1
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Hardtke HA, Zhang YJ. Collaborators or competitors: the communication between RNA polymerase II and the nucleosome during eukaryotic transcription. Crit Rev Biochem Mol Biol 2024; 59:1-19. [PMID: 38288999 PMCID: PMC11209794 DOI: 10.1080/10409238.2024.2306365] [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: 11/26/2023] [Accepted: 01/12/2024] [Indexed: 04/22/2024]
Abstract
Decades of scientific research have been devoted to unraveling the intricacies of eukaryotic transcription since the groundbreaking discovery of eukaryotic RNA polymerases in the late 1960s. RNA polymerase II, the polymerase responsible for mRNA synthesis, has always attracted the most attention. Despite its structural resemblance to its bacterial counterpart, eukaryotic RNA polymerase II faces a unique challenge in progressing transcription due to the presence of nucleosomes that package DNA in the nuclei. In this review, we delve into the impact of RNA polymerase II and histone signaling on the progression of eukaryotic transcription. We explore the pivotal points of interactions that bridge the RNA polymerase II and histone signaling systems. Finally, we present an analysis of recent cryo-electron microscopy structures, which captured RNA polymerase II-nucleosome complexes at different stages of the transcription cycle. The combination of the signaling crosstalk and the direct visualization of RNA polymerase II-nucleosome complexes provides a deeper understanding of the communication between these two major players in eukaryotic transcription.
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Affiliation(s)
- Haley A. Hardtke
- Department of Molecular Biosciences, University of Texas, Austin
| | - Y. Jessie Zhang
- Department of Molecular Biosciences, University of Texas, Austin
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2
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Corinti D, Paciotti R, Coletti C, Re N, Chiavarino B, Frison G, Crestoni ME, Fornarini S. IRMPD spectroscopy and quantum-chemical simulations of the reaction products of cisplatin with the dipeptide CysGly. J Inorg Biochem 2023; 247:112342. [PMID: 37536163 DOI: 10.1016/j.jinorgbio.2023.112342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023]
Abstract
The inorganic antineoplastic drug cisplatin was made to react in solution with the dipeptide cysteinylglycine (CysGly), chosen as a functional model of glutathione, and the reaction products were analyzed using electrospray ionization mass spectrometry (ESI-MS). Selected complexes, i.e., the primary substitution product cis-[PtCl(NH3)2(CysGly)]+ and the chelate cis-[PtCl(NH3)(CysGly)]+, were submitted to IR multiple photon dissociation (IRMPD) spectroscopy obtaining their vibrational features. The experimental IR ion spectra were compared with the calculated IR absorptions of different plausible isomeric families, finding CysGly to bind preferentially platinum(II) via its deprotonated thiolic group in the monovalent complex, cis-[PtCl(NH3)2(CysGly)]+, and to evolve in the S,N-bound chelate structure cis-[PtCl(NH3)(CysGly)]+ through the SH and NH2 functionality of the cysteine residue. Moreover, our findings indicate that the platination reaction does not affect the CysGly peptide bond, which remains in its trans configuration. These results provide additional insights into the reactivity of Pt(II)-complexes with glutathione which is involved in cellular cisplatin resistance.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy.
| | - Roberto Paciotti
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy.
| | - Cecilia Coletti
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Nazzareno Re
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Gilles Frison
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, LCT, F-75005 Paris, France
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
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3
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Okada T, Tomoike F. Distance-based global analysis of consistent cis-bonds in protein backbones. Heliyon 2023; 9:e18598. [PMID: 37576297 PMCID: PMC10413078 DOI: 10.1016/j.heliyon.2023.e18598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/15/2023] Open
Abstract
Biological polypeptides are known to contain cis-linkage in their main chain as a minor but important feature. Such anomalous connection of amino acids has different structural and functional effects on proteins. Experimental evidence of cis-bonds in proteins is mainly obtained using X-ray crystallography and other methods in the field of structural biology. To date, extensive analyses have been carried out on the experimentally found cis-bonds using the Protein Data Bank (PDB) entry-wise or residue-wise; however, their consistency in each protein has not been examined on a global scale. Data accumulation and advances in computational methodology enable the use of new approaches from a proteomic point of view. Here, we sought to carry out protein-wise analysis and describe a simple procedure for the detection and confirmation of cis-bonds from a set of experimental PDB chains for a protein to discriminate this type of bond from isomerizable and/or misassigned bonds. The resulting set of consistent cis bonds (found at identical positions in multiple chains) provides unprecedented insights into the trend of "high cis content" proteins and the upper limit of consistent cis bonds per polypeptide length. Recognizing such limit would not only be important for a practical check of upcoming structures, but also for the design of novel protein folds beyond the evolutionally-acquired repertoire.
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Affiliation(s)
- Tetsuji Okada
- Department of Life Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
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4
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Wieske LHE, Atilaw Y, Poongavanam V, Erdélyi M, Kihlberg J. Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds. Chemistry 2023; 29:e202202798. [PMID: 36286339 PMCID: PMC10107787 DOI: 10.1002/chem.202202798] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to adjust conformations in response to the polarity of the environment, i.e. molecular chameleonicity, is considered to be important for conferring both high aqueous solubility and high cell permeability to drugs in chemical space beyond Lipinski's rule of 5. We determined the conformational ensembles populated by the antiviral drugs asunaprevir, simeprevir, atazanavir and daclatasvir in polar (DMSO-d6 ) and non-polar (chloroform) environments with NMR spectroscopy. Daclatasvir was fairly rigid, whereas the first three showed large flexibility in both environments, that translated into major differences in solvent accessible 3D polar surface area within each conformational ensemble. No significant differences in size and polar surface area were observed between the DMSO-d6 and chloroform ensembles of these three drugs. We propose that such flexible compounds are characterized as "partial molecular chameleons" and hypothesize that their ability to adopt conformations with low polar surface area contributes to their membrane permeability and oral absorption.
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Affiliation(s)
- Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | | | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
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5
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Sec61 channel subunit Sbh1/Sec61β promotes ER translocation of proteins with suboptimal targeting sequences and is fine-tuned by phosphorylation. J Biol Chem 2023; 299:102895. [PMID: 36639027 PMCID: PMC9947333 DOI: 10.1016/j.jbc.2023.102895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
The highly conserved endoplasmic reticulum (ER) protein translocation channel contains one nonessential subunit, Sec61β/Sbh1, whose function is poorly understood so far. Its intrinsically unstructured cytosolic domain makes transient contact with ER-targeting sequences in the cytosolic channel vestibule and contains multiple phosphorylation sites suggesting a potential for regulating ER protein import. In a microscopic screen, we show that 12% of a GFP-tagged secretory protein library depends on Sbh1 for translocation into the ER. Sbh1-dependent proteins had targeting sequences with less pronounced hydrophobicity and often no charge bias or an inverse charge bias which reduces their insertion efficiency into the Sec61 channel. We determined that mutating two N-terminal, proline-flanked phosphorylation sites in the Sbh1 cytosolic domain to alanine phenocopied the temperature-sensitivity of a yeast strain lacking SBH1 and its ortholog SBH2. The phosphorylation site mutations reduced translocation into the ER of a subset of Sbh1-dependent proteins, including enzymes whose concentration in the ER lumen is critical for ER proteostasis. In addition, we found that ER import of these proteins depended on the activity of the phospho-S/T-specific proline isomerase Ess1 (PIN1 in mammals). We conclude that Sbh1 promotes ER translocation of substrates with suboptimal targeting sequences and that its activity can be regulated by a conformational change induced by N-terminal phosphorylation.
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Basak P, Zambelli B, Cabelli DE, Ciurli S, Maroney MJ. Pro5 is not essential for the formation of ‘Ni-hook’ in nickel superoxide dismutase. J Inorg Biochem 2022; 234:111858. [DOI: 10.1016/j.jinorgbio.2022.111858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/30/2022] [Accepted: 05/07/2022] [Indexed: 01/23/2023]
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7
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De Bei O, Marchetti M, Ronda L, Gianquinto E, Lazzarato L, Chirgadze DY, Hardwick SW, Cooper LR, Spyrakis F, Luisi BF, Campanini B, Bettati S. Cryo-EM structures of staphylococcal IsdB bound to human hemoglobin reveal the process of heme extraction. Proc Natl Acad Sci U S A 2022; 119:e2116708119. [PMID: 35357971 PMCID: PMC9168843 DOI: 10.1073/pnas.2116708119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/11/2022] [Indexed: 12/02/2022] Open
Abstract
Iron surface determinant B (IsdB) is a hemoglobin (Hb) receptor essential for hemic iron acquisition by Staphylococcus aureus. Heme transfer to IsdB is possible from oxidized Hb (metHb), but inefficient from Hb either bound to oxygen (oxyHb) or bound to carbon monoxide (HbCO), and encompasses a sequence of structural events that are currently poorly understood. By single-particle cryo-electron microscopy, we determined the structure of two IsdB:Hb complexes, representing key species along the heme extraction pathway. The IsdB:HbCO structure, at 2.9-Å resolution, provides a snapshot of the preextraction complex. In this early stage of IsdB:Hb interaction, the hemophore binds to the β-subunits of the Hb tetramer, exploiting a folding-upon-binding mechanism that is likely triggered by a cis/trans isomerization of Pro173. Binding of IsdB to α-subunits occurs upon dissociation of the Hb tetramer into α/β dimers. The structure of the IsdB:metHb complex reveals the final step of the extraction process, where heme transfer to IsdB is completed. The stability of the complex, both before and after heme transfer from Hb to IsdB, is influenced by isomerization of Pro173. These results greatly enhance current understanding of structural and dynamic aspects of the heme extraction mechanism by IsdB and provide insight into the interactions that stabilize the complex before the heme transfer event. This information will support future efforts to identify inhibitors of heme acquisition by S. aureus by interfering with IsdB:Hb complex formation.
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Affiliation(s)
- Omar De Bei
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
| | - Marialaura Marchetti
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
- Department of Medicine and Surgery, University of Parma, Parma 43126, Italy
| | - Luca Ronda
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
- Department of Medicine and Surgery, University of Parma, Parma 43126, Italy
- Institute of Biophysics, National Research Council, Pisa 56124, Italy
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Turin 10125, Italy
| | - Loretta Lazzarato
- Department of Drug Science and Technology, University of Turin, Turin 10125, Italy
| | - Dimitri Y. Chirgadze
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Steven W. Hardwick
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Lee R. Cooper
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin 10125, Italy
| | - Ben F. Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Barbara Campanini
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
- Department of Food and Drug, University of Parma, Parma 43124, Italy
| | - Stefano Bettati
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
- Department of Medicine and Surgery, University of Parma, Parma 43126, Italy
- Institute of Biophysics, National Research Council, Pisa 56124, Italy
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8
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Lawler JT, Harrilal CP, DeBlase AF, Sibert EL, McLuckey SA, Zwier TS. Single-conformation spectroscopy of cold, protonated DPG-containing peptides: switching β-turn types and formation of a sequential type II/II' double β-turn. Phys Chem Chem Phys 2022; 24:2095-2109. [PMID: 35019911 DOI: 10.1039/d1cp04852j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
D-Proline (DPro, DP) is widely utilized to form β-hairpin loops in engineered peptides that would otherwise be unstructured, most often as part of a DPG sub-unit that forms a β-turn. To observe whether DPG facilitated this effect in short protonated peptides, conformation specific IR-UV double resonance photofragment spectra of the cold (∼10 K) protonated DP and LP diastereomers of the pentapeptide YAPGA was carried out in the hydride stretch (2800-3700 cm-1) and amide I/II (1400-1800 cm-1) regions. A model localized Hamiltonian was developed to better describe the 1600-1800 cm-1 region commonly associated with the amide I vibrations. The CO stretch fundamentals experience extensive mixing with the N-H bending fundamentals of the NH3+ group in these protonated peptides. The model Hamiltonian accounts for experiment in quantitative detail. In the DP diastereomer, all the population is funneled into a single conformer which presented as a type II β-turn with A and DP in the i + 1 and i + 2 positions, respectively. This structure was not the anticipated type II' β-turn across DPG that we had hypothesized based on solution-phase propensities. Analysis of the conformational energy landscape shows that both steric and charge-induced effects play a role in the preferred formation of the type II β-turn. In contrast, the LP isomer forms three conformations with very different structures, none of which were type II/II' β-turns, confirming that LPG is not a β-turn former. Finally, single-conformation spectroscopy was also carried out on the extended peptide [YAADPGAAA + H]+ to determine whether moving the protonated N-terminus further from DPG would lead to β-hairpin formation. Despite funneling its entire population into a single peptide backbone structure, the assigned structure is not a β-hairpin, but a concatenated type II/type II' double β-turn that displaces the peptide backbone laterally by about 7.5 Å, but leaves the backbone oriented in its original direction.
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Affiliation(s)
- John T Lawler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | | | - Andrew F DeBlase
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Edwin L Sibert
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA. .,Gas Phase Chemical Physics, Sandia National Laboratories, Livermore, CA 94550, USA
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9
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Sahariah B, Sarma BK. Deciphering the Backbone Noncovalent Interactions that Stabilize Polyproline II Conformation and Reduce cis Proline Abundance in Polyproline Tracts. J Phys Chem B 2021; 125:13394-13405. [PMID: 34851647 DOI: 10.1021/acs.jpcb.1c07875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proline (Pro) has a higher propensity to adopt cis amide geometry than the other natural amino acids, and a poly-Pro (poly-P) tract can adopt either a polyproline I (PPI, all cis amide) or a polyproline II (PPII, all trans amide) helical conformation. Recent studies have revealed a reduced abundance of cis amide geometry among the inner Pro residues of a poly-P tract. However, the forces that stabilize the polyproline helices and the reason for the higher trans amide propensity of the inner Pro residues of a poly-P tract are poorly understood. Herein, we have studied both Pro and non-Pro PPII helical sequences and identified the backbone noncovalent interactions that are crucial to the higher stability of the trans Pro-amide geometry and the preference for a PPII helical conformation. We show the presence of reciprocal CO···CO interactions that extend over the whole PPII helical region. Interestingly, the CO···CO interactions strengthen with the increase in the PPII helical chain length and the inner CO groups possess stronger CO···CO interactions, which could explain the reduced cis abundance of the inner Pro residues of a poly-P tract. We also identified a much stronger (∼0.9 kcal·mol-1) nO → σ*Cα-Cβ interaction between the N-terminal CO oxygen lone pair and the antibonding orbital (σ*) of their Cα-Cβ bonds. As the nO → σ*Cα-Cβ interaction is possible only in the trans isomers of Pro, this interaction should be crucial for the stabilization of a PPII helix. Finally, an unusual nN(amide) → σ*C-N interaction (∼0.3 kcal·mol-1) was observed between the peptidic nitrogen lone pair (nN) and the antibonding orbital (σ*C-N) of the subsequent C-terminal peptide C-N bond. We propose a cumulative effect of these interactions in the stabilization of a PPII helix.
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Affiliation(s)
- Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
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10
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Herbst DA, Esbin MN, Louder RK, Dugast-Darzacq C, Dailey GM, Fang Q, Darzacq X, Tjian R, Nogales E. Structure of the human SAGA coactivator complex. Nat Struct Mol Biol 2021; 28:989-996. [PMID: 34811519 PMCID: PMC8660637 DOI: 10.1038/s41594-021-00682-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/05/2021] [Indexed: 12/16/2022]
Abstract
The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are noteworthy functional and compositional differences for this complex in metazoans. Here we present the cryogenic-electron microscopy (cryo-EM) structure of human SAGA (hSAGA) and show how the arrangement of distinct structural elements results in a globally divergent organization from that of yeast, with a different interface tethering the core module to the TRRAP subunit, resulting in a dramatically altered geometry of functional elements and with the integration of a metazoan-specific splicing module. Our hSAGA structure reveals the presence of an inositol hexakisphosphate (InsP6) binding site in TRRAP and an unusual property of its pseudo-(Ψ)PIKK. Finally, we map human disease mutations, thus providing the needed framework for structure-guided drug design of this important therapeutic target for human developmental diseases and cancer.
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Affiliation(s)
- Dominik A Herbst
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Meagan N Esbin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Robert K Louder
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Qianglin Fang
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Public Health, Sun Yat-sen University, Shenzhen, China
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Eva Nogales
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
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11
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Conformational Insights into the Control of CNF1 Toxin Activity by Peptidyl-Prolyl Isomerization: A Molecular Dynamics Perspective. Int J Mol Sci 2021; 22:ijms221810129. [PMID: 34576292 PMCID: PMC8467853 DOI: 10.3390/ijms221810129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/18/2022] Open
Abstract
The cytotoxic necrotizing factor 1 (CNF1) toxin from uropathogenic Escherichia coli constitutively activates Rho GTPases by catalyzing the deamidation of a critical glutamine residue located in the switch II (SWII). In crystallographic structures of the CNF1 catalytic domain (CNF1CD), surface-exposed P768 and P968 peptidyl-prolyl imide bonds (X-Pro) adopt an unusual cis conformation. Here, we show that mutation of each proline residue into glycine abrogates CNF1CD in vitro deamidase activity, while mutant forms of CNF1 remain functional on RhoA in cells. Using molecular dynamics simulations coupled to protein-peptide docking, we highlight the long-distance impact of peptidyl-prolyl cis-trans isomerization on the network of interactions between the loops bordering the entrance of the catalytic cleft. The energetically favorable isomerization of P768 compared with P968, induces an enlargement of loop L1 that fosters the invasion of CNF1CD catalytic cleft by a peptide encompassing SWII of RhoA. The connection of the P968 cis isomer to the catalytic cysteine C866 via a ladder of stacking interactions is alleviated along the cis-trans isomerization. Finally, the cis-trans conversion of P768 favors a switch of the thiol side chain of C866 from a resting to an active orientation. The long-distance impact of peptidyl-prolyl cis-trans isomerizations is expected to have implications for target modification.
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12
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Mori T, Terashi G, Matsuoka D, Kihara D, Sugita Y. Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps. J Chem Inf Model 2021; 61:3516-3528. [PMID: 34142833 PMCID: PMC9282639 DOI: 10.1021/acs.jcim.1c00230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural modeling of proteins from cryo-electron microscopy (cryo-EM) density maps is one of the challenging issues in structural biology. De novo modeling combined with flexible fitting refinement (FFR) has been widely used to build a structure of new proteins. In de novo prediction, artificial conformations containing local structural errors such as chirality errors, cis peptide bonds, and ring penetrations are frequently generated and cannot be easily removed in the subsequent FFR. Moreover, refinement can be significantly suppressed due to the low mobility of atoms inside the protein. To overcome these problems, we propose an efficient scheme for FFR, in which the local structural errors are fixed first, followed by FFR using an iterative simulated annealing (SA) molecular dynamics protocol with the united atom (UA) model in an implicit solvent model; we call this scheme "SAUA-FFR". The best model is selected from multiple flexible fitting runs with various biasing force constants to reduce overfitting. We apply our scheme to the decoys obtained from MAINMAST and demonstrate an improvement of the best model of eight selected proteins in terms of the root-mean-square deviation, MolProbity score, and RWplus score compared to the original scheme of MAINMAST. Fixing the local structural errors can enhance the formation of secondary structures, and the UA model enables progressive refinement compared to the all-atom model owing to its high mobility in the implicit solvent. The SAUA-FFR scheme realizes efficient and accurate protein structure modeling from medium-resolution maps with less overfitting.
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Affiliation(s)
- Takaharu Mori
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Daisuke Matsuoka
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Computer Science, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yuji Sugita
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.,RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN Center for Biosystems Dynamics Research, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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13
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Ramos J, Laux V, Haertlein M, Boeri Erba E, McAuley KE, Forsyth VT, Mossou E, Larsen S, Langkilde AE. Structural insights into protein folding, stability and activity using in vivo perdeuteration of hen egg-white lysozyme. IUCRJ 2021; 8:372-386. [PMID: 33953924 PMCID: PMC8086161 DOI: 10.1107/s2052252521001299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
This structural and biophysical study exploited a method of perdeuterating hen egg-white lysozyme based on the expression of insoluble protein in Escherichia coli followed by in-column chemical refolding. This allowed detailed comparisons with perdeuterated lysozyme produced in the yeast Pichia pastoris, as well as with unlabelled lysozyme. Both perdeuterated variants exhibit reduced thermal stability and enzymatic activity in comparison with hydrogenated lysozyme. The thermal stability of refolded perdeuterated lysozyme is 4.9°C lower than that of the perdeuterated variant expressed and secreted in yeast and 6.8°C lower than that of the hydrogenated Gallus gallus protein. However, both perdeuterated variants exhibit a comparable activity. Atomic resolution X-ray crystallographic analyses show that the differences in thermal stability and enzymatic function are correlated with refolding and deuteration effects. The hydrogen/deuterium isotope effect causes a decrease in the stability and activity of the perdeuterated analogues; this is believed to occur through a combination of changes to hydrophobicity and protein dynamics. The lower level of thermal stability of the refolded perdeuterated lysozyme is caused by the unrestrained Asn103 peptide-plane flip during the unfolded state, leading to a significant increase in disorder of the Lys97-Gly104 region following subsequent refolding. An ancillary outcome of this study has been the development of an efficient and financially viable protocol that allows stable and active perdeuterated lysozyme to be more easily available for scientific applications.
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Affiliation(s)
- Joao Ramos
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Valerie Laux
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Elisabetta Boeri Erba
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biologie Structurale, Université de Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Katherine E. McAuley
- Diamond Light Source, Didcot OX11 0DE, United Kingdom
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - V. Trevor Forsyth
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, United Kingdom
| | - Estelle Mossou
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, United Kingdom
| | - Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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14
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Mohanty AK, Choudhary S, Kaushik JK, Fisher AJ. Crystal structure of breast regression protein 39 (BRP39), a signaling glycoprotein expressed during mammary gland apoptosis, at 2.6 Å resolution. J Struct Biol 2021; 213:107737. [PMID: 33838225 DOI: 10.1016/j.jsb.2021.107737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/16/2022]
Abstract
Breast regression protein 39 (BRP39) is a 39 kDa protein that is a member of chitolectin class of glycosyl hydrolase family 18 (GH18). High expression levels of BRP39 have been detected in breast carcinoma. It helps in proliferation of cells during the progression of this disease and may act as a signaling factor. BRP39 may act as a potential candidate for rational structure-based drug design against breast carcinoma. In this study, we report the crystal structure of mouse recombinant BRP39 expressed in E. coli. The structure was solved by molecular replacement and refined to 2.6 Å resolution. The overall structure of BRP39 consisted of two globular domains: a large (β/α)8 triosephosphate isomerase (TIM) barrel domain and a small (α + β) domain. Three non-proline cis-peptides were detected in the sugar-binding cleft of BRP39, including Ser57-Phe58, Leu141-Tyr142, and Trp353-Ala354. The latter residues were conserved in other GH18 family members. It was notable that the conformation of critical Trp100 residue within the sugar-binding cleft was oriented away from the barrel. The side-chain conformation was found to be similar to that observed in chitinases, however, it was oriented into the barrel in other chitinase-like proteins (CLPs). The conformation of this critical residue may have significant implications in sugar binding. Further, two amino acid substitutions were observed in the sugar-binding groove of BRP39. The conserved Asn100 and Arg263 in Hcgp39 and other CLPs proteins (SPX-40 structures) were substituted by Lys101 and Lys264 in BRP39 which may have a significant impact on the sugar-binding properties.
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Affiliation(s)
- Ashok K Mohanty
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India.
| | - Suman Choudhary
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Jai K Kaushik
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Andrew J Fisher
- Department of Chemistry, University of California Davis, Davis, CA 95616, United States; Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, United States
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15
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Tronrud DE, Karplus PA. A complete Fourier-synthesis-based backbone-conformation-dependent library for proteins. Acta Crystallogr D Struct Biol 2021; 77:249-266. [DOI: 10.1107/s2059798320016344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/16/2020] [Indexed: 11/10/2022] Open
Abstract
While broadening the applicability of (φ/ψ)-dependent target values for the bond angles in the peptide backbone, sequence/conformation categories with too few residues to analyze via previous methods were encountered. Here, a method of describing a conformation-dependent library (CDL) using two-dimensional Fourier coefficients is reported where the number of coefficients for individual categories is determined via complete cross-validation. Sample sizes are increased further by selective blending of categories with similar patterns of conformational dependence. An additional advantage of the Fourier-synthesis-based CDL is that it uses continuous functions and has no artifactual steps near the edges of populated regions of φ/ψ space. A set of libraries for the seven main-chain bond angles, along with the ω and ζ angles, was created based on a set of Fourier analyses of 48 368 residues selected from high-resolution models in the wwPDB. This new library encompasses both trans- and cis-peptide bonds and outperforms currently used discrete CDLs.
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16
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Bojarska J, Remko M, Breza M, Madura I, Fruziński A, Wolf WM. A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI. Pharmaceuticals (Basel) 2020; 13:E338. [PMID: 33114370 PMCID: PMC7692516 DOI: 10.3390/ph13110338] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 11/16/2022] Open
Abstract
Proline is a unique, endogenous amino acid, prevalent in proteins and essential for living organisms. It is appreciated as a tecton for the rational design of new bio-active substances. Herein, we present a short overview of the subject. We analyzed 2366 proline-derived structures deposited in the Cambridge Structure Database, with emphasis on the angiotensin-converting enzyme inhibitors. The latter are the first-line antihypertensive and cardiological drugs. Their side effects prompt a search for improved pharmaceuticals. Characterization of tectons (molecular building blocks) and the resulting supramolecular synthons (patterns of intermolecular interactions) involving proline derivatives, as presented in this study, may be useful for in silico molecular docking and macromolecular modeling studies. The DFT, Hirshfeld surface and energy framework methods gave considerable insight into the nature of close inter-contacts and supramolecular topology. Substituents of proline entity are important for the formation and cooperation of synthons. Tectonic subunits contain proline moieties characterized by diverse ionization states: -N and -COOH(-COO-), -N+ and -COOH(-COO-), -NH and -COOH(-COO-), -NH+ and -COOH(-COO-), and -NH2+ and -COOH(-COO-). Furthermore, pharmacological profiles of ACE inhibitors and their impurities were determined via an in silico approach. The above data were used to develop comprehensive classification, which may be useful in further drug design studies.
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Affiliation(s)
- Joanna Bojarska
- Faculty of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (A.F.); (W.M.W.)
| | - Milan Remko
- Remedika, Luzna 9, 85104 Bratislava, Slovakia;
| | - Martin Breza
- Department of Physical Chemistry, Slovak Technical University, Radlinskeho 9, SK-81237 Bratislava, Slovakia;
| | - Izabela Madura
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
| | - Andrzej Fruziński
- Faculty of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (A.F.); (W.M.W.)
| | - Wojciech M. Wolf
- Faculty of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (A.F.); (W.M.W.)
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17
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Rein T. Peptidylprolylisomerases, Protein Folders, or Scaffolders? The Example of FKBP51 and FKBP52. Bioessays 2020; 42:e1900250. [DOI: 10.1002/bies.201900250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/12/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Theo Rein
- Department of Translational Science in Psychiatry, MunichMax Planck Institute of Psychiatry Munich 80804 Germany
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18
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Urbanek A, Popovic M, Elena-Real CA, Morató A, Estaña A, Fournet A, Allemand F, Gil AM, Cativiela C, Cortés J, Jiménez AI, Sibille N, Bernadó P. Evidence of the Reduced Abundance of Proline cis Conformation in Protein Poly Proline Tracts. J Am Chem Soc 2020; 142:7976-7986. [PMID: 32266815 DOI: 10.1021/jacs.0c02263] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proline is found in a cis conformation in proteins more often than other proteinogenic amino acids, where it influences structure and modulates function, being the focus of several high-resolution structural studies. However, until now, technical and methodological limitations have hampered the site-specific investigation of the conformational preferences of prolines present in poly proline (poly-P) homorepeats in their protein context. Here, we apply site-specific isotopic labeling to obtain high-resolution NMR data on the cis/trans equilibrium of prolines within the poly-P repeats of huntingtin exon 1, the causative agent of Huntington's disease. Screening prolines in different positions in long (poly-P11) and short (poly-P3) poly-P tracts, we found that, while the first proline of poly-P tracts adopts similar levels of cis conformation as isolated prolines, a length-dependent reduced abundance of cis conformers is observed for terminal prolines. Interestingly, the cis isomer could not be detected in inner prolines, in line with percentages derived from a large database of proline-centered tripeptides extracted from crystallographic structures. These results suggest a strong cooperative effect within poly-Ps that enhances their stiffness by diminishing the stability of the cis conformation. This rigidity is key to rationalizing the protection toward aggregation that the poly-P tract confers to huntingtin. Furthermore, the study provides new avenues to probe the structural properties of poly-P tracts in protein design as scaffolds or nanoscale rulers.
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Affiliation(s)
- Annika Urbanek
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier. 29, rue de Navacelles, 34090 Montpellier, France
| | - Matija Popovic
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier. 29, rue de Navacelles, 34090 Montpellier, France
| | - Carlos A Elena-Real
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier. 29, rue de Navacelles, 34090 Montpellier, France
| | - Anna Morató
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier. 29, rue de Navacelles, 34090 Montpellier, France
| | - Alejandro Estaña
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier. 29, rue de Navacelles, 34090 Montpellier, France.,LAAS-CNRS, Université de Toulouse, CNRS, 7 Avenue du Colonel Roche, 31400 Toulouse, France
| | - Aurélie Fournet
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier. 29, rue de Navacelles, 34090 Montpellier, France
| | - Frédéric Allemand
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier. 29, rue de Navacelles, 34090 Montpellier, France
| | - Ana M Gil
- Departamento de Quı́mica Orgánica, Instituto de Sı́ntesis Quı́mica y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Quı́mica Orgánica, Instituto de Sı́ntesis Quı́mica y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, 7 Avenue du Colonel Roche, 31400 Toulouse, France
| | - Ana I Jiménez
- Departamento de Quı́mica Orgánica, Instituto de Sı́ntesis Quı́mica y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Nathalie Sibille
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier. 29, rue de Navacelles, 34090 Montpellier, France
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier. 29, rue de Navacelles, 34090 Montpellier, France
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19
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Elbatrawi YM, Pedretty KP, Giddings N, Woodcock HL, Del Valle JR. δ-Azaproline and Its Oxidized Variants. J Org Chem 2020; 85:4207-4219. [DOI: 10.1021/acs.joc.9b03384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yassin M. Elbatrawi
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kyle P. Pedretty
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Nicole Giddings
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Juan R. Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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20
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Iyer BR, Gupta S, Noordeen H, Ravi R, Pawar MD, George A, Mahalakshmi R. Molecular Switch between Structural Compaction and Thermodynamic Stability by the Xxx-Pro Interface in Transmembrane β-Barrels. Biochemistry 2020; 59:303-314. [PMID: 31777252 DOI: 10.1021/acs.biochem.9b00731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transmembrane β-barrel scaffolds found in outer membrane proteins are formed and stabilized by a defined pattern of interstrand intraprotein H-bonds, in hydrophobic lipid bilayers. Introducing the conformationally constrained proline in β-barrels can cause significant destabilization of these structural regions that require H-bonding, with proline additionally acting as a secondary structure breaker. Membrane protein β-barrels are therefore expected to show poor tolerance to the presence of a transmembrane proline. Here, we assign a thermodynamic measure for the extent to which a single proline can be tolerated at the C-terminal interface of the model transmembrane β-barrel PagP. We find that proline drastically destabilizes PagP by 7.0 kcal mol-1 with respect to wild-type PagP (F161 → P161). Interestingly, strategic modulation of the preceding residue can modify the measured energetics. Placing a hydrophobic or bulky side chain as the preceding residue increases the thermodynamic stability by ≤8.0 kcal mol-1. While polar substituents at the preceding residue decrease the PagP stability, these residues demonstrate stronger tertiary packing interactions in the barrel and retain the catalytic activity of native PagP. This biophysical interplay between enhanced thermodynamic stability and attaining a structurally compact functional β-barrel scaffold highlights the detrimental effect caused by proline incorporation. Our findings also reveal alternative mechanisms that protein sequences can employ to salvage the structural integrity of transmembrane protein structures.
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Affiliation(s)
- Bharat Ramasubramanian Iyer
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Swadha Gupta
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Henna Noordeen
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Roshika Ravi
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Meera Daulatrao Pawar
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Anjana George
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
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21
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Ruiz-Estevez M, Staats J, Paatela E, Munson D, Katoku-Kikyo N, Yuan C, Asakura Y, Hostager R, Kobayashi H, Asakura A, Kikyo N. Promotion of Myoblast Differentiation by Fkbp5 via Cdk4 Isomerization. Cell Rep 2019; 25:2537-2551.e8. [PMID: 30485818 PMCID: PMC6350781 DOI: 10.1016/j.celrep.2018.11.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/29/2018] [Accepted: 10/31/2018] [Indexed: 01/10/2023] Open
Abstract
Fkbp5 is a widely expressed peptidyl prolyl isomerase that serves as a molecular chaperone through conformational changes of binding partners. Although it regulates diverse protein functions, little is known about its roles in myogenesis. We found here that Fkbp5 plays critical roles in myoblast differentiation through two mechanisms. First, it sequesters Cdk4 within the Hsp90 storage complex and prevents the formation of the cyclin D1-Cdk4 complex, which is a major inhibitor of differentiation. Second, Fkbp5 promotes cis-trans isomerization of the Thr172-Pro173 peptide bond in Cdk4 and inhibits phosphorylation of Thr172, an essential step for Cdk4 activation. Consistent with these in vitro findings, muscle regeneration is delayed in Fkbp5−/− mice. The related protein Fkbp4 also sequesters Cdk4 within the Hsp90 complex but does not isomerize Cdk4 or induce Thr173 phosphorylation despite its highly similar sequence. This study demonstrates protein isomerization as a critical regulatory mechanism of myogenesis by targeting Cdk4.
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Affiliation(s)
- Mercedes Ruiz-Estevez
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - James Staats
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ellen Paatela
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dane Munson
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nobuko Katoku-Kikyo
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ce Yuan
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yoko Asakura
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reilly Hostager
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hiroshi Kobayashi
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Atsushi Asakura
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Nobuaki Kikyo
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
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22
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Koehler M, Aravamudhan P, Guzman-Cardozo C, Dumitru AC, Yang J, Gargiulo S, Soumillion P, Dermody TS, Alsteens D. Glycan-mediated enhancement of reovirus receptor binding. Nat Commun 2019; 10:4460. [PMID: 31575869 PMCID: PMC6773860 DOI: 10.1038/s41467-019-12411-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/06/2019] [Indexed: 01/10/2023] Open
Abstract
Viral infection is an intricate process that requires the concerted action of both viral and host cell components. Entry of viruses into cells is initiated by interactions between viral proteins and their cell surface receptors. Despite recent progress, the molecular mechanisms underlying the multistep reovirus entry process are poorly understood. Using atomic force microscopy, we investigated how the reovirus σ1 attachment protein binds to both α-linked sialic acid (α-SA) and JAM-A cell-surface receptors. We discovered that initial σ1 binding to α-SA favors a strong multivalent anchorage to JAM-A. The enhanced JAM-A binding by virions following α-SA engagement is comparable to JAM-A binding by infectious subvirion particles (ISVPs) in the absence of α-SA. Since ISVPs have an extended σ1 conformer, this finding suggests that α-SA binding triggers a conformational change in σ1. These results provide new insights into the function of viral attachment proteins in the initiation of infection and open new avenues for the use of reoviruses as oncolytic agents.
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Affiliation(s)
- Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Pavithra Aravamudhan
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Microbial Pathogenesis, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Camila Guzman-Cardozo
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Microbial Pathogenesis, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Serena Gargiulo
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Terence S Dermody
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Center for Microbial Pathogenesis, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
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23
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Daza-Martin M, Starowicz K, Jamshad M, Tye S, Ronson GE, MacKay HL, Chauhan AS, Walker AK, Stone HR, Beesley JFJ, Coles JL, Garvin AJ, Stewart GS, McCorvie TJ, Zhang X, Densham RM, Morris JR. Isomerization of BRCA1-BARD1 promotes replication fork protection. Nature 2019; 571:521-527. [PMID: 31270457 DOI: 10.1038/s41586-019-1363-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 06/03/2019] [Indexed: 01/01/2023]
Abstract
The integrity of genomes is constantly threatened by problems encountered by the replication fork. BRCA1, BRCA2 and a subset of Fanconi anaemia proteins protect stalled replication forks from degradation by nucleases, through pathways that involve RAD51. The contribution and regulation of BRCA1 in replication fork protection, and how this role relates to its role in homologous recombination, is unclear. Here we show that BRCA1 in complex with BARD1, and not the canonical BRCA1-PALB2 interaction, is required for fork protection. BRCA1-BARD1 is regulated by a conformational change mediated by the phosphorylation-directed prolyl isomerase PIN1. PIN1 activity enhances BRCA1-BARD1 interaction with RAD51, thereby increasing the presence of RAD51 at stalled replication structures. We identify genetic variants of BRCA1-BARD1 in patients with cancer that exhibit poor protection of nascent strands but retain homologous recombination proficiency, thus defining domains of BRCA1-BARD1 that are required for fork protection and associated with cancer development. Together, these findings reveal a BRCA1-mediated pathway that governs replication fork protection.
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Affiliation(s)
- Manuel Daza-Martin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- The Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Katarzyna Starowicz
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Mohammed Jamshad
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Stephanie Tye
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
| | - George E Ronson
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Hannah L MacKay
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Anoop Singh Chauhan
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Alexandra K Walker
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Helen R Stone
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - James F J Beesley
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Jennifer L Coles
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Warwick Medical School, The University of Warwick, Coventry, UK
| | - Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Grant S Stewart
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Thomas J McCorvie
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
| | - Ruth M Densham
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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24
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Ovdiichuk O, Flauder L, Humbert-Voss E, Jamart-Grégoire B, Arrault A. δ-Azaproline: A versatile tool to design pseudopeptides by its incorporation via Nε or Nδ atoms. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2018.11.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Mukhopadhyay D, Gupta C, Theint T, Jaroniec CP. Peptide bond conformation in peptides and proteins probed by dipolar coupling-chemical shift tensor correlation solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 297:152-160. [PMID: 30396157 PMCID: PMC6289736 DOI: 10.1016/j.jmr.2018.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 05/30/2023]
Abstract
Multidimensional magic-angle spinning solid-state NMR experiments are described that permit cis and trans peptide bonds in uniformly 13C,15N-labeled peptides and proteins to be unambiguously distinguished in residue-specific manner by determining the relative orientations of the amide 13C' CSA and 1H-15N dipolar coupling tensors. The experiments are demonstrated for model peptides glycylglycine and 2,5-diketopiperazine containing trans and cis peptide bonds, respectively. Subsequently, the measurements are extended to two representative proteins that contain exclusively trans peptide bonds, microcrystalline B3 immunoglobulin domain of protein G and Y145Stop human prion protein amyloid fibrils, to illustrate their applicability to a wide range of protein systems.
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Affiliation(s)
- Dwaipayan Mukhopadhyay
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Chitrak Gupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Theint Theint
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States.
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26
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Thakkar BS, Svendsen JSM, Engh RA. Density Functional Studies on Secondary Amides: Role of Steric Factors in Cis/Trans Isomerization. Molecules 2018; 23:molecules23102455. [PMID: 30257481 PMCID: PMC6222500 DOI: 10.3390/molecules23102455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 11/16/2022] Open
Abstract
Cis/trans isomerization of amide bonds is a key step in a wide range of biological and synthetic processes. Occurring through C-N amide bond rotation, it also coincides with the activation of amides in enzymatic hydrolysis. In recently described QM studies of cis/trans isomerization in secondary amides using density functional methods, we highlighted that a peptidic prototype, such as glycylglycine methyl ester, can suitably represent the isomerization and complexities arising out of a larger molecular backbone, and can serve as the primary scaffold for model structures with different substitution patterns in order to assess and compare the steric effect of the substitution patterns. Here, we describe our theoretical assessment of such steric effects using tert-butyl as a representative bulky substitution. We analyze the geometries and relative stabilities of both trans and cis isomers, and effects on the cis/trans isomerization barrier. We also use the additivity principle to calculate absolute steric effects with a gradual increase in bulk. The study establishes that bulky substitutions significantly destabilize cis isomers and also increases the isomerization barrier, thereby synergistically hindering the cis/trans isomerization of secondary amides. These results provide a basis for the rationalization of kinetic and thermodynamic properties of peptides with potential applications in synthetic and medicinal chemistry.
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Affiliation(s)
- Balmukund S Thakkar
- Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.
| | | | - Richard A Engh
- Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.
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27
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Naseer MM, Hussain M, Bauzá A, Lo KM, Frontera A. Intramolecular Noncovalent Carbon Bonding Interaction Stabilizes the cis Conformation in Acylhydrazones. Chempluschem 2018; 83:881-885. [PMID: 31950685 DOI: 10.1002/cplu.201800329] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 12/14/2022]
Abstract
Noncovalent carbon bonding, a recently explored σ-hole interaction, was hitherto supposed to be a weak and structure-guided interaction. Here, its role in the intramolecular stabilization of the cis conformation of the amide moiety in acylhydrazones is described. The calculations reveal an electron donation from the lone pair of the nitrogen atom to the empty antibonding C-N orbital [LP(N)→BD*(C-N)] with a concomitant stabilization energy of E(2) =1.2 kcal mol-1 .
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Affiliation(s)
| | - Majid Hussain
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
| | - Kong Mun Lo
- Research Centre for Crystalline Materials School of Science and Technology, Sunway University, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
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28
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Lagu B, Kluge AF, Tozzo E, Fredenburg R, Bell EL, Goddeeris MM, Dwyer P, Basinski A, Senaiar RS, Jaleel M, Tiwari NK, Panigrahi SK, Krishnamurthy NR, Takahashi T, Patane MA. Selective PPARδ Modulators Improve Mitochondrial Function: Potential Treatment for Duchenne Muscular Dystrophy (DMD). ACS Med Chem Lett 2018; 9:935-940. [PMID: 30258544 DOI: 10.1021/acsmedchemlett.8b00287] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 07/31/2018] [Indexed: 01/14/2023] Open
Abstract
The X-ray structure of the previously reported PPARδ modulator 1 bound to the ligand binding domain (LBD) revealed that the amide moiety in 1 exists in the thermodynamically disfavored cis-amide orientation. Isosteric replacement of the cis-amide with five-membered heterocycles led to the identification of imidazole 17 (MA-0204), a potent, selective PPARδ modulator with good pharmacokinetic properties. MA-0204 was tested in vivo in mice and in vitro in patient-derived muscle myoblasts (from Duchenne Muscular Dystrophy (DMD) patients); 17 altered the expression of PPARδ target genes and improved fatty acid oxidation, which supports the therapeutic hypothesis for the study of MA-0204 in DMD patients.
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Affiliation(s)
- Bharat Lagu
- Mitobridge, Inc. (a wholly owned subsidiary of Astellas Pharma.), 1030 Massachusetts Avenue, Cambridge, Massachusetts 02138, United States
| | - Arthur F. Kluge
- Mitobridge, Inc. (a wholly owned subsidiary of Astellas Pharma.), 1030 Massachusetts Avenue, Cambridge, Massachusetts 02138, United States
| | - Effie Tozzo
- Mitobridge, Inc. (a wholly owned subsidiary of Astellas Pharma.), 1030 Massachusetts Avenue, Cambridge, Massachusetts 02138, United States
| | - Ross Fredenburg
- Mitobridge, Inc. (a wholly owned subsidiary of Astellas Pharma.), 1030 Massachusetts Avenue, Cambridge, Massachusetts 02138, United States
| | - Eric L. Bell
- Mitobridge, Inc. (a wholly owned subsidiary of Astellas Pharma.), 1030 Massachusetts Avenue, Cambridge, Massachusetts 02138, United States
| | - Matthew M. Goddeeris
- Mitobridge, Inc. (a wholly owned subsidiary of Astellas Pharma.), 1030 Massachusetts Avenue, Cambridge, Massachusetts 02138, United States
| | - Peter Dwyer
- Mitobridge, Inc. (a wholly owned subsidiary of Astellas Pharma.), 1030 Massachusetts Avenue, Cambridge, Massachusetts 02138, United States
| | - Andrew Basinski
- Mitobridge, Inc. (a wholly owned subsidiary of Astellas Pharma.), 1030 Massachusetts Avenue, Cambridge, Massachusetts 02138, United States
| | - Ramesh S. Senaiar
- Aurigene Discovery Technologies, Ltd., Bengaluru and Hyderabad, India
| | - Mahaboobi Jaleel
- Aurigene Discovery Technologies, Ltd., Bengaluru and Hyderabad, India
| | | | | | | | | | - Michael A. Patane
- Mitobridge, Inc. (a wholly owned subsidiary of Astellas Pharma.), 1030 Massachusetts Avenue, Cambridge, Massachusetts 02138, United States
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29
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Le DN, Hansen E, Khan HA, Kim B, Wiest O, Dong VM. Hydrogenation catalyst generates cyclic peptide stereocentres in sequence. Nat Chem 2018; 10:968-973. [PMID: 30061616 DOI: 10.1038/s41557-018-0089-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 05/22/2018] [Indexed: 11/09/2022]
Abstract
Molecular recognition plays a key role in enzyme-substrate specificity, the regulation of genes, and the treatment of diseases. Inspired by the power of molecular recognition in enzymatic processes, we sought to exploit its use in organic synthesis. Here we demonstrate how a synthetic rhodium-based catalyst can selectively bind a dehydroamino acid residue to initiate a sequential and stereoselective synthesis of cyclic peptides. Our combined experimental and theoretical study reveals the underpinnings of a cascade reduction that occurs with high stereocontrol and in one direction around a macrocyclic ring. As the catalyst can dissociate from the peptide, the C to N directionality of the hydrogenation reactions is controlled by catalyst-substrate recognition rather than a processive mechanism in which the catalyst remains bound to the macrocycle. This mechanistic insight provides a foundation for the use of cascade hydrogenations.
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Affiliation(s)
- Diane N Le
- Department of Chemistry, University of California, Irvine, CA, USA
| | - Eric Hansen
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Hasan A Khan
- Department of Chemistry, University of California, Irvine, CA, USA.,Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Byoungmoo Kim
- Department of Chemistry, University of California, Irvine, CA, USA.,Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA. .,Lab of Computational Chemistry and Drug Design, School of Chemical Biology and Biotechnology, Peking University, Shenzhen, China.
| | - Vy M Dong
- Department of Chemistry, University of California, Irvine, CA, USA.
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30
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Urushibara K, Ferrand Y, Liu Z, Masu H, Pophristic V, Tanatani A, Huc I. Frustrierte Helizität: Zusammenführung divergierender Enden einer stabilen aromatischen Amid‐Helix zu einem fluxionalen Makrocyclus. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ko Urushibara
- Department of Chemistry Faculty of Science Ochanomizu University 2-1-1 Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
- CBMN (UMR5248) Univ. Bordeaux – CNRS – IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| | - Yann Ferrand
- CBMN (UMR5248) Univ. Bordeaux – CNRS – IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| | - Zhiwei Liu
- Department of Chemistry &Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Hyuma Masu
- Center for Analytical Instrumentation Chiba University 1-33 Yayoi, Inage Chiba 263-8522 Japan
| | - Vojislava Pophristic
- Department of Chemistry &Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Aya Tanatani
- Department of Chemistry Faculty of Science Ochanomizu University 2-1-1 Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
| | - Ivan Huc
- CBMN (UMR5248) Univ. Bordeaux – CNRS – IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
- Department Pharmazie Ludwig-Maximilians-Universität Butenandtstraße 5–13 81377 München Deutschland
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31
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Discovery of d-amino acid oxidase inhibitors based on virtual screening against the lid-open enzyme conformation. Bioorg Med Chem Lett 2018; 28:1693-1698. [DOI: 10.1016/j.bmcl.2018.04.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 11/20/2022]
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32
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Urushibara K, Ferrand Y, Liu Z, Masu H, Pophristic V, Tanatani A, Huc I. Frustrated Helicity: Joining the Diverging Ends of a Stable Aromatic Amide Helix to Form a Fluxional Macrocycle. Angew Chem Int Ed Engl 2018; 57:7888-7892. [DOI: 10.1002/anie.201802159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Ko Urushibara
- Department of Chemistry Faculty of Science Ochanomizu University 2-1-1 Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
- CBMN (UMR5248), Univ. Bordeaux—CNRS—IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
| | - Yann Ferrand
- CBMN (UMR5248), Univ. Bordeaux—CNRS—IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
| | - Zhiwei Liu
- Department of Chemistry &Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Hyuma Masu
- Center for Analytical Instrumentation Chiba University 1–33 Yayoi, Inage Chiba 263-8522 Japan
| | - Vojislava Pophristic
- Department of Chemistry &Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Aya Tanatani
- Department of Chemistry Faculty of Science Ochanomizu University 2-1-1 Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
| | - Ivan Huc
- CBMN (UMR5248), Univ. Bordeaux—CNRS—IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
- Department Pharmazie Ludwig-Maximilians-Universität Butenandtstr. 5–13 81377 München Germany
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33
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Dilworth D, Gudavicius G, Xu X, Boyce AKJ, O’Sullivan C, Serpa JJ, Bilenky M, Petrochenko EV, Borchers CH, Hirst M, Swayne LA, Howard P, Nelson CJ. The prolyl isomerase FKBP25 regulates microtubule polymerization impacting cell cycle progression and genomic stability. Nucleic Acids Res 2018; 46:2459-2478. [PMID: 29361176 PMCID: PMC5861405 DOI: 10.1093/nar/gky008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 12/14/2017] [Accepted: 01/12/2018] [Indexed: 12/25/2022] Open
Abstract
FK506 binding proteins (FKBPs) catalyze the interconversion of cis-trans proline conformers in proteins. Importantly, FK506 drugs have anti-cancer and neuroprotective properties, but the effectors and mechanisms underpinning these properties are not well understood because the cellular function(s) of most FKBP proteins are unclear. FKBP25 is a nuclear prolyl isomerase that interacts directly with nucleic acids and is associated with several DNA/RNA binding proteins. Here, we show the catalytic FKBP domain binds microtubules (MTs) directly to promote their polymerization and stabilize the MT network. Furthermore, FKBP25 associates with the mitotic spindle and regulates entry into mitosis. This interaction is important for mitotic spindle dynamics, as we observe increased chromosome instability in FKBP25 knockdown cells. Finally, we provide evidence that FKBP25 association with chromatin is cell-cycle regulated by Protein Kinase C phosphorylation. This disrupts FKBP25-DNA contacts during mitosis while maintaining its interaction with the spindle apparatus. Collectively, these data support a model where FKBP25 association with chromatin and MTs is carefully choreographed to ensure faithful genome duplication. Additionally, they highlight that FKBP25 is a MT-associated FK506 receptor and potential therapeutic target in MT-associated diseases.
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Affiliation(s)
- David Dilworth
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Geoff Gudavicius
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Xiaoxue Xu
- Division of Medical Sciences and Island Medical Program, University of Victoria, Victoria V8P 5C2, Canada
| | - Andrew K J Boyce
- Division of Medical Sciences and Island Medical Program, University of Victoria, Victoria V8P 5C2, Canada
| | - Connor O’Sullivan
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Jason J Serpa
- University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Misha Bilenky
- BC Cancer Agency Genome Sciences Centre and the Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Evgeniy V Petrochenko
- University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Martin Hirst
- BC Cancer Agency Genome Sciences Centre and the Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Leigh Anne Swayne
- Division of Medical Sciences and Island Medical Program, University of Victoria, Victoria V8P 5C2, Canada
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Perry Howard
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Christopher J Nelson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
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34
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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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35
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Voronina L, Scutelnic V, Masellis C, Rizzo TR. Can Mutational Analysis Be Used To Assist Structure Determination of Peptides? J Am Chem Soc 2018; 140:2401-2404. [PMID: 29412650 DOI: 10.1021/jacs.7b11302] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mutational analysis is widely used to study the relationship between sequence and structure of proteins and peptides. It is often assumed that substituting a proline with another amino acid "locks" the peptide bond in the trans conformation, allowing only a subset of the initial molecular geometries to be observed. To test this assumption, we assess the result of substituting two prolines in the bradykinin sequence with alanine using field-asymmetric ion mobility spectrometry combined with cryogenic ion spectroscopy in the gas phase. While the structure of the mutant coincides with a part of the conformational space of the original peptide, the higher flexibility of the alanine backbone compared to proline allows it to access additional structures. We conclude that proline-to-nonproline substitutions are helpful to assign structures, but they should be used in conjunction with spectroscopic techniques that allow detailed comparison of the structures of the mutant and the native peptide.
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Affiliation(s)
- Liudmila Voronina
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM , Station 6, CH-1015 Lausanne, Switzerland
| | - Valeriu Scutelnic
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM , Station 6, CH-1015 Lausanne, Switzerland
| | - Chiara Masellis
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM , Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM , Station 6, CH-1015 Lausanne, Switzerland
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36
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Karachi S, Farrokhpour H, Abyar F. Ionization of the Conformers of cis
Nanotubular Cyclic Peptides in the Gas Phase: Effect of Size and Conformation on Ionization. J CHIN CHEM SOC-TAIP 2018. [DOI: 10.1002/jccs.201700179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sara Karachi
- Department of Chemistry; Isfahan University of Technology; Isfahan 84156-83111 Iran
| | - Hossein Farrokhpour
- Department of Chemistry; Isfahan University of Technology; Isfahan 84156-83111 Iran
| | - Fatemeh Abyar
- Chemical Engineering Department, Faculty of Engineering; Ardakan University; Ardakan Yazd 89518-95491 Iran
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37
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Alderson TR, Lee JH, Charlier C, Ying J, Bax A. Propensity for cis-Proline Formation in Unfolded Proteins. Chembiochem 2017; 19:37-42. [PMID: 29064600 DOI: 10.1002/cbic.201700548] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Indexed: 12/19/2022]
Abstract
In unfolded proteins, peptide bonds involving Pro residues exist in equilibrium between the minor cis and major trans conformations. Folded proteins predominantly contain trans-Pro bonds, and slow cis-trans Pro isomerization in the unfolded state is often found to be a rate-limiting step in protein folding. Moreover, kinases and phosphatases that act upon Ser/Thr-Pro motifs exhibit preferential recognition of either the cis- or trans-Pro conformer. Here, NMR spectra obtained at both atmospheric and high pressures indicate that the population of cis-Pro falls well below previous estimates, an effect attributed to the use of short peptides with charged termini in most prior model studies. For the intrinsically disordered protein α-synuclein, cis-Pro populations at all of its five X-Pro bonds are less than 5 %, with only modest ionic strength dependence and no detectable effect of the previously demonstrated interaction between the N- and C-terminal halves of the protein. Comparison to small peptides with the same amino-acid sequence indicates that peptides, particularly those with unblocked, oppositely charged amino and carboxyl end groups, strongly overestimate the amount of cis-Pro.
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Affiliation(s)
- T Reid Alderson
- Laboratory of Chemical Physics, National Institutes of Health, 5 Memorial Drive, Bethesda, MD, 20892, USA
| | - Jung Ho Lee
- Laboratory of Chemical Physics, National Institutes of Health, 5 Memorial Drive, Bethesda, MD, 20892, USA
| | - Cyril Charlier
- Laboratory of Chemical Physics, National Institutes of Health, 5 Memorial Drive, Bethesda, MD, 20892, USA
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institutes of Health, 5 Memorial Drive, Bethesda, MD, 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institutes of Health, 5 Memorial Drive, Bethesda, MD, 20892, USA
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38
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Thakkar BS, Svendsen JSM, Engh RA. Cis/Trans Isomerization in Secondary Amides: Reaction Paths, Nitrogen Inversion, and Relevance to Peptidic Systems. J Phys Chem A 2017; 121:6830-6837. [DOI: 10.1021/acs.jpca.7b05584] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Balmukund S. Thakkar
- Department of Chemistry, UiT The Arctic University of Norway, Tromsø-9037, Norway
| | | | - Richard A. Engh
- Department of Chemistry, UiT The Arctic University of Norway, Tromsø-9037, Norway
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39
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Wilk P, Uehlein M, Kalms J, Dobbek H, Mueller U, Weiss MS. Substrate specificity and reaction mechanism of human prolidase. FEBS J 2017; 284:2870-2885. [DOI: 10.1111/febs.14158] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/23/2017] [Accepted: 06/30/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Piotr Wilk
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
- Institut für Biologie, Strukturbiologie/Biochemie; Humboldt-Universität zu Berlin; Germany
| | - Monika Uehlein
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
| | - Jacqueline Kalms
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie; Humboldt-Universität zu Berlin; Germany
| | - Uwe Mueller
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
| | - Manfred S. Weiss
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
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40
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Das S, Bhadra P, Ramakumar S, Pal D. Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins. J Proteome Res 2017. [PMID: 28633522 DOI: 10.1021/acs.jproteome.7b00217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
cis-Peptide bonds, whose occurrence in proteins is rare but evolutionarily conserved, are implicated to play an important role in protein function. This has led to their previous use in a homology-independent, fragment-match-based protein function annotation method. However, proteins are not static molecules; dynamics is integral to their activity. This is nicely epitomized by the geometric isomerization of cis-peptide to trans form for molecular activity. Hence we have incorporated both static (cis-peptide) and dynamics information to improve the prediction of protein molecular function. Our results show that cis-peptide information alone cannot detect functional matches in cases where cis-trans isomerization exists but 3D coordinates have been obtained for only the trans isomer or when the cis-peptide bond is incorrectly assigned as trans. On the contrary, use of dynamics information alone includes false-positive matches for cases where fragments with similar secondary structure show similar dynamics, but the proteins do not share a common function. Combining the two methods reduces errors while detecting the true matches, thereby enhancing the utility of our method in function annotation. A combined approach, therefore, opens up new avenues of improving existing automated function annotation methodologies.
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Affiliation(s)
- Sreetama Das
- Department of Physics and ‡Department of Computational and Data Sciences, Indian Institute of Science , Bangalore 560012, India
| | - Pratiti Bhadra
- Department of Physics and ‡Department of Computational and Data Sciences, Indian Institute of Science , Bangalore 560012, India
| | - Suryanarayanarao Ramakumar
- Department of Physics and ‡Department of Computational and Data Sciences, Indian Institute of Science , Bangalore 560012, India
| | - Debnath Pal
- Department of Physics and ‡Department of Computational and Data Sciences, Indian Institute of Science , Bangalore 560012, India
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41
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Alderson TR, Benesch JLP, Baldwin AJ. Proline isomerization in the C-terminal region of HSP27. Cell Stress Chaperones 2017; 22:639-651. [PMID: 28547731 PMCID: PMC5465039 DOI: 10.1007/s12192-017-0791-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 12/12/2022] Open
Abstract
In mammals, small heat-shock proteins (sHSPs) typically assemble into interconverting, polydisperse oligomers. The dynamic exchange of sHSP oligomers is regulated, at least in part, by molecular interactions between the α-crystallin domain and the C-terminal region (CTR). Here we report solution-state nuclear magnetic resonance (NMR) spectroscopy investigations of the conformation and dynamics of the disordered and flexible CTR of human HSP27, a systemically expressed sHSP. We observed multiple NMR signals for residues in the vicinity of proline 194, and we determined that, while all observed forms are highly disordered, the extra resonances arise from cis-trans peptidyl-prolyl isomerization about the G193-P194 peptide bond. The cis-P194 state is populated to near 15% at physiological temperatures, and, although both cis- and trans-P194 forms of the CTR are flexible and dynamic, both states show a residual but differing tendency to adopt β-strand conformations. In NMR spectra of an isolated CTR peptide, we observed similar evidence for isomerization involving proline 182, found within the IPI/V motif. Collectively, these data indicate a potential role for cis-trans proline isomerization in regulating the oligomerization of sHSPs.
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Affiliation(s)
- T Reid Alderson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Justin L P Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Andrew J Baldwin
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
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42
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Momin M, Xin Y, Hamelberg D. Allosteric Fine-Tuning of the Binding Pocket Dynamics in the ITK SH2 Domain by a Distal Molecular Switch: An Atomistic Perspective. J Phys Chem B 2017; 121:6131-6138. [PMID: 28570811 DOI: 10.1021/acs.jpcb.7b03470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Although the regulation of function of proteins by allosteric interactions has been identified in many subcellular processes, molecular switches are also known to induce long-range conformational changes in proteins. A less well understood molecular switch involving cis-trans isomerization of a peptidyl-prolyl bond could induce a conformational change directly to the backbone that is propagated to other parts of the protein. However, these switches are elusive and hard to identify because they are intrinsic to biomolecules that are inherently dynamic. Here, we explore the conformational dynamics and free energy landscape of the SH2 domain of interleukin-2-inducible T-cell or tyrosine kinase (ITK) to fully understand the conformational coupling between the distal cis-trans molecular switch and its binding pocket of the phosphotyrosine motif. We use multiple microsecond-long all-atom molecular dynamics simulations in explicit water for over a total of 60 μs. We show that cis-trans isomerization of the Asn286-Pro287 peptidyl-prolyl bond is directly coupled to the dynamics of the binding pocket of the phosphotyrosine motif, in agreement with previous NMR experiments. Unlike the cis state that is localized and less dynamic in a single free energy basin, the trans state samples two distinct conformations of the binding pocket-one that recognizes the phosphotyrosine motif and the other that is somewhat similar to that of the cis state. The results provide an atomic-level description of a less well understood allosteric regulation by a peptidyl-prolyl cis-trans molecular switch that could aid in the understanding of normal and aberrant subcellular processes and the identification of these elusive molecular switches in other proteins.
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Affiliation(s)
- Mohamed Momin
- Department of Chemistry and ‡Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States
| | - Yao Xin
- Department of Chemistry and ‡Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry and ‡Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States
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43
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Singh MK, Manoj N. Structural role of a conserved active sitecisproline in theThermotoga maritimaacetyl esterase from the carbohydrate esterase family 7. Proteins 2017; 85:694-708. [DOI: 10.1002/prot.25249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/17/2016] [Accepted: 01/04/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Mrityunjay K. Singh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 Tamil Nadu India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 Tamil Nadu India
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44
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De S, Musil F, Ingram T, Baldauf C, Ceriotti M. Mapping and classifying molecules from a high-throughput structural database. J Cheminform 2017; 9:6. [PMID: 28203290 PMCID: PMC5289135 DOI: 10.1186/s13321-017-0192-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/17/2017] [Indexed: 11/10/2022] Open
Abstract
High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from computational searches, as well as the agglomeration of data of heterogeneous provenance leads to considerable challenges when it comes to navigating the database, representing its structure at a glance, understanding structure-property relations, eliminating duplicates and identifying inconsistencies. Here we present a case study, based on a data set of conformers of amino acids and dipeptides, of how machine-learning techniques can help addressing these issues. We will exploit a recently-developed strategy to define a metric between structures, and use it as the basis of both clustering and dimensionality reduction techniques-showing how these can help reveal structure-property relations, identify outliers and inconsistent structures, and rationalise how perturbations (e.g. binding of ions to the molecule) affect the stability of different conformers.
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Affiliation(s)
- Sandip De
- National Center for Computational Design and Discovery of Novel Materials (MARVEL), Lausanne, Switzerland.,Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Felix Musil
- National Center for Computational Design and Discovery of Novel Materials (MARVEL), Lausanne, Switzerland.,Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Teresa Ingram
- Theory Department of the Fritz Haber Institute, Faradayweg 4-6, 14195 Berlin-Dahlem, Germany
| | - Carsten Baldauf
- Theory Department of the Fritz Haber Institute, Faradayweg 4-6, 14195 Berlin-Dahlem, Germany
| | - Michele Ceriotti
- National Center for Computational Design and Discovery of Novel Materials (MARVEL), Lausanne, Switzerland.,Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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45
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46
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Li H, Jiang J, Luo Y. Identification of the protonation site of gaseous triglycine: the cis-peptide bond conformation as the global minimum. Phys Chem Chem Phys 2017; 19:15030-15038. [DOI: 10.1039/c7cp01997a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extensive ab initio investigations have been performed to characterize stable conformers of protonated triglycine (GGGH) in the gas phase.
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Affiliation(s)
- Hongbao Li
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- China
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- China
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47
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Wiedemann C, Ohlenschläger O, Mrestani-Klaus C, Bordusa F. NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state. Phys Chem Chem Phys 2017; 19:24115-24125. [DOI: 10.1039/c7cp03295a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The impact of ionic liquids on the chemical shifts and the cis/trans equilibrium state of a model peptide was systematically investigated by NMR spectroscopy.
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Affiliation(s)
- Christoph Wiedemann
- Institute of Biochemistry and Biotechnology
- Martin-Luther-University Halle-Wittenberg
- D-06120 Halle
- Germany
| | | | - Carmen Mrestani-Klaus
- Institute of Biochemistry and Biotechnology
- Martin-Luther-University Halle-Wittenberg
- D-06120 Halle
- Germany
| | - Frank Bordusa
- Institute of Biochemistry and Biotechnology
- Martin-Luther-University Halle-Wittenberg
- D-06120 Halle
- Germany
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48
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Properties of the Amide Bond Involving Proline 4,5-methanologues: an Experimental and Theoretical Study. Isr J Chem 2016. [DOI: 10.1002/ijch.201600106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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49
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Jangra H, Haindl MH, Achrainer F, Hioe J, Gschwind RM, Zipse H. Conformational Preferences in Small Peptide Models: The Relevance ofcis/trans-Conformations. Chemistry 2016; 22:13328-35. [DOI: 10.1002/chem.201601828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Harish Jangra
- Department of Chemistry; LMU München; Butenandstrasse 5-14 81377 München Germany
| | - Michael H. Haindl
- Institut für Organische Chemie; Universität Regensburg; 93053 Regensburg Germany
| | - Florian Achrainer
- Department of Chemistry; LMU München; Butenandstrasse 5-14 81377 München Germany
| | - Johnny Hioe
- Institut für Organische Chemie; Universität Regensburg; 93053 Regensburg Germany
| | - Ruth M. Gschwind
- Institut für Organische Chemie; Universität Regensburg; 93053 Regensburg Germany
| | - Hendrik Zipse
- Department of Chemistry; LMU München; Butenandstrasse 5-14 81377 München Germany
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50
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Dreßen M, Lahm H, Lahm A, Wolf K, Doppler S, Deutsch MA, Cleuziou J, Pabst von Ohain J, Schön P, Ewert P, Malcic I, Lange R, Krane M. A novel de novo TBX5 mutation in a patient with Holt-Oram syndrome leading to a dramatically reduced biological function. Mol Genet Genomic Med 2016; 4:557-67. [PMID: 27652283 PMCID: PMC5023941 DOI: 10.1002/mgg3.234] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 04/29/2016] [Accepted: 05/03/2016] [Indexed: 01/26/2023] Open
Abstract
Background The Holt–Oram syndrome (HOS) is an autosomal dominant disorder affecting 1/100.000 live births. It is defined by upper limb anomalies and congenital heart defects with variable severity. We describe a dramatic phenotype of a male, 15‐month‐old patient being investigated for strict diagnostic criteria of HOS. Methods and results Genetic analysis revealed a so far unpublished TBX5 mutation, which occurs de novo in the patient with healthy parents. TBX5 belongs to the large family of T‐box transcription factors playing major roles in morphogenesis and cell‐type specification. The mutation located in the DNA‐binding domain at position 920 (C→A) leads to an amino acid change at position 85 (proline → threonine). Three‐dimensional analysis of the protein structure predicted a cis to trans change in the respective peptide bond, thereby probably provoking major conformational and functional alterations of the protein. The p.Pro85Thr mutation showed a dramatically reduced activation (97%) of the NPPA promoter in luciferase assays and failed to induce NPPA expression in HEK 293 cells compared to wild‐type TBX5 protein. The mutation did not interfere with the nuclear localization of the protein. Conclusion These results suggest that the dramatic functional alteration of the p.Pro85Thr mutation leads to the distinctive phenotype of the patient.
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Affiliation(s)
- Martina Dreßen
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Harald Lahm
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Armin Lahm
- Bioinformatics Project Support Rome Italy
| | - Klaudia Wolf
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Stefanie Doppler
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Marcus-André Deutsch
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Julie Cleuziou
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Jelena Pabst von Ohain
- Department of Cardiovascular Surgery Division of Experimental Surgery German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Patric Schön
- Department of Paediatric Cardiology and Congenital Heart Defects German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Peter Ewert
- Department of Paediatric Cardiology and Congenital Heart Defects German Heart Center Munich at the Technical University of Munich Munich Germany
| | - Ivan Malcic
- Department of Pediatrics Division of Cardiology and Intensive Care Unit University Hospital Zagreb Zagreb Croatia
| | - Rüdiger Lange
- Department of Cardiovascular SurgeryDivision of Experimental SurgeryGerman Heart Center Munich at the Technical University of MunichMunichGermany; DZHK (German Center for Cardiovascular Research) - partner site Munich Heart AllianceMunichGermany
| | - Markus Krane
- Department of Cardiovascular SurgeryDivision of Experimental SurgeryGerman Heart Center Munich at the Technical University of MunichMunichGermany; DZHK (German Center for Cardiovascular Research) - partner site Munich Heart AllianceMunichGermany
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