. Recent advances of Pin1 inhibitors as potential anticancer agents. Bioorg Chem 2024; 144:107171. [PMID: 38325131 DOI: 10.1016/j.bioorg.2024.107171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Pin1 (proline isomerase peptidyl-prolyl isomerase NIMA-interacting-1), as a member of PPIase family, catalyzes cis-trans isomerization of pThr/Ser-Pro amide bonds of its substrate proteins, further regulating cell proliferation, division, apoptosis, and transformation. Pin1 is overexpressed in various cancers and is positively correlated with tumor initiation and progression. Pin1 inhibition can effectively reduce tumor growth and cancer stem cell expansion, block metastatic spread, and restore chemosensitivity, suggesting that targeting Pin1 may be an effective strategy for cancer treatment. Considering the promising therapeutic effects of Pin1 inhibitors on cancers, we herein are intended to comprehensively summarize the reported Pin1 inhibitors, mainly highlighting their structures, biological functions and binding modes, in hope of providing a reference for the future drug discovery.
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Affiliation(s)
- Yiru Bai
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Ziqiao Yuan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shuo Yuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China.
| | - Zhangxu He
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, China.
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4
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Yao XQ, Hamelberg D. Dissecting the Allosteric Fine-Tuning of Enzyme Catalysis. JACS AU 2024; 4:837-846. [PMID: 38425926 PMCID: PMC10900222 DOI: 10.1021/jacsau.3c00806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
Fully understanding the mechanism of allosteric regulation in biomolecules requires separating and examining all of the involved factors. In enzyme catalysis, allosteric effector binding shifts the structure and dynamics of the active site, leading to modified energetic (e.g., energy barrier) and dynamical (e.g., diffusion coefficient) factors underlying the catalyzed reaction rate. Such modifications can be subtle and dependent on the type of allosteric effector, representing a fine-tuning of protein function. The microscopic description of allosteric regulation at the level of function-dictating factors has prospective applications in fundamental and pharmaceutical sciences, which is, however, largely missing so far. Here, we characterize the allosteric fine-tuning of enzyme catalysis, using human Pin1 as an example, by performing more than half-millisecond all-atom molecular dynamics simulations. Changes of reaction kinetics and the dictating factors, including the free energy surface along the reaction coordinate and the diffusion coefficient of the reaction dynamics, under various enzyme and allosteric effector binding conditions are examined. Our results suggest equal importance of the energetic and dynamical factors, both of which can be modulated allosterically, and the combined effect determines the final allosteric output. We also reveal the potential dynamic basis for allosteric modulation using an advanced statistical technique to detect function-related conformational dynamics. Methods developed in this work can be applied to other allosteric systems.
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Affiliation(s)
- Xin-Qiu Yao
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
- Department
of Chemistry, University of Nebraska Omaha, Omaha, Nebraska 68182-0266, United
States
| | - Donald Hamelberg
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
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5
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Chen XR, Igumenova TI. Regulation of eukaryotic protein kinases by Pin1, a peptidyl-prolyl isomerase. Adv Biol Regul 2023; 87:100938. [PMID: 36496344 PMCID: PMC9992314 DOI: 10.1016/j.jbior.2022.100938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
The peptidyl-prolyl isomerase Pin1 cooperates with proline-directed kinases and phosphatases to regulate multiple oncogenic pathways. Pin1 specifically recognizes phosphorylated Ser/Thr-Pro motifs in proteins and catalyzes their cis-trans isomerization. The Pin1-catalyzed conformational changes determine the stability, activity, and subcellular localization of numerous protein substrates. We conducted a survey of eukaryotic protein kinases that are regulated by Pin1 and whose Pin1 binding sites have been identified. Our analyses reveal that Pin1 target sites in kinases do not fall exclusively within the intrinsically disordered regions of these enzymes. Rather, they fall into three groups based on their location: (i) within the catalytic kinase domain, (ii) in the C-terminal kinase region, and (iii) in regulatory domains. Some of the kinases downregulated by Pin1 activity are tumor-suppressing, and all kinases upregulated by Pin1 activity are functionally pro-oncogenic. These findings further reinforce the rationale for developing Pin1-specific inhibitors as attractive pharmaceuticals for cancer therapy.
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Affiliation(s)
- Xiao-Ru Chen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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6
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Born A, Soetbeer J, Henen MA, Breitgoff F, Polyhach Y, Jeschke G, Vögeli B. Ligand-specific conformational change drives interdomain allostery in Pin1. Nat Commun 2022; 13:4546. [PMID: 35927276 PMCID: PMC9352728 DOI: 10.1038/s41467-022-32340-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Pin1 is a two-domain cell regulator that isomerizes peptidyl-prolines. The catalytic domain (PPIase) and the other ligand-binding domain (WW) sample extended and compact conformations. Ligand binding changes the equilibrium of the interdomain conformations, but the conformational changes that lead to the altered domain sampling were unknown. Prior evidence has supported an interdomain allosteric mechanism. We recently introduced a magnetic resonance-based protocol that allowed us to determine the coupling of intra- and interdomain structural sampling in apo Pin1. Here, we describe ligand-specific conformational changes that occur upon binding of pCDC25c and FFpSPR. pCDC25c binding doubles the population of the extended states compared to the virtually identical populations of the apo and FFpSPR-bound forms. pCDC25c binding to the WW domain triggers conformational changes to propagate via the interdomain interface to the catalytic site, while FFpSPR binding displaces a helix in the PPIase that leads to repositioning of the PPIase catalytic loop.
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Affiliation(s)
- Alexandra Born
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO, USA
| | - Janne Soetbeer
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Morkos A Henen
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO, USA.,Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Frauke Breitgoff
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Beat Vögeli
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO, USA.
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7
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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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8
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Chen J. A Specific pSer/Thr-Pro Motif Generates Interdomain Communication Bifurcations of Two Modes of Pin1 in Solution Nuclear Magnetic Resonance. Biochemistry 2022; 61:1167-1180. [PMID: 35648841 DOI: 10.1021/acs.biochem.2c00255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Peptides mediate the interdomain communication of Pin1 (peptidyl-prolyl cis-trans isomerase) and can regulate its conformation and biochemical functions, providing an idea for drug design using Pin1. Two template peptide sequences have been widely used in the extended or compact state of Pin1 (Cdc25C, E-Q-P-L-pT-P-V-T-D-L; Pintide, W-F-Y-pS-P-R). The way in which specific pSer/Thr-Pro peptides regulate interdomain communication to achieve the opposite state is not clear. In this study, we subdivided the sequence composition of eight types of modified peptides and investigated the interaction with Pin1 by solution nuclear magnetic resonance and molecular dynamics. Demonstrating sequence dependence on the pSer-Pro or pThr-Pro motif and different residues in anchoring the WW domain, the Pin peptide (Pintide, PintideT, Pin25C, and Pin25CT) transmits this concentration accumulation to the PPIase domain, thus exhibiting two anchoring tendencies. However, the Cdc peptide (Cdc25C, Cdc25CS, Cdctide, and CdctideS) has a low binding energy that makes it difficult for the conformation to reach a steady state. In addition, Pin1 is influenced by both compact and extended states, regulated precisely by the sequence as well as by threonine or serine. These results provide new insight into the interdomain communication of Pin1 via pSer/Thr-Pro peptide binding.
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Affiliation(s)
- Jingqiu Chen
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima 739-8526, Japan
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9
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Born A, Henen MA, Nichols PJ, Vögeli B. On the use of residual dipolar couplings in multi-state structure calculation of two-domain proteins. MAGNETIC RESONANCE LETTERS 2022; 2:61-68. [PMID: 35734611 PMCID: PMC9210859 DOI: 10.1016/j.mrl.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Residual dipolar couplings (RDCs) are powerful nuclear magnetic resonance (NMR) probes for the structure calculation of biomacromolecules. Typically, an alignment tensor that defines the orientation of the entire molecule relative to the magnetic field is determined either before refinement of individual bond vectors or simultaneously with this refinement. For single-domain proteins this approach works well since all bond vectors can be described within the same coordinate frame, which is given by the alignment tensor. However, novel approaches are sought after for systems where no universal alignment tensor can be used. Here, we present an approach that can be applied to two-domain proteins that enables the calculation of multiple states within each domain as well as with respect to the relative positions of the two domains.
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Affiliation(s)
- Alexandra Born
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, 12801 East 17 Avenue, Aurora, CO 80045, USA
| | - Morkos A. Henen
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, 12801 East 17 Avenue, Aurora, CO 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Parker J. Nichols
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, 12801 East 17 Avenue, Aurora, CO 80045, USA
| | - Beat Vögeli
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, 12801 East 17 Avenue, Aurora, CO 80045, USA
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10
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Born A, Soetbeer J, Breitgoff F, Henen MA, Sgourakis N, Polyhach Y, Nichols PJ, Strotz D, Jeschke G, Vögeli B. Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance. J Am Chem Soc 2021; 143:16055-16067. [PMID: 34579531 DOI: 10.1021/jacs.1c06289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteins composed of multiple domains allow for structural heterogeneity and interdomain dynamics that may be vital for function. Intradomain structures and dynamics can influence interdomain conformations and vice versa. However, no established structure determination method is currently available that can probe the coupling of these motions. The protein Pin1 contains separate regulatory and catalytic domains that sample "extended" and "compact" states, and ligand binding changes this equilibrium. Ligand binding and interdomain distance have been shown to impact the activity of Pin1, suggesting interdomain allostery. In order to characterize the conformational equilibrium of Pin1, we describe a novel method to model the coupling between intra- and interdomain dynamics at atomic resolution using multistate ensembles. The method uses time-averaged nuclear magnetic resonance (NMR) restraints and double electron-electron resonance (DEER) data that resolve distance distributions. While the intradomain calculation is primarily driven by exact nuclear Overhauser enhancements (eNOEs), J couplings, and residual dipolar couplings (RDCs), the relative domain distribution is driven by paramagnetic relaxation enhancement (PREs), RDCs, interdomain NOEs, and DEER. Our data support a 70:30 population of the compact and extended states in apo Pin1. A multistate ensemble describes these conformations simultaneously, with distinct conformational differences located in the interdomain interface stabilizing the compact or extended states. We also describe correlated conformations between the catalytic site and interdomain interface that may explain allostery driven by interdomain contact.
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Affiliation(s)
- Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
| | - Janne Soetbeer
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Frauke Breitgoff
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States.,Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Nikolaos Sgourakis
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
| | - Dean Strotz
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
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11
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Zhang M, Frederick TE, VanPelt J, Case DA, Peng JW. Coupled intra- and interdomain dynamics support domain cross-talk in Pin1. J Biol Chem 2020; 295:16585-16603. [PMID: 32963105 PMCID: PMC7864058 DOI: 10.1074/jbc.ra120.015849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/19/2020] [Indexed: 11/06/2022] Open
Abstract
The functional mechanisms of multidomain proteins often exploit interdomain interactions, or "cross-talk." An example is human Pin1, an essential mitotic regulator consisting of a Trp-Trp (WW) domain flexibly tethered to a peptidyl-prolyl isomerase (PPIase) domain, resulting in interdomain interactions important for Pin1 function. Substrate binding to the WW domain alters its transient contacts with the PPIase domain via means that are only partially understood. Accordingly, we have investigated Pin1 interdomain interactions using NMR paramagnetic relaxation enhancement (PRE) and molecular dynamics (MD) simulations. The PREs show that apo-Pin1 samples interdomain contacts beyond the range suggested by previous structural studies. They further show that substrate binding to the WW domain simultaneously alters interdomain separation and the internal conformation of the WW domain. A 4.5-μs all-atom MD simulation of apo-Pin1 suggests that the fluctuations of interdomain distances are correlated with fluctuations of WW domain interresidue contacts involved in substrate binding. Thus, the interdomain/WW domain conformations sampled by apo-Pin1 may already include a range of conformations appropriate for binding Pin1's numerous substrates. The proposed coupling between intra-/interdomain conformational fluctuations is a consequence of the dynamic modular architecture of Pin1. Such modular architecture is common among cell-cycle proteins; thus, the WW-PPIase domain cross-talk mechanisms of Pin1 may be relevant for their mechanisms as well.
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Affiliation(s)
- Meiling Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Thomas E Frederick
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jamie VanPelt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Jeffrey W Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.
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12
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Allostery and Epistasis: Emergent Properties of Anisotropic Networks. ENTROPY 2020; 22:e22060667. [PMID: 33286439 PMCID: PMC7517209 DOI: 10.3390/e22060667] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 11/17/2022]
Abstract
Understanding the underlying mechanisms behind protein allostery and non-additivity of substitution outcomes (i.e., epistasis) is critical when attempting to predict the functional impact of mutations, particularly at non-conserved sites. In an effort to model these two biological properties, we extend the framework of our metric to calculate dynamic coupling between residues, the Dynamic Coupling Index (DCI) to two new metrics: (i) EpiScore, which quantifies the difference between the residue fluctuation response of a functional site when two other positions are perturbed with random Brownian kicks simultaneously versus individually to capture the degree of cooperativity of these two other positions in modulating the dynamics of the functional site and (ii) DCIasym, which measures the degree of asymmetry between the residue fluctuation response of two sites when one or the other is perturbed with a random force. Applied to four independent systems, we successfully show that EpiScore and DCIasym can capture important biophysical properties in dual mutant substitution outcomes. We propose that allosteric regulation and the mechanisms underlying non-additive amino acid substitution outcomes (i.e., epistasis) can be understood as emergent properties of an anisotropic network of interactions where the inclusion of the full network of interactions is critical for accurate modeling. Consequently, mutations which drive towards a new function may require a fine balance between functional site asymmetry and strength of dynamic coupling with the functional sites. These two tools will provide mechanistic insight into both understanding and predicting the outcome of dual mutations.
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13
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Cohn GM, Liefwalker DF, Langer EM, Sears RC. PIN1 Provides Dynamic Control of MYC in Response to Extrinsic Signals. Front Cell Dev Biol 2020; 8:224. [PMID: 32300594 PMCID: PMC7142217 DOI: 10.3389/fcell.2020.00224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/16/2020] [Indexed: 01/05/2023] Open
Abstract
PIN1 is a phosphorylation-directed member of the peptidyl-prolyl cis/trans isomerase (PPIase) family that facilitates conformational changes in phosphorylated targets such as c-MYC (MYC). Following signaling events that mediate phosphorylation of MYC at Serine 62, PIN1 establishes structurally distinct pools of MYC through its trans-cis and cis-trans isomerization activity at Proline 63. Through these isomerization steps, PIN1 functionally regulates MYC's stability, the molecular timing of its DNA binding and transcriptional activity, and its subnuclear localization. Recently, our group showed that Serine 62 phosphorylated MYC can associate with the inner basket of the nuclear pore (NP) in a PIN1-dependent manner. The poised euchromatin at the NP basket enables rapid cellular response to environmental signals and cell stress, and PIN1-mediated trafficking of MYC calibrates this response. In this perspective, we describe the molecular aspects of PIN1 target recognition and PIN1's function in the context of its temporal and spatial regulation of MYC.
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Affiliation(s)
- Gabriel M Cohn
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Daniel F Liefwalker
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Ellen M Langer
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health and Science University, Portland, OR, United States.,Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States
| | - Rosalie C Sears
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health and Science University, Portland, OR, United States.,Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States.,Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, United States
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14
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Pu W, Zheng Y, Peng Y. Prolyl Isomerase Pin1 in Human Cancer: Function, Mechanism, and Significance. Front Cell Dev Biol 2020; 8:168. [PMID: 32296699 PMCID: PMC7136398 DOI: 10.3389/fcell.2020.00168] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/29/2020] [Indexed: 02/05/2023] Open
Abstract
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) is an evolutionally conserved and unique enzyme that specifically catalyzes the cis-trans isomerization of phosphorylated serine/threonine-proline (pSer/Thr-Pro) motif and, subsequently, induces the conformational change of its substrates. Mounting evidence has demonstrated that Pin1 is widely overexpressed and/or overactivated in cancer, exerting a critical influence on tumor initiation and progression via regulation of the biological activity, protein degradation, or nucleus-cytoplasmic distribution of its substrates. Moreover, Pin1 participates in the cancer hallmarks through activating some oncogenes and growth enhancers, or inactivating some tumor suppressors and growth inhibitors, suggesting that Pin1 could be an attractive target for cancer therapy. In this review, we summarize the findings on the dysregulation, mechanisms, and biological functions of Pin1 in cancer cells, and also discuss the significance and potential applications of Pin1 dysregulation in human cancer.
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Affiliation(s)
- Wenchen Pu
- Laboratory of Molecular Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yuanyuan Zheng
- Laboratory of Molecular Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yong Peng
- Laboratory of Molecular Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University Collaborative Innovation Center of Biotherapy, Chengdu, China
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15
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Chen D, Wang L, Lee TH. Post-translational Modifications of the Peptidyl-Prolyl Isomerase Pin1. Front Cell Dev Biol 2020; 8:129. [PMID: 32195254 PMCID: PMC7064559 DOI: 10.3389/fcell.2020.00129] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/14/2020] [Indexed: 12/14/2022] Open
Abstract
The peptidyl-prolyl cis/trans isomerase (PPIase) Pin1 is a unique enzyme that only binds to Ser/Thr-Pro peptide motifs after phosphorylation and regulates the conformational changes of the bond. The Pin1-catalyzed isomerization upon phosphorylation can have profound effects on substrate biological functions, including their activity, stability, assembly, and subcellular localization, affecting its role in intracellular signaling, transcription, and cell cycle progression. The functions of Pin1 are regulated by post-translational modifications (PTMs) in many biological processes, which include phosphorylation, ubiquitination, SUMOylation and oxidation. Phosphorylation of different Pin1 sites regulates Pin1 enzymatic activity, binding ability, localization, and ubiquitination by different kinases under various cellular contexts. Moreover, SUMOylation and oxidation have been shown to downregulate Pin1 activity. Although Pin1 is tightly regulated under physiological conditions, deregulation of Pin1 PTMs contributes to the development of human diseases including cancer and Alzheimer's disease (AD). Therefore, manipulating the PTMs of Pin1 may be a promising therapeutic option for treating various human diseases. In this review, we focus on the molecular mechanisms of Pin1 regulation by PTMs and the major impact of Pin1 PTMs on the progression of cancer and AD.
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Affiliation(s)
- Dongmei Chen
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Long Wang
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Tae Ho Lee
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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16
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Born A, Henen MA, Vögeli B. Activity and Affinity of Pin1 Variants. MOLECULES (BASEL, SWITZERLAND) 2019; 25:molecules25010036. [PMID: 31861908 PMCID: PMC6983177 DOI: 10.3390/molecules25010036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/07/2019] [Accepted: 12/18/2019] [Indexed: 12/14/2022]
Abstract
Pin1 is a peptidyl-prolyl isomerase responsible for isomerizing phosphorylated S/T-P motifs. Pin1 has two domains that each have a distinct ligand binding site, but only its PPIase domain has catalytic activity. Vast evidence supports interdomain allostery of Pin1, with binding of a ligand to its regulatory WW domain impacting activity in the PPIase domain. Many diverse studies have made mutations in Pin1 in order to elucidate interactions that are responsible for ligand binding, isomerase activity, and interdomain allostery. Here, we summarize these mutations and their impact on Pin1′s structure and function.
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Affiliation(s)
- Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.)
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.)
- Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.)
- Correspondence: ; Tel.: +1-303-724-1627
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17
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Yao XQ, Hamelberg D. Detecting Functional Dynamics in Proteins with Comparative Perturbed-Ensembles Analysis. Acc Chem Res 2019; 52:3455-3464. [PMID: 31793290 DOI: 10.1021/acs.accounts.9b00485] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recent advances have made all-atom molecular dynamics (MD) a powerful tool to sample the conformational energy landscape. There are still however three major challenges in the application of MD to biological systems: accuracy of force field, time scale, and the analysis of simulation trajectories. Significant progress in addressing the first two challenges has been made and extensively reviewed previously. This Account focuses on strategies of analyzing simulation data of biomolecules that also covers ways to properly design simulations and validate simulation results. In particular, we examine an approach named comparative perturbed-ensembles analysis, which we developed to efficiently detect dynamics in protein MD simulations that can be linked to biological functions. In our recent studies, we implemented this approach to understand allosteric regulations in several disease-associated human proteins. The central task of a comparative perturbed-ensembles analysis is to compare two or more conformational ensembles of a system generated by MD simulations under distinct perturbation conditions. Perturbations can be different sequence variations, ligand-binding conditions, and other physical/chemical modifications of the system. Each simulation is long enough (e.g., microsecond-long) to ensure sufficient sampling of the local substate. Then, sophisticated bioinformatic and statistical tools are applied to extract function-related information from the simulation data, including principal component analysis, residue-residue contact analysis, difference contact network analysis (dCNA) based on the graph theory, and statistical analysis of side-chain conformations. Computational findings are further validated with experimental data. By comparing distinct conformational ensembles, functional micro- to millisecond dynamics can be inferred. In contrast, such a time scale is difficult to reach in a single simulation; even when reached for a single condition of a system, it is elusive as to what dynamical motions are related to functions without, for example, comparing free and substrate-bound proteins at the minimum. We illustrate our approach with three examples. First, we discuss using the approach to identify allosteric pathways in cyclophilin A (CypA), a member of a ubiquitous class of peptidyl-prolyl cis-trans isomerase enzymes. By comparing side-chain torsion-angle distributions of CypA in wild-type and mutant forms, we identified three pathways: two are consistent with recent nuclear magnetic resonance experiments, whereas the third is a novel pathway. Second, we show how the approach enables a dynamical-evolution analysis of the human cyclophilin family. In the analysis, both conserved and divergent conformational dynamics across three cyclophilin isoforms (CypA, CypD, and CypE) were summarized. The conserved dynamics led to the discovery of allosteric networks resembling those found in CypA. A residue wise determinant underlying the unique dynamics in CypD was also detected and validated with additional mutational MD simulations. In the third example, we applied the approach to elucidate a peptide sequence-dependent allosteric mechanism in human Pin 1, a phosphorylation-dependent peptidyl-prolyl isomerase. We finally present our outlook of future directions. Especially, we envisage how the approach could help open a new avenue in drug discovery.
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Affiliation(s)
- Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
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18
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Namanja AT, Xu J, Wu H, Sun Q, Upadhyay AK, Sun C, Van Doren SR, Petros AM. NMR-based fragment screening and lead discovery accelerated by principal component analysis. JOURNAL OF BIOMOLECULAR NMR 2019; 73:675-685. [PMID: 31541395 DOI: 10.1007/s10858-019-00279-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
Protein-based NMR spectroscopy has proven to be a very robust method for finding fragment leads to protein targets. However, one limitation of protein-based NMR is that the data acquisition and analysis can be time consuming. In order to streamline the scoring of protein-based NMR fragment screening data and the determination of ligand affinities using 2D NMR experiments we have developed a data analysis workflow based on principal component analysis (PCA) within the TREND NMR Pro software package. We illustrate this using four different proteins and sets of ligands which interact with these proteins over a range of affinities. Also, these PCA-based methods can be successfully applied even to systems where ligand binding to target proteins is in intermediate or even slow exchange on the NMR time scale. Finally, these methods will work for scoring of fragment binding data using protein spectra that are either highly overlapped or lower in resolution.
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Affiliation(s)
- Andrew T Namanja
- Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Jia Xu
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA
- Department of Radiology, University of Iowa, Iowa City, IA, 52242, USA
| | - Haihong Wu
- Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Qi Sun
- Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Anup K Upadhyay
- Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Chaohong Sun
- Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Steven R Van Doren
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA.
| | - Andrew M Petros
- Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL, 60064, USA.
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19
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Born A, Nichols PJ, Henen MA, Chi CN, Strotz D, Bayer P, Tate SI, Peng JW, Vögeli B. Backbone and side-chain chemical shift assignments of full-length, apo, human Pin1, a phosphoprotein regulator with interdomain allostery. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:85-89. [PMID: 30353504 PMCID: PMC9205186 DOI: 10.1007/s12104-018-9857-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/19/2018] [Indexed: 05/27/2023]
Abstract
Pin1 is a human peptidyl-prolyl cis-trans isomerase important for the regulation of phosphoproteins that are implicated in many diseases including cancer and Alzheimer's. Further biophysical study of Pin1 will elucidate the importance of the two-domain system to regulate its own activity. Here, we report near-complete backbone and side-chain 1H, 13C and 15N NMR chemical shift assignments of full-length, apo Pin1 for the purpose of studying interdomain allostery and dynamics.
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Affiliation(s)
- Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123, Uppsala, Sweden
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zürich, ETH-Hönggerberg, Zurich, Switzerland
| | - Peter Bayer
- Strukturelle und Medizinische Biochemie, Universität Duisburg-Essen, Universitätsstrasse 2-5, 45117, Essen, Germany
| | - Shin-Ichi Tate
- Department of Mathematical and Life Sciences, Hiroshima University, Hiroshima, Japan
| | - Jeffrey W Peng
- Department of Chemistry and Biochemistry & Department of Physics, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA.
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Research Center 1 South, Room 9103, 12801 East 17th Avenue, Aurora, CO, 80045, USA.
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20
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Zhu W, Li Y, Liu M, Zhu J, Yang Y. Uncorrelated Effect of Interdomain Contact on Pin1 Isomerase Activity Reveals Positive Catalytic Cooperativity. J Phys Chem Lett 2019; 10:1272-1278. [PMID: 30821977 DOI: 10.1021/acs.jpclett.9b00052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pin1 is a two-domain peptidyl-prolyl isomerase (PPIase) associated with neurodegeneration and tumorigenesis. The two domains, a WW and a PPIase domain, are connected by a flexible linker, making Pin1 adopt various conformations ranging from compact to extended, wherein Pin1 exhibits different extents of interdomain contact. Previous studies have shown that weakening interdomain contact increases the isomerase activity of Pin1. Here, we propose an NMR chemical shift correlation-analysis-based method that will be general for two-domain proteins to gauge two-state populations of Pin1, and we report a linker-modified mutant of Pin1 with enhanced interdomain contact and increased isomerase activity, with the latter suggesting an uncorrelated effect of interdomain contact on isomerase activity. Thus, although bindings of different substrates in the WW domain impose opposite effects on interdomain contact, in both cases, it may promote isomerization, implying cooperativity between substrate binding in the WW domain and isomerization in the PPIase domain.
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Affiliation(s)
- Wenkai Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics , Chinese Academy of Sciences , Wuhan 430071 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics , Chinese Academy of Sciences , Wuhan 430071 , People's Republic of China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics , Chinese Academy of Sciences , Wuhan 430071 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics , Chinese Academy of Sciences , Wuhan 430071 , People's Republic of China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics , Chinese Academy of Sciences , Wuhan 430071 , People's Republic of China
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21
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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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22
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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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23
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Byrne C, Belnou M, Baulieu E, Lequin O, Jacquot Y. Electronic circular dichroism and nuclear magnetic resonance studies of peptides derived from the FKBP52‐interacting β‐turn of the hERα ligand‐binding domain. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Cillian Byrne
- Sorbonne Université, Ecole Normale SupérieurePSL University, CNRS UMR 7203, Laboratoire des Biomolécules Paris France
- Institut Baulieu, Université Paris‐SaclayINSERM UMR 1195, Neuroprotection and Neuroregeneration Le Kremlin Bicêtre France
| | - Mathilde Belnou
- Sorbonne Université, Ecole Normale SupérieurePSL University, CNRS UMR 7203, Laboratoire des Biomolécules Paris France
| | - Etienne‐Emile Baulieu
- Institut Baulieu, Université Paris‐SaclayINSERM UMR 1195, Neuroprotection and Neuroregeneration Le Kremlin Bicêtre France
| | - Olivier Lequin
- Sorbonne Université, Ecole Normale SupérieurePSL University, CNRS UMR 7203, Laboratoire des Biomolécules Paris France
| | - Yves Jacquot
- Sorbonne Université, Ecole Normale SupérieurePSL University, CNRS UMR 7203, Laboratoire des Biomolécules Paris France
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24
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El Boustani M, De Stefano L, Caligiuri I, Mouawad N, Granchi C, Canzonieri V, Tuccinardi T, Giordano A, Rizzolio F. A Guide to PIN1 Function and Mutations Across Cancers. Front Pharmacol 2019; 9:1477. [PMID: 30723410 PMCID: PMC6349750 DOI: 10.3389/fphar.2018.01477] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022] Open
Abstract
PIN1 is a member of a family of peptidylprolyl isomerases that bind phosphoproteins and catalyze the rapid cis-trans isomerization of proline peptidyl bonds, resulting in an alteration of protein structure, function, and stability. PIN1 is overexpressed in human cancers, suggesting it promotes tumorigenesis, but depending on the cellular context, it also acts as a tumor suppressor. Here, we review the role of PIN1 in cancer and the regulation of PIN1 expression, and catalog the single nucleotide polymorphisms, and mutations in PIN1 gene associated with cancer. In addition, we provide a 3D model of the protein to localize the mutated residues.
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Affiliation(s)
- Maguie El Boustani
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy.,Doctoral School in Molecular Biomedicine, University of Trieste, Trieste, Italy
| | - Lucia De Stefano
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy.,Doctoral School in Chemistry, University of Trieste, Trieste, Italy
| | - Isabella Caligiuri
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy
| | - Nayla Mouawad
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy.,Department of Pharmacy, University of Pisa, Pisa, Italy
| | | | | | | | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, United States
| | - Flavio Rizzolio
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy.,Department of Molecular Science and Nanosystems, Ca' Foscari University of Venice, Venice, Italy
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25
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Lee YM, Liou YC. Gears-In-Motion: The Interplay of WW and PPIase Domains in Pin1. Front Oncol 2018; 8:469. [PMID: 30460195 PMCID: PMC6232885 DOI: 10.3389/fonc.2018.00469] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/04/2018] [Indexed: 01/22/2023] Open
Abstract
Pin1 belongs to the family of the peptidyl-prolyl cis-trans isomerase (PPIase), which is a class of enzymes that catalyze the cis/trans isomerization of the Proline residue. Pin1 is unique and only catalyzes the phosphorylated Serine/Threonine-Proline (S/T-P) motifs of a subset of proteins. Since the discovery of Pin1 as a key protein in cell cycle regulation, it has been implicated in numerous diseases, ranging from cancer to neurodegenerative diseases. The main features of Pin1 lies in its two main domains: the WW (two conserved tryptophan) domain and the PPIase domain. Despite extensive studies trying to understand the mechanisms of Pin1 functions, how these two domains contribute to the biological roles of Pin1 in cellular signaling requires more investigations. The WW domain of Pin1 is known to have a higher affinity to its substrate than that of the PPIase domain. Yet, the WW domain seems to prefer the trans configuration of phosphorylated S/T-P motif, while the PPIase catalyzes the cis to trans isomerasion. Such contradicting information has generated much confusion as to the actual mechanism of Pin1 function. In addition, dynamic allostery has been suggested to be important for Pin1 function. Henceforth, in this review, we will be looking at the progress made in understanding the function of Pin1, and how these understandings can aid us in overcoming the diseases implicated by Pin1 such as cancer during drug development.
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Affiliation(s)
- Yew Mun Lee
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Yih-Cherng Liou
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
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26
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Zhang M, Case DA, Peng JW. Propagated Perturbations from a Peripheral Mutation Show Interactions Supporting WW Domain Thermostability. Structure 2018; 26:1474-1485.e5. [PMID: 30197038 DOI: 10.1016/j.str.2018.07.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 06/21/2018] [Accepted: 07/25/2018] [Indexed: 12/18/2022]
Abstract
Inter-residue interactions stabilize protein folds and facilitate allosteric communication. Predicting which interactions are crucial and understanding why remain challenging. We highlight this through studies of a single peripheral mutation (Q33E) on the surface of the Pin1 WW domain that causes an unexpected loss of thermostability. Nuclear magnetic resonance studies attribute the loss to reorganizations of electrostatic and hydrophobic interactions, resulting in propagated conformational perturbations. The propagation demonstrates the cooperative response of Pin1 WW to external perturbations, consistent with its allosteric behavior within Pin1. Microsecond molecular dynamics simulations suggest the wild-type fold relies on couplings between a surface electrostatic network and a highly conserved hydrophobic core; Q33E directly perturbs the former, thereby disrupting the latter. These couplings suggest that predictions of mutation consequences that assume dominance of a single interaction type can be limiting, and highlight challenges in predicting protein mutational landscapes.
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Affiliation(s)
- Meiling Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, 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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27
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Momin M, Yao XQ, Thor W, Hamelberg D. Substrate Sequence Determines Catalytic Activities, Domain-Binding Preferences, and Allosteric Mechanisms in Pin1. J Phys Chem B 2018; 122:6521-6527. [DOI: 10.1021/acs.jpcb.8b03819] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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28
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Enhanced Sampling of Interdomain Motion Using Map-Restrained Langevin Dynamics and NMR: Application to Pin1. J Mol Biol 2018; 430:2164-2180. [PMID: 29775635 DOI: 10.1016/j.jmb.2018.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/04/2018] [Accepted: 05/05/2018] [Indexed: 11/20/2022]
Abstract
Many signaling proteins consist of globular domains connected by flexible linkers that allow for substantial domain motion. Because these domains often serve as complementary functional modules, the possibility of functionally important domain motions arises. To explore this possibility, we require knowledge of the ensemble of protein conformations sampled by interdomain motion. Measurements of NMR residual dipolar couplings (RDCs) of backbone HN bonds offer a per-residue characterization of interdomain dynamics, as the couplings are sensitive to domain orientation. A challenge in reaching this potential is the need to interpret the RDCs as averages over dynamic ensembles of domain conformations. Here, we address this challenge by introducing an efficient protocol for generating conformational ensembles appropriate for flexible, multi-domain proteins. The protocol uses map-restrained self-guided Langevin dynamics simulations to promote collective, interdomain motion while restraining the internal domain motion to near rigidity. Critically, the simulations retain an all-atom description for facile inclusion of site-specific NMR RDC restraints. The result is the rapid generation of conformational ensembles consistent with the RDC data. We illustrate this protocol on human Pin1, a two-domain peptidyl-prolyl isomerase relevant for cancer and Alzheimer's disease. The results include the ensemble of domain orientations sampled by Pin1, as well as those of a dysfunctional variant, I28A-Pin1. The differences between the ensembles corroborate our previous spin relaxation results that showed weakened interdomain contact in the I28A variant relative to wild type. Our protocol extends our abilities to explore the functional significance of protein domain motions.
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29
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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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30
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Campitelli P, Guo J, Zhou HX, Ozkan SB. Hinge-Shift Mechanism Modulates Allosteric Regulations in Human Pin1. J Phys Chem B 2018; 122:5623-5629. [PMID: 29361231 DOI: 10.1021/acs.jpcb.7b11971] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery, which is regulation from distant sites, plays a major role in biology. While traditional allostery is described in terms of conformational change upon ligand binding as an underlying principle, it is possible to have allosteric regulations without significant conformational change through modulating the conformational dynamics by altering the local effective elastic modulus of the protein upon ligand binding. Pin1 utilizes this dynamic allostery to regulate its function. It is a modular protein containing a WW domain and a larger peptidyl prolyl isomerase domain (PPIase) that isomerizes phosphoserine/threonine-proline (pS/TP) motifs. The WW domain serves as a docking module, whereas catalysis solely takes place within the PPIase domain. Here, we analyze the change in the dynamic flexibility profile of the PPIase domain upon ligand binding to the WW domain. Substrate binding to the WW domain induces the formation of a new rigid hinge site around the interface of the two domains and loosens the flexibility of a rigid site existing in the Apo form around the catalytic site. This hinge-shift mechanism enhances the dynamic coupling of the catalytic positions with the PPIase domain, where the rest of the domain can cooperatively respond to the local conformational changes around the catalytic site, leading to an increase in catalytic efficiency.
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Affiliation(s)
- Paul Campitelli
- Department of Physics and Center for Biological Physics , Arizona State University , Tempe , Arizona 85287 , United States
| | - Jingjing Guo
- School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , China
| | - Huan-Xiang Zhou
- Department of Chemistry and Department of Physics , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics , Arizona State University , Tempe , Arizona 85287 , United States
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31
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Mahoney BJ, Zhang M, Zintsmaster JS, Peng JW. Extended Impact of Pin1 Catalytic Loop Phosphorylation Revealed by S71E Phosphomimetic. J Mol Biol 2018; 430:710-721. [PMID: 29317221 DOI: 10.1016/j.jmb.2017.12.021] [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] [Received: 08/17/2017] [Revised: 12/19/2017] [Accepted: 12/31/2017] [Indexed: 11/24/2022]
Abstract
Pin1 is a two-domain human protein that catalyzes the cis-trans isomerization of phospho-Ser/Thr-Pro (pS/T-P) motifs in numerous cell-cycle regulatory proteins. These pS/T-P motifs bind to Pin1's peptidyl-prolyl isomerase (PPIase) domain in a catalytic pocket, between an extended catalytic loop and the PPIase domain core. Previous studies showed that post-translational phosphorylation of S71 in the catalytic loop decreases substrate binding affinity and isomerase activity. To define the origins for these effects, we investigated a phosphomimetic Pin1 mutant, S71E-Pin1, using solution NMR. We find that S71E perturbs not only its host loop but also the nearby PPIase core. The perturbations identify a local network of hydrogen bonds and salt bridges that is more extended than previously thought, and includes interactions between the catalytic loop and the α2/α3 turn in the PPIase core. Explicit-solvent molecular dynamics simulations and phylogenetic analysis suggest that these interactions act as conserved "latches" between the loop and PPIase core that enhance binding of phosphorylated substrates, as they are absent in PPIases lacking pS/T-P specificity. Our results suggest that S71 is a hub residue within an electrostatic network primed for phosphorylation, and may illustrate a common mechanism of phosphorylation-mediated allostery.
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Affiliation(s)
- Brendan J Mahoney
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, United States
| | - Meiling Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, United States
| | - John S Zintsmaster
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, United States
| | - Jeffrey W Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, United States.
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32
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Csizmok V, Montecchio M, Lin H, Tyers M, Sunnerhagen M, Forman-Kay JD. Multivalent Interactions with Fbw7 and Pin1 Facilitate Recognition of c-Jun by the SCF Fbw7 Ubiquitin Ligase. Structure 2017; 26:28-39.e2. [PMID: 29225075 DOI: 10.1016/j.str.2017.11.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/07/2017] [Accepted: 11/08/2017] [Indexed: 01/09/2023]
Abstract
Many regulatory proteins, including the transcription factor c-Jun, are highly enriched in disordered protein regions that govern growth, division, survival, differentiation, and response to signals. The stability of c-Jun is controlled by poorly understood regulatory interactions of its disordered region with both the E3 ubiquitin ligase SCFFbw7 and prolyl cis-trans isomerase Pin1. We use nuclear magnetic resonance and fluorescence studies of c-Jun to demonstrate that multisite c-Jun phosphorylation is required for high-affinity interaction with Fbw7. We show that the Pin1 WW and PPIase domains interact in a dynamic complex with multiply phosphorylated c-Jun. Importantly, Pin1 isomerizes a pSer-Pro peptide bond at the c-Jun N terminus that affects binding to Fbw7 and thus modulates the ubiquitin-mediated degradation of c-Jun. Our findings support the general principle that multiple weak binding motifs within disordered regions can synergize to yield high-affinity interactions and provide rapidly evolvable means to build and fine-tune regulatory events.
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Affiliation(s)
- Veronika Csizmok
- Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Meri Montecchio
- Department of Physics, Chemistry and Biology, Linköping University, 58183 Linköping, Sweden
| | - Hong Lin
- Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Linköping University, 58183 Linköping, Sweden
| | - Julie D Forman-Kay
- Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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33
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Wang J, Kawasaki R, Uewaki JI, Rashid AUR, Tochio N, Tate SI. Dynamic Allostery Modulates Catalytic Activity by Modifying the Hydrogen Bonding Network in the Catalytic Site of Human Pin1. Molecules 2017; 22:molecules22060992. [PMID: 28617332 PMCID: PMC6152768 DOI: 10.3390/molecules22060992] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 06/13/2017] [Accepted: 06/13/2017] [Indexed: 02/01/2023] Open
Abstract
Allosteric communication among domains in modular proteins consisting of flexibly linked domains with complimentary roles remains poorly understood. To understand how complementary domains communicate, we have studied human Pin1, a representative modular protein with two domains mutually tethered by a flexible linker: a WW domain for substrate recognition and a peptidyl-prolyl isomerase (PPIase) domain. Previous studies of Pin1 showed that physical contact between the domains causes dynamic allostery by reducing conformation dynamics in the catalytic domain, which compensates for the entropy costs of substrate binding to the catalytic site and thus increases catalytic activity. In this study, the S138A mutant PPIase domain, a mutation that mimics the structural impact of the interdomain contact, was demonstrated to display dynamic allostery by rigidification of the α2-α3 loop that harbors the key catalytic residue C113. The reduced dynamics of the α2-α3 loop stabilizes the C113-H59 hydrogen bond in the hydrogen-bonding network of the catalytic site. The stabilized hydrogen bond between C113 and H59 retards initiation of isomerization, which explains the reduced isomerization rate by ~20% caused by the S138A mutation. These results provide new insight into the interdomain allosteric communication of Pin1.
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Affiliation(s)
- Jing Wang
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Ryosuke Kawasaki
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Jun-Ichi Uewaki
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Arif U R Rashid
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Naoya Tochio
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Shin-Ichi Tate
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
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34
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Fine-tuning the extent and dynamics of binding cleft opening as a potential general regulatory mechanism in parvulin-type peptidyl prolyl isomerases. Sci Rep 2017; 7:44504. [PMID: 28300139 PMCID: PMC5353683 DOI: 10.1038/srep44504] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/06/2017] [Indexed: 11/23/2022] Open
Abstract
Parvulins or rotamases form a distinct group within peptidyl prolyl cis-trans isomerases. Their exact mode of action as well as the role of conserved residues in the family are still not unambiguously resolved. Using backbone S2 order parameters and NOEs as restraints, we have generated dynamic structural ensembles of three distinct parvulins, SaPrsA, TbPin1 and CsPinA. The resulting ensembles are in good agreement with the experimental data but reveal important differences between the three enzymes. The largest difference can be attributed to the extent of the opening of the substrate binding cleft, along which motional mode the three molecules occupy distinct regions. Comparison with a wide range of other available parvulin structures highlights structural divergence along the bottom of the binding cleft acting as a hinge during the opening-closing motion. In the prototype WW-domain containing parvulin, Pin1, this region is also important in forming contacts with the WW domain known to modulate enzymatic activity of the catalytic domain. We hypothesize that modulation of the extent and dynamics of the identified ‘breathing motion’ might be one of the factors responsible for functional differences in the distinct parvulin subfamilies.
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35
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Vöhringer-Martinez E, Dörner C. Conformational Substrate Selection Contributes to the Enzymatic Catalytic Reaction Mechanism of Pin1. J Phys Chem B 2016; 120:12444-12453. [DOI: 10.1021/acs.jpcb.6b09187] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Esteban Vöhringer-Martinez
- Departamento de Físico-Química,
Facultad de Ciencias Químicas, Universidad de Concepción, 4030000 Concepción, Chile
| | - Ciro Dörner
- Departamento de Físico-Química,
Facultad de Ciencias Químicas, Universidad de Concepción, 4030000 Concepción, Chile
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36
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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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37
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The Dynamic Basis for Signal Propagation in Human Pin1-WW. Structure 2016; 24:1464-75. [PMID: 27499442 DOI: 10.1016/j.str.2016.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/11/2016] [Accepted: 06/14/2016] [Indexed: 12/23/2022]
Abstract
Allostery is the structural manifestation of information transduction in biomolecules. Its hallmark is conformational change induced by perturbations at a distal site. An increasing body of evidence demonstrates the presence of allostery in very flexible and even disordered proteins, encouraging a thermodynamic description of this phenomenon. Still, resolving such processes at atomic resolution is difficult. Here we establish a protocol to determine atomistic thermodynamic models of such systems using high-resolution solution state nuclear magnetic resonance data and extensive molecular simulations. Using this methodology, we study information transduction in the WW domain of a key cell-cycle regulator Pin1. Pin1 binds promiscuously to phospho-Ser/Thr-Pro motifs, however, disparate structural and dynamic responses have been reported upon binding different ligands. Our model consists of two topologically distinct states whose relative population may be specifically skewed by an incoming ligand. This model provides a canonical basis for the understanding of multi-functionality in Pin1.
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38
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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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39
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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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40
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Doyle CM, Rumfeldt JA, Broom HR, Sekhar A, Kay LE, Meiering EM. Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts. Biochemistry 2016; 55:1346-61. [PMID: 26849066 DOI: 10.1021/acs.biochem.5b01133] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemical shifts of backbone amide protons in proteins are sensitive reporters of local structural stability and conformational heterogeneity, which can be determined from their readily measured linear and nonlinear temperature-dependences, respectively. Here we report analyses of amide proton temperature-dependences for native dimeric Cu, Zn superoxide dismutase (holo pWT SOD1) and structurally diverse mutant SOD1s associated with amyotrophic lateral sclerosis (ALS). Holo pWT SOD1 loses structure with temperature first at its periphery and, while having extremely high global stability, nevertheless exhibits extensive conformational heterogeneity, with ∼1 in 5 residues showing evidence for population of low energy alternative states. The holo G93A and E100G ALS mutants have moderately decreased global stability, whereas V148I is slightly stabilized. Comparison of the holo mutants as well as the marginally stable immature monomeric unmetalated and disulfide-reduced (apo(2SH)) pWT with holo pWT shows that changes in the local structural stability of individual amides vary greatly, with average changes corresponding to differences in global protein stability measured by differential scanning calorimetry. Mutants also exhibit altered conformational heterogeneity compared to pWT. Strikingly, substantial increases as well as decreases in local stability and conformational heterogeneity occur, in particular upon maturation and for G93A. Thus, the temperature-dependence of amide shifts for SOD1 variants is a rich source of information on the location and extent of perturbation of structure upon covalent changes and ligand binding. The implications for potential mechanisms of toxic misfolding of SOD1 in disease and for general aspects of protein energetics, including entropy-enthalpy compensation, are discussed.
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Affiliation(s)
| | | | | | | | - Lewis E Kay
- Program in Molecular Structure and Function, Hospital for Sick Children , Toronto, Canada
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41
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Abstract
The functions of many proteins are regulated through allostery, whereby effector binding at a distal site changes the functional activity (e.g., substrate binding affinity or catalytic efficiency) at the active site. Most allosteric studies have focused on thermodynamic properties, in particular, substrate binding affinity. Changes in substrate binding affinity by allosteric effectors have generally been thought to be mediated by conformational transitions of the proteins or, alternatively, by changes in the broadness of the free energy basin of the protein conformational state without shifting the basin minimum position. When effector binding changes the free energy landscape of a protein in conformational space, the change affects not only thermodynamic properties but also dynamic properties, including the amplitudes of motions on different time scales and rates of conformational transitions. Here we assess the roles of conformational dynamics in allosteric regulation. Two cases are highlighted where NMR spectroscopy and molecular dynamics simulation have been used as complementary approaches to identify residues possibly involved in allosteric communication. Perspectives on contentious issues, for example, the relationship between picosecond-nanosecond local and microsecond-millisecond conformational exchange dynamics, are presented.
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Affiliation(s)
- Jingjing Guo
- School of Chemistry and Chemical Engineering, Henan Normal University , Xinxiang, Henan 453007, People's Republic of China
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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42
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Namanja AT, Wang J, Buettner R, Colson L, Chen Y. Allosteric Communication across STAT3 Domains Associated with STAT3 Function and Disease-Causing Mutation. J Mol Biol 2016; 428:579-589. [PMID: 26774853 DOI: 10.1016/j.jmb.2016.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 01/03/2016] [Accepted: 01/06/2016] [Indexed: 01/10/2023]
Abstract
STAT3 is a member of STAT (signal transducer and activator of transcription) transcription activators. Aberration in STAT3 activity due to constitutive activation or mutations leads to diseases such as cancer and hyper-immunoglobulin E syndrome (HIES). STAT3 contains several structured domains including the Src homology 2 domain (SH2), linker domain (LD), DNA-binding domain (DBD) and the coiled-coil domain. Here we report the discovery of inter-domain allosteric communications in STAT3 from studies using nuclear magnetic resonance (NMR) and other methods. We found that pTyr-peptide interactions with SH2 cause structural and dynamics changes in LD and DBD. The inter-domain allosteric effect is likely mediated by the flexibility in the hydrophobic core. In addition, a mutation in LD found in HIES (I568F) induces NMR chemical shift perturbation in SH2, DBD and the coiled-coil domain, suggesting conformational changes in these domains. Consistent with conformational changes in SH2, the I568F mutant reduces SH2's binding affinity to a pTyr-containing peptide. This study provides an example of dynamics-dependent allosteric effects, and due to the structural conservation of the STAT family of proteins, the inter-domain allosteric communication observed in STAT3 likely occurs in other STATs.
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Affiliation(s)
- Andrew T Namanja
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Jianghai Wang
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Ralf Buettner
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Loren Colson
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Yuan Chen
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
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43
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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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Pre-Anchoring of Pin1 to Unphosphorylated c-Myc in a Fuzzy Complex Regulates c-Myc Activity. Structure 2015; 23:2267-2279. [PMID: 26655473 DOI: 10.1016/j.str.2015.10.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 12/27/2022]
Abstract
Hierarchic phosphorylation and concomitant Pin1-mediated proline isomerization of the oncoprotein c-Myc controls its cellular stability and activity. However, the molecular basis for Pin1 recognition and catalysis of c-Myc and other multisite, disordered substrates in cell regulation and disease is unclear. By nuclear magnetic resonance, surface plasmon resonance, and molecular modeling, we show that Pin1 subdomains jointly pre-anchor unphosphorylated c-Myc1-88 in the Pin1 interdomain cleft in a disordered, or "fuzzy", complex at the herein named Myc Box 0 (MB0) conserved region N-terminal to the highly conserved Myc Box I (MBI). Ser62 phosphorylation in MBI intensifies previously transient MBI-Pin1 interactions in c-Myc1-88 binding, and increasingly engages Pin1PPIase and its catalytic region with maintained MB0 interactions. In cellular assays, MB0 mutated c-Myc shows decreased Pin1 interaction, increased protein half-life, but lowered rates of Myc-driven transcription and cell proliferation. We propose that dynamic Pin1 recognition of MB0 contributes to the regulation of c-Myc activity in cells.
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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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Stereochemical Control in the Still-Wittig Rearrangement Synthesis of Cyclohexyl (Z)-Alkene Inhibitors of Pin1. PLoS One 2015; 10:e0139543. [PMID: 26445009 PMCID: PMC4596862 DOI: 10.1371/journal.pone.0139543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/14/2015] [Indexed: 11/29/2022] Open
Abstract
Three stereoisomeric inhibitors of Pin1: (2R,5S)-, (2S,5R)- and (2S,5S)-Ac–pSer–Ψ[(Z)CH = C]–pipecolyl(Pip)–2-(2-naphthyl)ethylamine 1, that mimic L-pSer–D-Pro, D-pSer–L-Pro, and D-pSer–D-Pro amides respectively, were synthesized by a 13-step route. The newly formed stereogenic centers in the pipecolyl ring were introduced by Luche reduction, followed by stereospecific [2,3]-Still-Wittig rearrangement. The (Z)- to (E)-alkene ratio in the rearrangements were consistently 5.5 to 1. The stereochemistry at the original Ser α-carbon controlled the stereochemistry of the Luche reduction, but it did not affect the stereochemical outcome of the rearrangement, which consistently gave the (Z)-alkene. The epimerized by-product, (2S,5S)-10, resulting from the work-up after Na/NH3 debenzylation of (2S,5R)-9, was carried on to the (2S,5S)-1 isomer. Compound (2S,5S)-10 was resynthesized from the Luche reduction by-product, (2R,3R)-3, and the stereochemistry was confirmed by comparison of the optical rotations. The IC50 values for (2R,5S)-1, (2S,5R)-1 and (2S,5S)-1 Pin1 inhibition were: 52, 85, and 140 μM, respectively.
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Huang KY, Horng JC. Modulating the Affinities of Phosphopeptides for the Human Pin1 WW Domain Using 4-Substituted Proline Derivatives. Biochemistry 2015; 54:6186-94. [DOI: 10.1021/acs.biochem.5b00880] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kuei-Yen Huang
- Department
of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC
- Frontier
Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC
| | - Jia-Cherng Horng
- Department
of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC
- Frontier
Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC
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Guo J, Zhou HX. Dynamically Driven Protein Allostery Exhibits Disparate Responses for Fast and Slow Motions. Biophys J 2015; 108:2771-4. [DOI: 10.1016/j.bpj.2015.04.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/13/2015] [Accepted: 04/24/2015] [Indexed: 12/29/2022] Open
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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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50
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Etzkorn FA, Zhao S. Stereospecific phosphorylation by the central mitotic kinase Cdk1-cyclin B. ACS Chem Biol 2015; 10:952-6. [PMID: 25603287 DOI: 10.1021/cb500815b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The cis vs trans conformation, or shape, of phosphoserine-proline (pSer-Pro), a prevalent motif in cell cycle proteins, may play a significant role in regulating mitosis. We demonstrate that Cdk1-cyclin B, the central mitotic kinase, is specific for the trans conformation, not cis, of synthetic, locked Ser-Pro 11-residue peptide substrates, using LC-MSMS detection and sequencing of phosphorylated products. This substrate stereospecificity may contribute an additional level of mitotic regulation.
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Affiliation(s)
- Felicia A. Etzkorn
- Virginia Tech, Department
of Chemistry, Blacksburg, Virginia 24061, United States
| | - Song Zhao
- Virginia Tech, Department
of Chemistry, Blacksburg, Virginia 24061, United States
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