1
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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Cheng Y, Hyodo T, Yamaguchi K, Ohwada T, Otani Y. Complete amide cis- trans switching synchronized with disulfide bond formation and cleavage in a proline-mimicking system. Chem Commun (Camb) 2024; 60:6158-6161. [PMID: 38804552 DOI: 10.1039/d4cc01096e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
A typical naturally occurring disulfide structure in proteins is an 8-membered disulfide ring formed between two adjacent cysteine (Cys-Cys) residues. Based on this structure, we designed 7- to 9-membered disulfide ring molecules, embedded in the 7-azabicyclo[2.2.1]heptane skeleton, that switch their conformation from exclusively trans-amide to exclusively cis-amide upon redox transformation from dithiol to disulfide, and vice versa. Constrained shape of disulfide rings is rare in nature, and the present molecular structure is expected to be a useful fundamental component for the construction of new conformation-switching systems.
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Affiliation(s)
- Yuhe Cheng
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Tadashi Hyodo
- School of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Kentaro Yamaguchi
- School of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Tomohiko Ohwada
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Yuko Otani
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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3
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Breunig SL, Chapman AM, LeBon J, Quijano JC, Ranasinghe M, Rawson J, Demeler B, Ku HT, Tirrell DA. 4S-fluorination of ProB29 in insulin lispro slows fibril formation. J Biol Chem 2024; 300:107332. [PMID: 38703998 PMCID: PMC11154709 DOI: 10.1016/j.jbc.2024.107332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 05/06/2024] Open
Abstract
Recombinant insulin is a life-saving therapeutic for millions of patients affected by diabetes mellitus. Standard mutagenesis has led to insulin variants with improved control of blood glucose; for instance, the fast-acting insulin lispro contains two point mutations that suppress dimer formation and expedite absorption. However, insulins undergo irreversible denaturation, a process accelerated for the insulin monomer. Here we replace ProB29 of insulin lispro with 4R-fluoroproline, 4S-fluoroproline, and 4,4-difluoroproline. All three fluorinated lispro variants reduce blood glucose in diabetic mice, exhibit similar secondary structure as measured by CD, and rapidly dissociate from the zinc- and resorcinol-bound hexamer upon dilution. Notably, however, we find that 4S-fluorination of ProB29 delays the formation of undesired insulin fibrils that can accumulate at the injection site in vivo and can complicate insulin production and storage. These results demonstrate how subtle molecular changes achieved through non-canonical amino acid mutagenesis can improve the stability of protein therapeutics.
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Affiliation(s)
- Stephanie L Breunig
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Alex M Chapman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Jeanne LeBon
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope, Duarte, California, USA
| | - Janine C Quijano
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope, Duarte, California, USA
| | - Maduni Ranasinghe
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Jeffrey Rawson
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope, Duarte, California, USA
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana, USA
| | - Hsun Teresa Ku
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope, Duarte, California, USA; Irell & Manella Graduate School of Biological Science, City of Hope, Duarte, California, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.
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4
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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5
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Jeong J, Usman M, Li Y, Zhou XZ, Lu KP. Pin1-Catalyzed Conformation Changes Regulate Protein Ubiquitination and Degradation. Cells 2024; 13:731. [PMID: 38727267 PMCID: PMC11083468 DOI: 10.3390/cells13090731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 05/13/2024] Open
Abstract
The unique prolyl isomerase Pin1 binds to and catalyzes cis-trans conformational changes of specific Ser/Thr-Pro motifs after phosphorylation, thereby playing a pivotal role in regulating the structure and function of its protein substrates. In particular, Pin1 activity regulates the affinity of a substrate for E3 ubiquitin ligases, thereby modulating the turnover of a subset of proteins and coordinating their activities after phosphorylation in both physiological and disease states. In this review, we highlight recent advancements in Pin1-regulated ubiquitination in the context of cancer and neurodegenerative disease. Specifically, Pin1 promotes cancer progression by increasing the stabilities of numerous oncoproteins and decreasing the stabilities of many tumor suppressors. Meanwhile, Pin1 plays a critical role in different neurodegenerative disorders via the regulation of protein turnover. Finally, we propose a novel therapeutic approach wherein the ubiquitin-proteasome system can be leveraged for therapy by targeting pathogenic intracellular targets for TRIM21-dependent degradation using stereospecific antibodies.
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Affiliation(s)
- Jessica Jeong
- Departments of Biochemistry and Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5C1, Canada; (J.J.)
- Robarts Research Institute, Western University, London, ON N6A 5B7, Canada
| | - Muhammad Usman
- Departments of Biochemistry and Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5C1, Canada; (J.J.)
- Robarts Research Institute, Western University, London, ON N6A 5B7, Canada
| | - Yitong Li
- Departments of Biochemistry and Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5C1, Canada; (J.J.)
- Robarts Research Institute, Western University, London, ON N6A 5B7, Canada
| | - Xiao Zhen Zhou
- Departments of Biochemistry and Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5C1, Canada; (J.J.)
- Department of Pathology and Laboratory Medicine, and Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5C1, Canada
- Lawson Health Research Institute, Western University, London, ON N6C 2R5, Canada
| | - Kun Ping Lu
- Departments of Biochemistry and Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5C1, Canada; (J.J.)
- Robarts Research Institute, Western University, London, ON N6A 5B7, Canada
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6
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Bharambe N, Li Z, Seiferth D, Balakrishna AM, Biggin PC, Basak S. Cryo-EM structures of prokaryotic ligand-gated ion channel GLIC provide insights into gating in a lipid environment. Nat Commun 2024; 15:2967. [PMID: 38580666 PMCID: PMC10997623 DOI: 10.1038/s41467-024-47370-w] [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: 02/22/2023] [Accepted: 03/28/2024] [Indexed: 04/07/2024] Open
Abstract
GLIC, a proton-activated prokaryotic ligand-gated ion channel, served as a model system for understanding the eukaryotic counterparts due to their structural and functional similarities. Despite extensive studies conducted on GLIC, the molecular mechanism of channel gating in the lipid environment requires further investigation. Here, we present the cryo-EM structures of nanodisc-reconstituted GLIC at neutral and acidic pH in the resolution range of 2.6 - 3.4 Å. In our apo state at pH 7.5, the extracellular domain (ECD) displays conformational variations compared to the existing apo structures. At pH 4.0, three distinct conformational states (C1, C2 and O states) are identified. The protonated structures exhibit a compacted and counter-clockwise rotated ECD compared with our apo state. A gradual widening of the pore in the TMD is observed upon reducing the pH, with the widest pore in O state, accompanied by several layers of water pentagons. The pore radius and molecular dynamics (MD) simulations suggest that the O state represents an open conductive state. We also observe state-dependent interactions between several lipids and proteins that may be involved in the regulation of channel gating. Our results provide comprehensive insights into the importance of lipids impact on gating.
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Affiliation(s)
- Nikhil Bharambe
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Zhuowen Li
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - David Seiferth
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Sandip Basak
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 639798, Singapore.
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7
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Zhao Z, Wang M, Miller MC, He Z, Xu X, Zhou Y, Mayo KH, Tai G. Isomerization of proline-46 in the N-terminal tail of galectin-3 enhances T cell apoptosis via the ROS-ERK pathway. Int J Biol Macromol 2024; 256:128304. [PMID: 37992938 DOI: 10.1016/j.ijbiomac.2023.128304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/11/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023]
Abstract
Galectin-3 (Gal-3) is unique in the galectin family, due to the presence of a long N-terminal tail (NT) arising from its conserved carbohydrate recognition domain (CRD). Although functional significance of the NT has remained elusive, our previous studies demonstrated the importance of NT prolines to Gal-3 function. Here, we show that during the time Gal-3 stands in solution for three or more days, Gal-3 NT undergoes a slow, intra-molecular, time-dependent conformational/dynamical change associated with proline cis-trans isomerization. From initial dissolution of Gal-3 in buffer to three days in solution, Gal-3-mediated T cell apoptosis is enhanced from 23 % to 37 %. Western blotting and flow cytometry show that the enhancement occurs via the ROS-ERK pathway, and not by the PKC-ERK pathway. To assess which proline(s) is (are) responsible for this effect, we individually mutated all 14 NT prolines within the first 68 residues to alanines, and assessed their effect on ROS production. Our study shows that isomerization of P46 alone is responsible for the upregulation of ROS and T cell apoptosis. NMR studies show that this unique effect is mediated by a change in dynamic interactions between the NT and CRD F-face, which in turn leads to this change in Gal-3 function.
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Affiliation(s)
- Zihan Zhao
- Engineering Research Center of Glycoconjugates, Ministry of Education, Jilin Province Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Menghui Wang
- Engineering Research Center of Glycoconjugates, Ministry of Education, Jilin Province Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Michelle C Miller
- Department of Biochemistry, Molecular Biology & Biophysics, 6-155 Jackson Hall, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zhen He
- Engineering Research Center of Glycoconjugates, Ministry of Education, Jilin Province Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Xuejiao Xu
- Engineering Research Center of Glycoconjugates, Ministry of Education, Jilin Province Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Yifa Zhou
- Engineering Research Center of Glycoconjugates, Ministry of Education, Jilin Province Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Kevin H Mayo
- Department of Biochemistry, Molecular Biology & Biophysics, 6-155 Jackson Hall, University of Minnesota, Minneapolis, MN 55455, USA
| | - Guihua Tai
- Engineering Research Center of Glycoconjugates, Ministry of Education, Jilin Province Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China.
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8
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Breunig S, Quijano JC, Donohue C, Henrickson A, Demeler B, Ku HT, Tirrell DA. Incorporation of Aliphatic Proline Residues into Recombinantly Produced Insulin. ACS Chem Biol 2023; 18:2574-2581. [PMID: 37960878 PMCID: PMC10728891 DOI: 10.1021/acschembio.3c00561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023]
Abstract
Analogs of proline can be used to expand the chemical space about the residue while maintaining its uniquely restricted conformational space. Here, we demonstrate the incorporation of 4R-methylproline, 4S-methylproline, and 4-methyleneproline into recombinant insulin expressed in Escherichia coli. These modified proline residues, introduced at position B28, change the biophysical properties of insulin: Incorporation of 4-methyleneproline at B28 accelerates fibril formation, while 4-methylation speeds dissociation from the pharmaceutically formulated hexamer. This work expands the scope of proline analogs amenable to incorporation into recombinant proteins and demonstrates how noncanonical amino acid mutagenesis can be used to engineer the therapeutically relevant properties of protein drugs.
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Affiliation(s)
- Stephanie
L. Breunig
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Janine C. Quijano
- Department
of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Institute City
of Hope, Duarte, California 91010, United States
| | - Cecile Donohue
- Department
of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Institute City
of Hope, Duarte, California 91010, United States
| | - Amy Henrickson
- Department
of Chemistry and Biochemistry, University
of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Borries Demeler
- Department
of Chemistry and Biochemistry, University
of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
- Department
of Chemistry and Biochemistry, University
of Montana, Missoula, Montana 59801, United States
| | - Hsun Teresa Ku
- Department
of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Institute City
of Hope, Duarte, California 91010, United States
- Irell &
Manella Graduate School of Biological Science, City of Hope, Duarte, California 91010, United
States
| | - David A. Tirrell
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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9
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Qiu R, Li X, Huang K, Bai W, Zhou D, Li G, Qin Z, Li Y. Cis-trans isomerization of peptoid residues in the collagen triple-helix. Nat Commun 2023; 14:7571. [PMID: 37989738 PMCID: PMC10663571 DOI: 10.1038/s41467-023-43469-8] [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: 06/10/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023] Open
Abstract
Cis-peptide bonds are rare in proteins, and building blocks less favorable to the trans-conformer have been considered destabilizing. Although proline tolerates the cis-conformer modestly among all amino acids, for collagen, the most prevalent proline-abundant protein, all peptide bonds must be trans to form its hallmark triple-helix structure. Here, using host-guest collagen mimetic peptides (CMPs), we discover that surprisingly, even the cis-enforcing peptoid residues (N-substituted glycines) form stable triple-helices. Our interrogations establish that these peptoid residues entropically stabilize the triple-helix by pre-organizing individual peptides into a polyproline-II helix. Moreover, noting that the cis-demanding peptoid residues drastically reduce the folding rate, we design a CMP whose triple-helix formation can be controlled by peptoid cis-trans isomerization, enabling direct targeting of fibrotic remodeling in myocardial infarction in vivo. These findings elucidate the principles of peptoid cis-trans isomerization in protein folding and showcase the exploitation of cis-amide-favoring residues in building programmable and functional peptidomimetics.
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Affiliation(s)
- Rongmao Qiu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
| | - Xiaojing Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
| | - Kui Huang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
| | - Weizhe Bai
- Cardiac Surgery and Structural Heart Disease Unit of Cardiovascular Center, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
| | - Daoning Zhou
- Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
| | - Gang Li
- Cardiac Surgery and Structural Heart Disease Unit of Cardiovascular Center, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China.
| | - Zhao Qin
- Department of Civil & Environmental Engineering, College of Engineering & Computer Science, Syracuse University, Syracuse, New York, 13244, USA.
| | - Yang Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China.
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China.
- Cardiac Surgery and Structural Heart Disease Unit of Cardiovascular Center, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China.
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10
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Stauffer W, Bobardt M, Ure D, Foster R, Gallay P. The Cyclophilin Inhibitor Rencofilstat Decreases HCV-Induced Hepatocellular Carcinoma Independently of Its Antiviral Activity. Viruses 2023; 15:2099. [PMID: 37896876 PMCID: PMC10612079 DOI: 10.3390/v15102099] [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: 09/01/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
There is an urgent need for the identification of new drugs that inhibit HCV-induced hepatocellular carcinoma (HCC). Our work demonstrates that cyclophilin inhibitors (CypIs) represent such new drugs. We demonstrate that the nonimmunosuppressive cyclosporine A (CsA) analog (CsAa) rencofilstat possesses dual therapeutic activities for the treatment of HCV infection and HCV-induced HCC. Specifically, we show that the HCV infection of humanized mice results in the progressive development of HCC. This is true for the four genotypes tested (1 to 4). Remarkably, we demonstrate that rencofilstat inhibits the development of HCV-induced HCC in mice even when added 16 weeks after infection when HCC is well established. Importantly, we show that rencofilstat drastically reduces HCC progression independently of its anti-HCV activity. Indeed, the CypI rencofilstat inhibits HCC, while other anti-HCV agents such as NS5A (NS5Ai) and NS5B (NS5Bi) fail to reduce HCC. In conclusion, this study shows for the first time that the CypI rencofilstat represents a potent therapeutic agent for the treatment of HCV-induced HCC.
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Affiliation(s)
- Winston Stauffer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (W.S.); (M.B.)
| | - Michael Bobardt
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (W.S.); (M.B.)
| | - Daren Ure
- Hepion Pharmaceuticals Inc., Edison, NJ 08837, USA; (D.U.); (R.F.)
| | - Robert Foster
- Hepion Pharmaceuticals Inc., Edison, NJ 08837, USA; (D.U.); (R.F.)
| | - Philippe Gallay
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (W.S.); (M.B.)
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11
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Chang Z, Wang S, Huang J, Chen G, Tang Z, Wang R, Zhao D. Copper catalyzed Shono-type oxidation of proline residues in peptide. SCIENCE ADVANCES 2023; 9:eadj3090. [PMID: 37703373 PMCID: PMC10881060 DOI: 10.1126/sciadv.adj3090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/11/2023] [Indexed: 09/15/2023]
Abstract
Since the initial report in 1975, the Shono oxidation has become a powerful tool to functionalize the α position of amines, including proline derivatives, by electrochemical oxidation. However, the application of electrochemical Shono oxidations is restricted to the preparation of simple building blocks and homogeneous Shono-type oxidation of proline derivatives remains challenging. The late-stage functionalization at proline residues embedded within peptides is highly important as substitutions about the proline ring are known to affect biological and pharmacological activities. Here, we show that homogenous copper-catalyzed oxidation conditions complement the Shono oxidation and this general protocol can be applied to a series of formal C-C coupling reactions with a variety of nucleophiles using a one-pot procedure. This protocol shows good tolerance toward 19 proteinogenic amino acids and was used to functionalize several representative bioactive peptides, including captopril, enalapril, Smac, and endomorphin-2. Last, peptide cyclization can also be achieved by using an appropriately positioned side-chain hydroxyl moiety.
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Affiliation(s)
- Zhe Chang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Si Wang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jialin Huang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Geshuyi Chen
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Zhanyong Tang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Rui Wang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Depeng Zhao
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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12
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Stauffer W, Bobardt M, Ure D, Foster R, Gallay P. The Cyclophilin Inhibitor Rencofilstat Decreases HCV-induced Hepatocellular Carcinoma Independently of Its Antiviral Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553982. [PMID: 37645728 PMCID: PMC10462172 DOI: 10.1101/2023.08.19.553982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
There is an urgent need for the identification of new drugs that inhibit HCV-induced hepatocellular carcinoma (HCC). Our work demonstrates that cyclophilin inhibitors (CypI) represent such new drugs. We demonstrated that the non-immunosuppressive cyclosporine A (CsA) analog (CsAa) rencofilstat possesses dual therapeutic activities for the treatment of HCV infection and HCV-induced HCC. Specifically, we showed that HCV infection of humanized mice results in the progressive development of HCC. This was true for four genotypes tested (1 to 4). Remarkably, we demonstrated that rencofilstat inhibits the development of HCV-induced HCC in mice even when added 16 weeks post-infection when HCC is well established. Importantly, we showed that rencofilstat drastically reduces HCC progression independently of its anti-HCV activity. Indeed, the CypI rencofilstat inhibits HCC while other anti-HCV agents such as NS5A (NS5Ai) and NS5B (NS5Bi) fail to reduce HCC. In conclusion, this study shows for the first time that the CypI rencofilstat represents a potent therapeutic agent for the treatment of HCV-induced HCC.
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Affiliation(s)
- Winston Stauffer
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Michael Bobardt
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Daren Ure
- Hepion Pharmaceuticals Inc., Edison, New Jersey, USA
| | - Robert Foster
- Hepion Pharmaceuticals Inc., Edison, New Jersey, USA
| | - Philippe Gallay
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, California, USA
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13
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Chiliveri SC, Shen Y, Baber JL, Ying J, Sagar V, Wistow G, Anfinrud P, Bax A. Experimental NOE, Chemical Shift, and Proline Isomerization Data Provide Detailed Insights into Amelotin Oligomerization. J Am Chem Soc 2023; 145:18063-18074. [PMID: 37548612 PMCID: PMC10436275 DOI: 10.1021/jacs.3c05710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Indexed: 08/08/2023]
Abstract
Amelotin is an intrinsically disordered protein (IDP) rich in Pro residues and is involved in hydroxyapatite mineralization. It rapidly oligomerizes under physiological conditions of pH and pressure but reverts to its monomeric IDP state at elevated pressure. We identified a 105-residue segment of the protein that becomes ordered upon oligomerization, and we used pressure-jump NMR spectroscopy to measure long-range NOE contacts that exist exclusively in the oligomeric NMR-invisible state. The kinetics of oligomerization and dissociation were probed at the residue-specific level, revealing that the oligomerization process is initiated in the C-terminal half of the segment. Using pressure-jump NMR, the degree of order in the oligomer at the sites of Pro residues was probed by monitoring changes in cis/trans equilibria relative to the IDP state after long-term equilibration under oligomerizing conditions. Whereas most Pro residues revert to trans in the oligomeric state, Pro-49 favors a cis configuration and three Pro residues retain an unchanged cis fraction, pointing to their local lack of order in the oligomeric state. NOE contacts and secondary 13C chemical shifts in the oligomeric state indicate the presence of an 11-residue α-helix, preceded by a small intramolecular antiparallel β-sheet, with slower formation of long-range intermolecular interactions to N-terminal residues. Although none of the models generated by AlphaFold2 for the amelotin monomer was consistent with experimental data, subunits of a hexamer generated by AlphaFold-Multimer satisfied intramolecular NOE and chemical shift data and may provide a starting point for developing atomic models for the oligomeric state.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Yang Shen
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - James L. Baber
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Jinfa Ying
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Vatsala Sagar
- Section
on Molecular Structure and Function, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Graeme Wistow
- Section
on Molecular Structure and Function, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Philip Anfinrud
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
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14
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Tran P, Crawford T, Ragnarsson L, Deuis JR, Mobli M, Sharpe SJ, Schroeder CI, Vetter I. Structural Conformation and Activity of Spider-Derived Inhibitory Cystine Knot Peptide Pn3a Are Modulated by pH. ACS OMEGA 2023; 8:26276-26286. [PMID: 37521635 PMCID: PMC10373202 DOI: 10.1021/acsomega.3c02664] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
Numerous spider venom-derived gating modifier toxins exhibit conformational heterogeneity during purification by reversed-phase high-performance liquid chromatography (RP-HPLC). This conformational exchange is especially peculiar for peptides containing an inhibitor cystine knot motif, which confers excellent structural stability under conditions that are not conducive to disulfide shuffling. This phenomenon is often attributed to proline cis/trans isomerization but has also been observed in peptides that do not contain a proline residue. Pn3a is one such peptide forming two chromatographically distinguishable peaks that readily interconvert following the purification of either conformer. The nature of this exchange was previously uncharacterized due to the fast rate of conversion in solution, making isolation of the conformers impossible. In the present study, an N-terminal modification of Pn3a enabled the isolation of the individual conformers, allowing activity assays to be conducted on the individual conformers using electrophysiology. The conformers were analyzed separately by nuclear magnetic resonance spectroscopy (NMR) to study their structural differences. RP-HPLC and NMR were used to study the mechanism of exchange. The later-eluting conformer was the active conformer with a rigid structure that corresponds to the published structure of Pn3a, while NMR analysis revealed the earlier-eluting conformer to be inactive and disordered. The exchange was found to be pH-dependent, arising in acidic solutions, possibly due to reversible disruption and formation of intramolecular salt bridges. This study reveals the nature of non-proline conformational exchange observed in Pn3a and possibly other disulfide-rich peptides, highlighting that the structure and activity of some disulfide-stabilized peptides can be dramatically susceptible to disruption.
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Affiliation(s)
- Poanna Tran
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
| | - Theo Crawford
- Centre
for Advanced Imaging, The University of
Queensland, Brisbane, Queensland 4072, Australia
| | - Lotten Ragnarsson
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
| | - Jennifer R. Deuis
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
| | - Mehdi Mobli
- Centre
for Advanced Imaging, The University of
Queensland, Brisbane, Queensland 4072, Australia
| | - Simon J. Sharpe
- Molecular
Medicine Program, Research Institute, The
Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Christina I. Schroeder
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
- Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702-1201, United States
- Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Irina Vetter
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
- School
of Pharmacy, The University of Queensland, Brisbane, Queensland 4102, Australia
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15
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Gurung D, Danielson JA, Tasnim A, Zhang JT, Zou Y, Liu JY. Proline Isomerization: From the Chemistry and Biology to Therapeutic Opportunities. BIOLOGY 2023; 12:1008. [PMID: 37508437 PMCID: PMC10376262 DOI: 10.3390/biology12071008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
Proline isomerization, the process of interconversion between the cis- and trans-forms of proline, is an important and unique post-translational modification that can affect protein folding and conformations, and ultimately regulate protein functions and biological pathways. Although impactful, the importance and prevalence of proline isomerization as a regulation mechanism in biological systems have not been fully understood or recognized. Aiming to fill gaps and bring new awareness, we attempt to provide a wholistic review on proline isomerization that firstly covers what proline isomerization is and the basic chemistry behind it. In this section, we vividly show that the cause of the unique ability of proline to adopt both cis- and trans-conformations in significant abundance is rooted from the steric hindrance of these two forms being similar, which is different from that in linear residues. We then discuss how proline isomerization was discovered historically followed by an introduction to all three types of proline isomerases and how proline isomerization plays a role in various cellular responses, such as cell cycle regulation, DNA damage repair, T-cell activation, and ion channel gating. We then explore various human diseases that have been linked to the dysregulation of proline isomerization. Finally, we wrap up with the current stage of various inhibitors developed to target proline isomerases as a strategy for therapeutic development.
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Affiliation(s)
- Deepti Gurung
- Department of Medicine, University of Toledo College of Medicine, Toledo, OH 43614, USA
- Department of Cell and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Jacob A Danielson
- Department of Medicine, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Afsara Tasnim
- Department of Bioengineering, University of Toledo College of Engineering, Toledo, OH 43606, USA
| | - Jian-Ting Zhang
- Department of Cell and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Yue Zou
- Department of Cell and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Jing-Yuan Liu
- Department of Medicine, University of Toledo College of Medicine, Toledo, OH 43614, USA
- Department of Cell and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
- Department of Bioengineering, University of Toledo College of Engineering, Toledo, OH 43606, USA
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16
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Xiong R, Xu L, Tang Y, Cao M, Li H. Identifying the protonation site and the scope of non-proline cis-peptide bond conformations: a first-principles study on protonated oligopeptides. Phys Chem Chem Phys 2023; 25:13989-13998. [PMID: 37194311 DOI: 10.1039/d3cp00690e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The existence of non-proline cis-peptide bond conformations of protonated triglycine proposed by us has been verified through a recent IR-IR double resonance experiment. However, the scope of such unique structures in protonated oligopeptides and whether protonation at amide oxygen is more stable than that at traditional amino nitrogen remain unsolved. In this study, the most stable conformers of a series of protonated oligopeptides were fully searched. Our findings reveal that the special cis-peptide bond structure appears with high energies for diglycine and is energetically less favored for tetra- and pentapeptides, while it acts as the global minimum only for tripeptides. To explore the formation mechanism of the cis-peptide bond, electrostatic potential analysis, and intramolecular interactions were analyzed. Advanced theoretical calculations confirmed that amino nitrogen is still preferred as the protonated site in most cases except glycylalanylglycine(GAG). The energy difference between the two protonated isomers of GAG is only 0.03 kcal mol-1, indicating that the tripeptide is most likely to be protonated on the amide oxygen first. We also conducted chemical (infrared (IR)) and electronic (X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure spectra (NEXAFS)) structure calculations of these peptides to identify their notable differences unambiguously. This study thus provides valuable information for exploring the scope of cis-peptide bond conformation and the competition between two different protonated ways.
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Affiliation(s)
- Rui Xiong
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education, Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui, 230601, China.
| | - Li Xu
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education, Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui, 230601, China.
| | - Yong Tang
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education, Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui, 230601, China.
| | - Mengge Cao
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education, Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui, 230601, China.
| | - Hongbao Li
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education, Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui, 230601, China.
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17
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Jin Z, Vighi A, Dong Y, Bureau JA, Ignea C. Engineering membrane architecture for biotechnological applications. Biotechnol Adv 2023; 64:108118. [PMID: 36773706 DOI: 10.1016/j.biotechadv.2023.108118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Cellular membranes, predominantly described as a dynamic bilayer, are composed of different lipids, transmembrane proteins, and carbohydrates. Most research on biological membranes focuses on the identification, characterization, and mechanistic aspects of their different components. These studies provide a fundamental understanding of membrane structure, function, and dynamics, establishing a basis for the development of membrane engineering strategies. To date, approaches in this field concentrate on membrane adaptation to harsh conditions during industrial fermentation, which can be caused by temperature, osmotic, or organic solvent stress. With advances in the field of metabolic engineering and synthetic biology, recent breakthroughs include proof of concept microbial production of essential medicines, such as cannabinoids and vinblastine. However, long pathways, low yields, and host adaptation continue to pose challenges to the efficient scale up production of many important compounds. The lipid bilayer is profoundly linked to the activity of heterologous membrane-bound enzymes and transport of metabolites. Therefore, strategies for improving enzyme performance, facilitating pathway reconstruction, and enabling storage of products to increase the yields directly involve cellular membranes. At the forefront of membrane engineering research are re-emerging approaches in lipid research and synthetic biology that manipulate membrane size and composition and target lipid profiles across species. This review summarizes engineering strategies applied to cellular membranes and discusses the challenges and future perspectives, particularly with regards to their applications in host engineering and bioproduction.
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Affiliation(s)
- Zimo Jin
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Asia Vighi
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Yueming Dong
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | | | - Codruta Ignea
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada.
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18
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Aittoniemi J, Jensen MØ, Pan AC, Shaw DE. Desensitization dynamics of the AMPA receptor. Structure 2023:S0969-2126(23)00096-5. [PMID: 37059095 DOI: 10.1016/j.str.2023.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/17/2022] [Accepted: 03/21/2023] [Indexed: 04/16/2023]
Abstract
To perform their physiological functions, amino methyl propionic acid receptors (AMPARs) cycle through active, resting, and desensitized states, and dysfunction in AMPAR activity is associated with various neurological disorders. Transitions among AMPAR functional states, however, are largely uncharacterized at atomic resolution and are difficult to examine experimentally. Here, we report long-timescale molecular dynamics simulations of dimerized AMPAR ligand-binding domains (LBDs), whose conformational changes are tightly coupled to changes in AMPAR functional states, in which we observed LBD dimer activation and deactivation upon ligand binding and unbinding at atomic resolution. Importantly, we observed the ligand-bound LBD dimer transition from the active conformation to several other conformations, which may correspond with distinct desensitized conformations. We also identified a linker region whose structural rearrangements heavily affected the transitions to and among these putative desensitized conformations, and confirmed, using electrophysiology experiments, the importance of the linker region in these functional transitions.
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Affiliation(s)
| | | | | | - David E Shaw
- D. E. Shaw Research, New York, NY 10036, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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19
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Izquierdo PG, Charvet CL, Neveu C, Green AC, Tattersall JEH, Holden-Dye L, O'Connor V. Modelling organophosphate intoxication in C. elegans highlights nicotinic acetylcholine receptor determinants that mitigate poisoning. PLoS One 2023; 18:e0284786. [PMID: 37083685 PMCID: PMC10121051 DOI: 10.1371/journal.pone.0284786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
Organophosphate intoxication via acetylcholinesterase inhibition executes neurotoxicity via hyper stimulation of acetylcholine receptors. Here, we use the organophosphate paraoxon-ethyl to treat C. elegans and use its impact on pharyngeal pumping as a bio-assay to model poisoning through these neurotoxins. This assay provides a tractable measure of acetylcholine receptor mediated contraction of body wall muscle. Investigation of the time dependence of organophosphate treatment and the genetic determinants of the drug-induced inhibition of pumping highlight mitigating modulation of the effects of paraoxon-ethyl. We identified mutants that reduce acetylcholine receptor function protect against the consequence of intoxication by organophosphates. Data suggests that reorganization of cholinergic signalling is associated with organophosphate poisoning. This reinforces the under investigated potential of using therapeutic approaches which target a modulation of nicotinic acetylcholine receptor function to treat the poisoning effects of this important class of neurotoxins.
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Affiliation(s)
- Patricia G Izquierdo
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Claude L Charvet
- French National Institute for Agricultural Research (INRA), Infectiologie Animale et Santé Publique, Nouzilly, France
| | - Cedric Neveu
- French National Institute for Agricultural Research (INRA), Infectiologie Animale et Santé Publique, Nouzilly, France
| | - A Christopher Green
- Dstl, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - John E H Tattersall
- Dstl, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Lindy Holden-Dye
- Dstl, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Vincent O'Connor
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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20
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Nesci S. Protein folding and unfolding: proline cis-trans isomerization at the c subunits of F 1 F O -ATPase might open a high conductance ion channel. Proteins 2022; 90:2001-2005. [PMID: 35532281 PMCID: PMC9790210 DOI: 10.1002/prot.26383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 12/30/2022]
Abstract
The c subunits, which constitute the c-ring apparatus of the F1 FO -ATPase, could be the main components of the mitochondrial permeability transition pore (mPTP). The well-known modulator of the mPTP formation and opening is the cyclophilin D (CyPD), a peptidyl-prolyl cis-trans isomerase. On the loop, which connects the two hairpin α-helix of c subunit, is present the unique proline residue (Pro40 ) that could be a biological target of CyPD. Indeed, the proline cis-trans isomerization might provide the switch that interconverts the open/closed states of the pore by pulling out the c-ring lipid plug.
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Affiliation(s)
- Salvatore Nesci
- Department of Veterinary Medical SciencesUniversity of Bolognavia Tolara di Sopra, 40Ozzano Emilia40064
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21
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Identification and molecular evolution of the La and LARP genes in 16 plant species: A focus on the Gossypium hirsutum. Int J Biol Macromol 2022; 224:1101-1117. [DOI: 10.1016/j.ijbiomac.2022.10.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
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22
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Thurston R, Zantop V, Park KS, Maid H, Seitz A, Heinrich MR. pH-Dependent Conformational Switching of Amide Bonds─from Full trans to Full cis and Vice Versa. Org Lett 2022; 24:3488-3492. [PMID: 35544347 DOI: 10.1021/acs.orglett.2c00938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Strategies enabling the pH-dependent conformational switching of amide bonds from trans to cis, and vice versa, are yet limited in the sense that, in a suitable pH range, one rotamer may be stabilized to a large extent while the complementary pH range only leads to a mixture of isomers. By exploiting the effects of steric demand and the interaction of the amide carbonyl with a positive charge, we herein present the first examples for reversible pH-dependent switching from full trans to full cis.
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Affiliation(s)
- Ryan Thurston
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Viviane Zantop
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Kristen Sodam Park
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Harald Maid
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Organic Chemistry II, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Anke Seitz
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
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23
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Schnitzer T, Rackl JW, Wennemers H. Stereoselective Peptide Catalysis in Complex Environments – From River Water to Cell Lysates. Chem Sci 2022; 13:8963-8967. [PMID: 36091207 PMCID: PMC9365096 DOI: 10.1039/d2sc02044k] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/27/2022] [Indexed: 11/21/2022] Open
Abstract
Many stereoselective peptide catalysts have been established. They consist, like nature's catalysts, of amino acids but have significantly lower molecular weights than enzymes. Whereas enzymes operate with exquisite chemoselectivity in complex biological environments, peptide catalysts are used in pure organic solvents and at higher concentrations. Can a peptide catalyst exhibit chemoselectivity reminiscent of enzymes? Here, we investigated the properties of tripeptide catalysts in complex mixtures in hydrophobic and aqueous solvents. We challenged the catalysts with biomolecules bearing functional groups that could interfere by coordination or reaction with the peptide, the substrates, or intermediates. H-dPro-αMePro-Glu-NHC12H15 emerged through tailoring of the trans/cis ratio of the tertiary amide as a conformationally well-defined tripeptide that catalyzes C–C bond formations with high reactivity and stereoselectivity – regardless of the solvent and compound composition. The chemoselectivity of the tripeptide is so high that it even catalyzes reactions in cell lysates. The findings provoke the question of the potential role of peptide catalysis in nature and during the evolution of enzymes. The reactivity, stereo-, and chemoselectivity of a tripeptide are so high that it catalyzes conjugate addition reactions with high stereoselectivity in complex compound mixtures—even in cell lysates.![]()
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Affiliation(s)
- Tobias Schnitzer
- Laboratory of Organic Chemistry, ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Jonas W Rackl
- Laboratory of Organic Chemistry, ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
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24
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Vettore LA, Westbrook RL, Tennant DA. Proline metabolism and redox; maintaining a balance in health and disease. Amino Acids 2021; 53:1779-1788. [PMID: 34291343 PMCID: PMC8651533 DOI: 10.1007/s00726-021-03051-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/10/2021] [Indexed: 02/06/2023]
Abstract
Proline is a non-essential amino acid with key roles in protein structure/function and maintenance of cellular redox homeostasis. It is available from dietary sources, generated de novo within cells, and released from protein structures; a noteworthy source being collagen. Its catabolism within cells can generate ATP and reactive oxygen species (ROS). Recent findings suggest that proline biosynthesis and catabolism are essential processes in disease; not only due to the role in new protein synthesis as part of pathogenic processes but also due to the impact of proline metabolism on the wider metabolic network through its significant role in redox homeostasis. This is particularly clear in cancer proliferation and metastatic outgrowth. Nevertheless, the precise identity of the drivers of cellular proline catabolism and biosynthesis, and the overall cost of maintaining appropriate balance is not currently known. In this review, we explore the major drivers of proline availability and consumption at a local and systemic level with a focus on cancer. Unraveling the main factors influencing proline metabolism in normal physiology and disease will shed light on new effective treatment strategies.
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Affiliation(s)
- Lisa A Vettore
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Rebecca L Westbrook
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Daniel A Tennant
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK.
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25
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Ventura CR, Wiedman GR. Substituting azobenzene for proline in melittin to create photomelittin: A light-controlled membrane active peptide. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183759. [PMID: 34506797 DOI: 10.1016/j.bbamem.2021.183759] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/30/2022]
Abstract
In this article we present the synthesis and characterization of a new form of the membrane active peptide melittin: photomelittin. This peptide was created by substituting the proline residue in melittin for a synthetic azobenzene amino acid derivative. This azobenzene altered the membrane activity of the peptide while retaining much of the secondary structure. Furthermore, the peptide demonstrates added light-dependent activity in leakage assays. There is a 1.5-fold increase in activity when exposed to UV light as opposed to visible light. The peptides further exhibit light-dependent hemolytic activity against human red blood cells. This will enable future studies optimizing photomelittin and other azobenzene-containing membrane active peptides for uses in medicine, drug delivery, and other biotechnological applications.
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Affiliation(s)
- Cristina R Ventura
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States of America.
| | - Gregory R Wiedman
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States of America.
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26
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Nin-Hill A, Mueller NPF, Molteni C, Rovira C, Alfonso-Prieto M. Photopharmacology of Ion Channels through the Light of the Computational Microscope. Int J Mol Sci 2021; 22:12072. [PMID: 34769504 PMCID: PMC8584574 DOI: 10.3390/ijms222112072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
The optical control and investigation of neuronal activity can be achieved and carried out with photoswitchable ligands. Such compounds are designed in a modular fashion, combining a known ligand of the target protein and a photochromic group, as well as an additional electrophilic group for tethered ligands. Such a design strategy can be optimized by including structural data. In addition to experimental structures, computational methods (such as homology modeling, molecular docking, molecular dynamics and enhanced sampling techniques) can provide structural insights to guide photoswitch design and to understand the observed light-regulated effects. This review discusses the application of such structure-based computational methods to photoswitchable ligands targeting voltage- and ligand-gated ion channels. Structural mapping may help identify residues near the ligand binding pocket amenable for mutagenesis and covalent attachment. Modeling of the target protein in a complex with the photoswitchable ligand can shed light on the different activities of the two photoswitch isomers and the effect of site-directed mutations on photoswitch binding, as well as ion channel subtype selectivity. The examples presented here show how the integration of computational modeling with experimental data can greatly facilitate photoswitchable ligand design and optimization. Recent advances in structural biology, both experimental and computational, are expected to further strengthen this rational photopharmacology approach.
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Affiliation(s)
- Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain; (A.N.-H.); (C.R.)
| | - Nicolas Pierre Friedrich Mueller
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany;
- Faculty of Mathematics and Natural Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Carla Molteni
- Physics Department, King’s College London, London WC2R 2LS, UK;
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain; (A.N.-H.); (C.R.)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany;
- Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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27
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Sanchez CA, Gadais C, Diarra S, Bordessa A, Lensen N, Chelain E, Brigaud T. Synthesis of enantiopure α-Tfm-proline and α-Tfm-pipecolic acid from oxazolo-pyrrolidines and -piperidines. Org Biomol Chem 2021; 19:6771-6775. [PMID: 34292288 DOI: 10.1039/d1ob01173a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Enantiopure α-Tfm-proline and α-Tfm-pipecolic acid were synthesized starting from commercially available diesters and ethyl trifluoroacetate. A Strecker type reaction on intermediate chiral Tfm-oxazolo-pyrrolidine and -piperidine provided the corresponding nitrile precursor of enantiopure (R) and (S) α-Tfm-proline and α-Tfm-pipecolic acid. The C-terminal peptide coupling reaction of α-Tfm-pipecolic acid has been successfully achieved.
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Affiliation(s)
- Clément A Sanchez
- CY Cergy Paris Université, CNRS, BioCIS, 95000, Cergy Pontoise, France.
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28
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Catalini S, Rossi B, Tortora M, Foggi P, Gessini A, Masciovecchio C, Bruni F. Hydrogen Bonding and Solvation of a Proline-Based Peptide Model in Salt Solutions. Life (Basel) 2021; 11:life11080824. [PMID: 34440568 PMCID: PMC8400059 DOI: 10.3390/life11080824] [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: 07/26/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
The hydrogen bonding of water and water/salt mixtures around the proline-based tripeptide model glycyl-l-prolyl-glycinamide·HCl (GPG-NH2) is investigated here by multi-wavelength UV resonance Raman spectroscopy (UVRR) to clarify the role of ion–peptide interactions in affecting the conformational stability of this peptide. The unique sensitivity and selectivity of the UVRR technique allow us to efficiently probe the hydrogen bond interaction between water molecules and proline residues in different solvation conditions, along with its influence on trans to cis isomerism in the hydrated tripeptide. The spectroscopic data suggest a relevant role played by the cations in altering the solvation shell at the carbonyl site of proline., while the fluoride and chloride anions were found to promote the establishment of the strongest interactions on the C=O site of proline. This latter effect is reflected in the greater stabilization of the trans conformers of the tripeptide in the presence of these specific ions. The molecular view provided by UVRR experiments was complemented by the results of circular dichroism (CD) measurements that show a strong structural stabilizing effect on the β-turn motif of GPG-NH2 observed in the presence of KF as a co-solute.
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Affiliation(s)
- Sara Catalini
- European Laboratory for Non-Linear Spectroscopy, LENS, Via Nello Carrara, 1, 50019 Sesto Fiorentino, Italy; (S.C.); (P.F.)
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
- Correspondence:
| | - Mariagrazia Tortora
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
- Area Science Park, Padriciano, 99, 34149 Trieste, Italy
| | - Paolo Foggi
- European Laboratory for Non-Linear Spectroscopy, LENS, Via Nello Carrara, 1, 50019 Sesto Fiorentino, Italy; (S.C.); (P.F.)
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
| | - Claudio Masciovecchio
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
| | - Fabio Bruni
- Dipartimento di Scienze, Università degli Studi Roma Tre, Via della Vasca Navale, 84, 00146 Roma, Italy;
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29
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Sengupta A, Rognoni LE, Merkel U, Žoldák G, Rief M. SlyD Accelerates trans-to- cis Prolyl Isomerization in a Mechanosignaling Protein under Load. J Phys Chem B 2021; 125:8712-8721. [PMID: 34279937 DOI: 10.1021/acs.jpcb.1c03648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prolyl isomerization is recognized as one of the key regulatory mechanisms, which plays a crucial role in cell signaling, ion channel gating, phage virus infection, and molecular timing. This isomerization is usually slow but often accelerated by an enzyme, called peptidyl-prolyl isomerase (PPIase). In the current project, we investigate using single-molecule force spectroscopy (SMFS) the impact of a bacterial PPIase, SlyD, on the cis-trans isomerization of the proline 2225 (P2225) in an isolated 20th domain of a cytoskeletal mechanosensing protein filamin-A (FlnA20). To explore the FlnA20-PPIase interaction, we have used multiple SMFS modes, like constant velocity, constant distance, and jumping trap experiments. In our previous study, we reported the unique nature of the P2225, which is conserved in all naturally occurring filamins and can slowly (minutes) interconvert between cis-trans isomers, in absence of any PPIase. Our current results show a staggering 25-fold acceleration of the trans-to-cis isomerization rate in the presence of saturating SlyD concentration (7.25 μM) compared to the unenzymatic condition. A SlyD concentration-dependent depletion of the trans isomeric lifetime was also observed. Additionally, we observed that SlyD stabilizes the cis-isomer in the native state of FlnA20 by ∼2 kBT. This is the first single-molecule observation of the cis-trans isomerization catalysis by a PPIase in a mechanosensing protein.
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Affiliation(s)
- Abhigyan Sengupta
- Technische Universität München, Physik Department, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 8, D-85748 Garching, Germany
| | - Lorenz E Rognoni
- Technische Universität München, Physik Department, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 8, D-85748 Garching, Germany
| | - Ulrich Merkel
- Technische Universität München, Physik Department, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 8, D-85748 Garching, Germany
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Trieda SNP 1, 040 11Košice, Slovakia
| | - Matthias Rief
- Technische Universität München, Physik Department, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 8, D-85748 Garching, Germany
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30
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Abstract
![]()
Since the establishment
of site-specific mutagenesis of single
amino acids to interrogate protein function in the 1970s, biochemists
have sought to tailor protein structure in the native cell environment.
Fine-tuning the chemical properties of proteins is an indispensable
way to address fundamental mechanistic questions. Unnatural amino
acids (UAAs) offer the possibility to expand beyond the 20 naturally
occurring amino acids in most species and install new and useful chemical
functions. Here, we review the literature about advances in UAA incorporation
technology from chemoenzymatic aminoacylation of modified tRNAs to in vitro translation systems to genetic encoding of UAAs
in the native cell environment and whole organisms. We discuss innovative
applications of the UAA technology to challenges in bioengineering
and medicine.
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Affiliation(s)
- Mia A Shandell
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, U.K
| | - Zhongping Tan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Virginia W Cornish
- Department of Chemistry, Columbia University, New York, New York 10027, United States.,Department of Systems Biology, Columbia University, New York, New York 10027, United States
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31
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Breunig SL, Tirrell DA. Incorporation of proline analogs into recombinant proteins expressed in Escherichia coli. Methods Enzymol 2021; 656:545-571. [PMID: 34325798 DOI: 10.1016/bs.mie.2021.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Proline residues are unique in the extent to which they constrain the conformational space available to the protein backbone. Because the conformational preferences of proline cannot be recapitulated by any of the other proteinogenic amino acids, standard mutagenesis approaches that seek to introduce new chemical functionality at proline positions unavoidably perturb backbone flexibility. Here, we detail the incorporation of proline analogs into recombinant proteins in Escherichia coli via a residue-specific mutagenesis strategy. This approach results in global replacement of proline residues with high yields of the recombinant protein of interest, minimal genetic manipulation, and maintenance of backbone conformational constraints.
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Affiliation(s)
- Stephanie L Breunig
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States.
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32
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Guan X, Wang S, Shi G, Zhang J, Wan X. Thermoswitching of Helical Inversion of Dynamic Polyphenylacetylenes through cis-trans Isomerization of Amide Pendants. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00538] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xiaoyan Guan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Sheng Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ge Shi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jie Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xinhua Wan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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33
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Asymmetric opening of the homopentameric 5-HT 3A serotonin receptor in lipid bilayers. Nat Commun 2021; 12:1074. [PMID: 33594077 PMCID: PMC7887223 DOI: 10.1038/s41467-021-21016-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop receptor family are key players in fast signal transduction throughout the nervous system. They have been shown to be modulated by the lipid environment, however the underlying mechanism is not well understood. We report three structures of the Cys-loop 5-HT3A serotonin receptor (5HT3R) reconstituted into saposin-based lipid bilayer discs: a symmetric and an asymmetric apo state, and an asymmetric agonist-bound state. In comparison to previously published 5HT3R conformations in detergent, the lipid bilayer stabilises the receptor in a more tightly packed, ‘coupled’ state, involving a cluster of highly conserved residues. In consequence, the agonist-bound receptor conformation adopts a wide-open pore capable of conducting sodium ions in unbiased molecular dynamics (MD) simulations. Taken together, we provide a structural basis for the modulation of 5HT3R by the membrane environment, and a model for asymmetric activation of the receptor. Pentameric ligand-gated ion channels (pLGICs) are key players in neurotransmission and have been shown to be modulated by the lipid environment, however the underlying mechanism is not well understood. Here, the authors report structures of the pLGIC 5-HT3A serotonin receptor reconstituted into lipid bilayer discs and reveal lipid–protein interactions as well as asymmetric activation of the homopentameric receptor.
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34
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Gibbs E, Chakrapani S. Structure, Function and Physiology of 5-Hydroxytryptamine Receptors Subtype 3. Subcell Biochem 2021; 96:373-408. [PMID: 33252737 DOI: 10.1007/978-3-030-58971-4_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
5-hydroxytryptamine receptor subtype 3 (5-HT3R) is a pentameric ligand-gated ion channel (pLGIC) involved in neuronal signaling. It is best known for its prominent role in gut-CNS signaling though there is growing interest in its other functions, particularly in modulating non-serotonergic synaptic activity. Recent advances in structural biology have provided mechanistic understanding of 5-HT3R function and present new opportunities for the field. This chapter gives a broad overview of 5-HT3R from a physiological and structural perspective and then discusses the specific details of ion permeation, ligand binding and allosteric coupling between these two events. Biochemical evidence is summarized and placed within a physiological context. This perspective underscores the progress that has been made as well as outstanding challenges and opportunities for future 5-HT3R research.
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Affiliation(s)
- Eric Gibbs
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA. .,Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.
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35
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Shimizu S, Takada M, Wada K, Ikake H, Muroga Y. Conformational transition of Poly-L-proline studied by IR, NMR, and SAXS. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.123424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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36
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Sanchez CA, Gadais C, Chaume G, Girard S, Chelain E, Brigaud T. Enantiopure 5-CF 3-Proline: Synthesis, Incorporation in Peptides, and Tuning of the Peptide Bond Geometry. Org Lett 2021; 23:382-387. [PMID: 33369434 DOI: 10.1021/acs.orglett.0c03880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The straightforward synthesis of enantiopure 5-(R)-and 5-(S)-trifluoromethylproline is reported. The key steps are a Ruppert-Prakash reagent addition on l-pyroglutamic esters followed by an elimination reaction and a selective reduction. The solution-phase and solid-phase incorporation of this unprotected enantiopure fluorinated amino acid in a short peptide chain was demonstrated. Compared to proline, the CF3 group provides a decrease of the trans to cis amide bond isomerization energy and an increase of the cis conformer population.
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Affiliation(s)
- Clément A Sanchez
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Charlène Gadais
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Grégory Chaume
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Sylvaine Girard
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Evelyne Chelain
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Thierry Brigaud
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
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37
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Cholesterol content in the membrane promotes key lipid-protein interactions in a pentameric serotonin-gated ion channel. Biointerphases 2021; 15:061018. [PMID: 33397116 DOI: 10.1116/6.0000561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs), embedded in the lipid membranes of nerve cells, mediate fast synaptic transmission and are major pharmaceutical targets. Because of their complexity and the limited knowledge of their structure, their working mechanisms have still to be fully unraveled at the molecular level. Over the past few years, evidence that the lipid membrane may modulate the function of membrane proteins, including pLGICs, has emerged. Here, we investigate, by means of molecular dynamics simulations, the behavior of the lipid membrane at the interface with the 5-HT3A receptor (5-HT3AR), a representative pLGIC which is the target of nausea-suppressant drugs, in a nonconductive state. Three lipid compositions are studied, spanning different concentrations of the phospholipids, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, and of cholesterol, hence a range of viscosities. A variety of lipid interactions and persistent binding events to different parts of the receptor are revealed in the investigated models, providing snapshots of the dynamical environment at the membrane-receptor interface. Some of these events result in lipid intercalation within the transmembrane domain, and others reach out to protein key sections for signal transmission and receptor activation, such as the Cys-loop and the M2-M3 loop. In particular, phospholipids, with their long hydrophobic tails, play an important role in these interactions, potentially providing a bridge between these two structures. A higher cholesterol content appears to promote lipid persistent binding to the receptor.
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38
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Park HS, Kang YK. Puckering transition of the proline residue along the pseudorotational path: revisited. NEW J CHEM 2021. [DOI: 10.1039/d1nj01361k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Puckering transitions of the proline residue for Ac-Pro-X with trans and cis prolyl peptide bonds were explored along the pseudorotation phase angle using DFT methods in the gas phase and in water.
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Affiliation(s)
- Hae Sook Park
- Department of Nursing
- Cheju Halla University
- Cheju 63092
- Republic of Korea
| | - Young Kee Kang
- Department of Chemistry
- Chungbuk National University
- Cheongju
- Republic of Korea
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39
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Maschio MC, Fregoni J, Molteni C, Corni S. Proline isomerization effects in the amyloidogenic protein β2-microglobulin. Phys Chem Chem Phys 2021; 23:356-367. [DOI: 10.1039/d0cp04780e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protein β2-microglobulin can aggregate in insoluble amyloid fibrils. By relying on extensive sampling simulations, we study the Pro32 isomerization as a possible triggering factor leading to structural modifications in β2-m.
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Affiliation(s)
| | - Jacopo Fregoni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
| | - Carla Molteni
- Department of Physics
- King's College London
- Strand
- London WC2R 2LS
- UK
| | - Stefano Corni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
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40
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Schmidpeter PAM, Rheinberger J, Nimigean CM. Prolyl isomerization controls activation kinetics of a cyclic nucleotide-gated ion channel. Nat Commun 2020; 11:6401. [PMID: 33328472 PMCID: PMC7744796 DOI: 10.1038/s41467-020-20104-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/11/2020] [Indexed: 01/21/2023] Open
Abstract
SthK, a cyclic nucleotide-modulated ion channel from Spirochaeta thermophila, activates slowly upon cAMP increase. This is reminiscent of the slow, cAMP-induced activation reported for the hyperpolarization-activated and cyclic nucleotide-gated channel HCN2 in the family of so-called pacemaker channels. Here, we investigate slow cAMP-induced activation in purified SthK channels using stopped-flow assays, mutagenesis, enzymatic catalysis and inhibition assays revealing that the cis/trans conformation of a conserved proline in the cyclic nucleotide-binding domain determines the activation kinetics of SthK. We propose that SthK exists in two forms: trans Pro300 SthK with high ligand binding affinity and fast activation, and cis Pro300 SthK with low affinity and slow activation. Following channel activation, the cis/trans equilibrium, catalyzed by prolyl isomerases, is shifted towards trans, while steady-state channel activity is unaffected. Our results reveal prolyl isomerization as a regulatory mechanism for SthK, and potentially eukaryotic HCN channels. This mechanism could contribute to electrical rhythmicity in cells.
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Affiliation(s)
- Philipp A. M. Schmidpeter
- grid.5386.8000000041936877XWeill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065 USA
| | - Jan Rheinberger
- grid.5386.8000000041936877XWeill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065 USA ,grid.4830.f0000 0004 0407 1981Present Address: University of Groningen, Groningen, Netherlands
| | - Crina M. Nimigean
- grid.5386.8000000041936877XWeill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065 USA ,grid.5386.8000000041936877XWeill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065 USA
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Kaji MD, Geary TG, Beech RN. A Functional Comparison of Homopentameric Nicotinic Acetylcholine Receptors (ACR-16) Receptors From Necator americanus and Ancylostoma ceylanicum. Front Mol Neurosci 2020; 13:601102. [PMID: 33324163 PMCID: PMC7725692 DOI: 10.3389/fnmol.2020.601102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022] Open
Abstract
Effective control of hookworm infections in humans and animals relies on using a small group of anthelmintics. Many of these drugs target cholinergic ligand-gated ion channels, yet the direct activity of anthelmintics has only been studied in a subset of these receptors, primarily in the non-parasitic nematode, Caenorhabditis elegans. Here we report the characterization of a homopentameric ionotropic acetylcholine receptor (AChR), ACR-16, from Necator americanus and Ancylostoma ceylanicum, the first known characterization of human hookworm ion channels. We used two-electrode voltage clamp electrophysiology in Xenopus laevis oocytes to determine the pharmacodynamics of cholinergics and anthelmintics on ACR-16 from both species of hookworm. The A. ceylanicum receptor (Ace-ACR-16) was more sensitive to acetylcholine (EC50 = 20.64 ± 0.32 μM) and nicotine (EC50 = 24.37 ± 2.89 μM) than the N. americanus receptor (Nam-ACR-16) (acetylcholine EC50 = 170.1 ± 19.23 μM; nicotine EC50 = 597.9 ± 59.12 μM), at which nicotine was a weak partial agonist (% maximal acetylcholine response = 30.4 ± 7.4%). Both receptors were inhibited by 500 μM levamisole (Ace-ACR-16 = 65.1 ± 14.3% inhibition, Nam-ACR-16 = 79.5 ± 7.7% inhibition), and responded to pyrantel, but only Ace-ACR-16 responded to oxantel. We used in silico homology modeling to investigate potential structural differences that account for the differences in agonist binding and identified a loop E isoleucine 130 of Nam-ACR-16 as possibly playing a role in oxantel insensitivity. These data indicate that key functional differences exist among ACR-16 receptors from closely related species and suggest mechanisms for differential drug sensitivity.
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Affiliation(s)
- Mark D. Kaji
- Institute of Parasitology, McGill University, Montreal, QC, Canada
| | - Timothy G. Geary
- Institute of Parasitology, McGill University, Montreal, QC, Canada
- School of Biological Sciences, Queen’s University-Belfast, Belfast, United Kingdom
| | - Robin N. Beech
- Institute of Parasitology, McGill University, Montreal, QC, Canada
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42
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Gomila AMJ, Rustler K, Maleeva G, Nin-Hill A, Wutz D, Bautista-Barrufet A, Rovira X, Bosch M, Mukhametova E, Petukhova E, Ponomareva D, Mukhamedyarov M, Peiretti F, Alfonso-Prieto M, Rovira C, König B, Bregestovski P, Gorostiza P. Photocontrol of Endogenous Glycine Receptors In Vivo. Cell Chem Biol 2020; 27:1425-1433.e7. [PMID: 32846115 DOI: 10.1016/j.chembiol.2020.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/14/2020] [Accepted: 08/04/2020] [Indexed: 12/15/2022]
Abstract
Glycine receptors (GlyRs) are indispensable for maintaining excitatory/inhibitory balance in neuronal circuits that control reflexes and rhythmic motor behaviors. Here we have developed Glyght, a GlyR ligand controlled with light. It is selective over other Cys-loop receptors, is active in vivo, and displays an allosteric mechanism of action. The photomanipulation of glycinergic neurotransmission opens new avenues to understanding inhibitory circuits in intact animals and to developing drug-based phototherapies.
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Affiliation(s)
- Alexandre M J Gomila
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Karin Rustler
- University of Regensburg, Institute of Organic Chemistry, Regensburg 93053, Germany
| | - Galyna Maleeva
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain; Aix-Marseille Université, INSERM, INS, Institut de Neurosciences des Systèmes, Marseille 13005, France
| | - Alba Nin-Hill
- University of Barcelona, Department of Inorganic and Organic Chemistry, Institute of Theoretical Chemistry (IQTCUB), Barcelona 08028, Spain
| | - Daniel Wutz
- University of Regensburg, Institute of Organic Chemistry, Regensburg 93053, Germany
| | - Antoni Bautista-Barrufet
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Xavier Rovira
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Miquel Bosch
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Elvira Mukhametova
- Aix-Marseille Université, INSERM, INS, Institut de Neurosciences des Systèmes, Marseille 13005, France; Kazan Federal University, Open Lab of Motor Neurorehabilitation, Kazan, Russia
| | - Elena Petukhova
- Institute of Neurosciences, Kazan State Medical University, Kazan, Russia
| | - Daria Ponomareva
- Institute of Neurosciences, Kazan State Medical University, Kazan, Russia
| | | | - Franck Peiretti
- Aix Marseille Université, INSERM 1263, INRA 1260, C2VN, Marseille, France
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany; Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Carme Rovira
- University of Barcelona, Department of Inorganic and Organic Chemistry, Institute of Theoretical Chemistry (IQTCUB), Barcelona 08028, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08003 Spain.
| | - Burkhard König
- University of Regensburg, Institute of Organic Chemistry, Regensburg 93053, Germany.
| | - Piotr Bregestovski
- Aix-Marseille Université, INSERM, INS, Institut de Neurosciences des Systèmes, Marseille 13005, France; Institute of Neurosciences, Kazan State Medical University, Kazan, Russia.
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08003 Spain; CIBER-BBN, Madrid 28001 Spain.
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43
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Ohwada T, Otani Y. Lactam Amide Spinning. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.1006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tomohiko Ohwada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
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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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Han L, Shan Q. Pair of Residue Substitutions at the Outer Mouth of the Channel Pore Act as Inputs for a Boolean Logic "OR" Gate Based on the Glycine Receptor. ACS Chem Neurosci 2020; 11:3409-3417. [PMID: 32970400 DOI: 10.1021/acschemneuro.0c00522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The glycine receptor (GlyR) is a ligand-activated chloride channel, whose mutations are the major cause of hereditary hyperekplexia. The hyperekplexia-causing R271Q mutation, which is located at the extracellular outer mouth of the channel pore, dramatically impairs the GlyR function manifesting a reduced sensitivity toward glycine. This study reports that a second mutation, S273D, rescues the function of the R271Q GlyR to that of the wild-type (WT) GlyR. Surprisingly, the S273D mutation, when introduced to the WT GlyR, does not further increase the receptor function. In other words, the compromised function of the 271Q 273S GlyR (i.e., the R271Q GlyR) can be rescued to WT levels by the introduction of either, or both, of the Q271R and S273D substitutions. From the perspective of Boolean logic gates, the Q271R and S273D substitutions act as inputs for an OR gate based on the GlyR. Further experiments revealed that the negative-charge carried by the 273 residue is essential for the expression of the OR gate and that the expression of the OR gate is residue-position-specific. In addition, mechanistic investigation implied that the 273 residue influences the 271 residue, which might underpin the unique nonadditive OR gate relationship between these two residues. Such an ion-channel-based OR gate, expressing output in the form of electrical current, could potentially be developed to digitally manipulate neuronal activity.
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Affiliation(s)
- Lu Han
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Qiang Shan
- Laboratory for Synaptic Plasticity, Shantou University Medical College, Shantou, Guangdong 515041, China
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
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46
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Tian Y, Chen S, Shan Q. Charged residues at the pore extracellular half of the glycine receptor facilitate channel gating: a potential role played by electrostatic repulsion. J Physiol 2020; 598:4643-4661. [PMID: 32844405 DOI: 10.1113/jp279288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 07/29/2020] [Indexed: 02/05/2023] Open
Abstract
KEY POINTS The Arg271Gln mutation of the glycine receptor (GlyR) causes hereditary hyperekplexia. This mutation dramatically compromises GlyR function; however, the underlying mechanism is not yet known. This study, by employing function and computation methods, proposes that charged residues (including the Arg residue) at the pore extracellular half from each of the five subunits of the homomeric α1 GlyR, create an electrostatic repulsive potential to widen the pore, thereby facilitating channel opening. This mechanism explains how the Arg271Gln mutation, in which the positively charged Arg residue is substituted by the neutral Gln residue, compromises GlyR function. This study furthers our understanding of the biophysical mechanism underlying the Arg271Gln mutation compromising GlyR function. ABSTRACT The R271(19')Q mutation in the α1 subunit of the glycine receptor (GlyR) chloride channel causes hereditary hyperekplexia. This mutation dramatically compromises channel function; however, the underlying mechanism is not yet known. The R271 residue is located at the extracellular half of the channel pore. In this study, an Arg-scanning mutagenesis was performed at the pore extracellular half from the 262(10') to the 272(20') position on the background of the α1 GlyR carrying the hyperekplexia-causing mutation R271(19')Q. It was found that the placement of the Arg residue rescued channel function to an extent inversely correlated with the distance between the residue and the pore central axis (perpendicular to the plane of the lipid bilayer). Accordingly, it was hypothesized that the placed Arg residues from each of the five subunits of the homomeric α1 GlyR create an electrostatic repulsive potential to widen the pore, thereby facilitating channel opening. This hypothesis was quantitatively verified by theoretical computation via exploiting basic laws of electrostatics and thermodynamics, and further supported by more experimental findings that the placement of another positively charged Lys residue or even a negatively charged Asp residue also rescued channel function in the same manner. This study provides a novel mechanism via which charged residues in the pore region facilitate channel gating, not only for the disease-causing 19'R residue in the GlyR, but also potentially for charged residues in the same region of other ion channels.
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Affiliation(s)
- Yao Tian
- Chern Institute of Mathematics, Nankai University, Tianjin, 300071, China
| | - Shijie Chen
- Laboratory for Synaptic Plasticity, Shantou University Medical College, Shantou, Guangdong, 515041, China
| | - Qiang Shan
- Laboratory for Synaptic Plasticity, Shantou University Medical College, Shantou, Guangdong, 515041, China
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47
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Silzel JW, Murphree TA, Paranji RK, Guttman MM, Julian RR. Probing the Stability of Proline Cis/Trans Isomers in the Gas Phase with Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1974-1980. [PMID: 32808771 DOI: 10.1021/jasms.0c00242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although most peptide bonds in proteins exist in the trans configuration, when cis peptide bonds do occur, they can have major impact on protein structure and function. The rapid identification of cis peptide bonds is therefore an important task. Peptide bonds containing proline are more likely to adopt the cis configuration because the ring connecting the side chain and backbone in proline flattens the energetic landscape relative to amino acids with free side chains. Examples of cis proline isomers have been identified in both solution and in the gas phase by a variety of structure-probing methods. Mass spectrometry is an attractive potential method for identifying cis proline due to its speed and sensitivity; however, the question remains of whether cis/trans proline isomers originating in solution are preserved during ionization and manipulation within a mass spectrometer. Herein, we investigate the gas-phase stability of isolated solution-phase cis and trans proline isomers using a synthetic peptide sequence with a Tyr-Pro-Pro motif. A variety of dissociation methods were explored to evaluate their potential to distinguish cis/trans configuration, including collision-induced dissociation, radical-directed dissociation, and photodissociation. Only photodissociation employed in conjunction with extremely gentle electrospray and charge solvation by 18-crown-6 ether was able to distinguish cis/trans isomers for our model peptide, suggesting that any thermal activation during transfer or while in the gas phase leads to isomer scrambling. Furthermore, the necessity for 18-crown-6 suggests that intramolecular charge solvation taking place during electrospray ionization can override cis/trans isomer homogeneity. Overall, the results suggest that solution-phase cis/trans proline isomers are fragile and easily lost during electrospray, requiring careful selection of instrument parameters and consideration of charge solvation to prevent cis/trans scrambling.
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Affiliation(s)
- Jacob W Silzel
- Department of Chemistry, University of California, 501 Big Springs Road, Riverside, California 92521, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Rajan K Paranji
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Miklos M Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ryan R Julian
- Department of Chemistry, University of California, 501 Big Springs Road, Riverside, California 92521, United States
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48
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Juza R, Vlcek P, Mezeiova E, Musilek K, Soukup O, Korabecny J. Recent advances with 5-HT 3 modulators for neuropsychiatric and gastrointestinal disorders. Med Res Rev 2020; 40:1593-1678. [PMID: 32115745 DOI: 10.1002/med.21666] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/10/2019] [Accepted: 02/11/2020] [Indexed: 12/17/2022]
Abstract
Serotonin (5-hydroxytryptophan [5-HT]) is a biologically active amine expressed in platelets, in gastrointestinal (GI) cells and, to a lesser extent, in the central nervous system (CNS). This biogenic compound acts through the activation of seven 5-HT receptors (5-HT1-7 Rs). The 5-HT3 R is a ligand-gated ion channel belonging to the Cys-loop receptor family. There is a wide variety of 5-HT3 R modulators, but only receptor antagonists (known as setrons) have been used clinically for chemotherapy-induced nausea and vomiting and irritable bowel syndrome treatment. However, since the discovery of the setrons in the mid-1980s, a large number of studies have been published exploring new potential applications due their potency in the CNS and mild side effects. The results of these studies have revealed new potential applications, including the treatment of neuropsychiatric disorders such as schizophrenia, depression, anxiety, and drug abuse. In this review, we provide information related to therapeutic potential of 5-HT3 R antagonists on GI and neuropsychiatric disorders. The major attention is paid to the structure, function, and pharmacology of novel 5-HT3 R modulators developed over the past 10 years.
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Affiliation(s)
- Radomir Juza
- National Institute of Mental Health, Klecany, Czech Republic
- Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Premysl Vlcek
- National Institute of Mental Health, Klecany, Czech Republic
- Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Eva Mezeiova
- Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Kamil Musilek
- Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czech Republic
- Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jan Korabecny
- National Institute of Mental Health, Klecany, Czech Republic
- Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
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49
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Lang SM, Bernhardt TM, Bakker JM, Barnett RN, Landman U. Energetic Stabilization of Carboxylic Acid Conformers by Manganese Atoms and Clusters. J Phys Chem A 2020; 124:4990-4997. [DOI: 10.1021/acs.jpca.0c03315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sandra M. Lang
- Institute of Surface Chemistry and Catalysis, University of Ulm, Albert-Einstein-Allee 47, 89069 Ulm, Germany
| | - Thorsten M. Bernhardt
- Institute of Surface Chemistry and Catalysis, University of Ulm, Albert-Einstein-Allee 47, 89069 Ulm, Germany
| | - Joost M. Bakker
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Robert N. Barnett
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332-0430, United States
| | - Uzi Landman
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332-0430, United States
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50
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Qi J, Gao Y, Jia H, Richter M, Huang L, Cao Y, Yang H, Zheng Q, Berger R, Liu J, Lin X, Lu H, Cheng Z, Ouyang M, Feng X, Du S, Gao HJ. Force-Activated Isomerization of a Single Molecule. J Am Chem Soc 2020; 142:10673-10680. [PMID: 32459961 DOI: 10.1021/jacs.0c00192] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding and controlling isomerization at the single molecular level should provide new insight into the molecular dynamics and design guidelines of functional devices. Scanning tunneling microscopy (STM) has been demonstrated to be a powerful tool to study isomerization of single molecules on a substrate, by either electric field or inelastic electron tunneling mechanisms. A similar molecular isomerization process can in principle be induced by mechanical force; however, relevant study has remained elusive. Here, we demonstrate that isomerization of a N,N-dimethylamino-dianthryl-benzene molecule on Ag(100) can be mechanically driven by the STM tip. The existence of an out-of-plane dimethylamino group in the molecule is found to play a pivotal role in the isomerization process by providing a steric hindrance effect for asymmetric interaction between the STM tip and the molecule. This underlying mechanism is further confirmed by performing molecular dynamics simulations, which show agreement with experimental results. Our work opens the opportunity to manipulate the molecular configuration on the basis of mechanical force.
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Affiliation(s)
- Jing Qi
- Institute of Physics and University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China
| | - Yixuan Gao
- Institute of Physics and University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China
| | - Haihong Jia
- Institute of Physics and University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China
| | - Marcus Richter
- Center for Advancing Electronics Dresden (cfaed) and Department of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden 01069, Germany
| | - Li Huang
- Institute of Physics and University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China
| | - Yun Cao
- Institute of Physics and University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China
| | - Huan Yang
- Institute of Physics and University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China
| | - Qi Zheng
- Institute of Physics and University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China
| | - Reinhard Berger
- Center for Advancing Electronics Dresden (cfaed) and Department of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden 01069, Germany
| | - Junzhi Liu
- Center for Advancing Electronics Dresden (cfaed) and Department of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden 01069, Germany
| | - Xiao Lin
- Institute of Physics and University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongliang Lu
- Institute of Physics and University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhihai Cheng
- Department of Physics and Beijing Key Laboratory of Optoelectronic Functional Materials & Micro-nano Devices, Renmin University of China, Beijing 100872, China
| | - Min Ouyang
- Department of Physics and Center for Nanophysics and Advanced Materials, University of Maryland, College Park, Maryland 20742, United States
| | - Xinliang Feng
- Center for Advancing Electronics Dresden (cfaed) and Department of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden 01069, Germany.,School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shixuan Du
- Institute of Physics and University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China
| | - Hong-Jun Gao
- Institute of Physics and University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China
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