1
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Wagner WJ, Moyle AB, Wagner ND, Rempel DL, Gross ML. Evaluating Chemical Footprinting-Induced Perturbation of Protein Higher Order Structure. Anal Chem 2024; 96:9693-9703. [PMID: 38815160 PMCID: PMC11238718 DOI: 10.1021/acs.analchem.4c01735] [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] [Indexed: 06/01/2024]
Abstract
Specific amino acid footprinting mass spectrometry (MS) is an increasingly utilized method for elucidating protein higher order structure (HOS). It does this by adding to certain amino acid residues a mass tag, whose reaction extent depends on solvent accessibility and microenvironment of the protein. Unlike reactive free radicals and carbenes, these specific footprinters react slower than protein unfolding. Thus, their footprinting, under certain conditions, provokes structural changes to the protein, leading to labeling on non-native structures. It is critical to establish conditions (i.e., reagent concentrations, time of reaction) to ensure that the structure of the protein following footprinting remains native. Here, we compare the efficacy of five methods in assessing protein HOS following footprinting at the intact protein level and then further localize the perturbation at the peptide level. Three are MS-based methods that provide dose-response plot analysis, evaluation of Poisson distributions of precursor and products, and determination of the average number of modifications. These MS-based methods reliably and effectively indicate HOS perturbation at the intact protein level, whereas spectroscopic methods (circular dichroism (CD) and dynamic light scattering (DLS)) are less sensitive in monitoring subtle HOS perturbation caused by footprinting. Evaluation of HOS at the peptide level indicates regions that are sensitive to localized perturbations. Peptide-level analysis also provides higher resolution of the HOS perturbation, and we recommend using it for future footprinting studies. Overall, this work shows conclusive evidence for HOS perturbation caused by footprinting. Implementation of quality control workflows can identify conditions to avoid the perturbation, for footprinting, allowing accurate and reliable identification of protein structural changes that accompany, for example, ligand interactions, mutations, and changes in solution environment.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| | - Austin B Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| | - Don L Rempel
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
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2
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Li Q, Min J, Zhang J, Reches M, Shen Y, Su R, Wang Y, Qi W. Enzyme-Driven, Switchable Catalysis Based on Dynamic Self-Assembly of Peptides. Angew Chem Int Ed Engl 2023; 62:e202309830. [PMID: 37602955 DOI: 10.1002/anie.202309830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 08/22/2023]
Abstract
Covalent regulatory systems of enzymes are widely used to modulate biological enzyme activities. Inspired by the regulation of reactive-site phosphorylation in organisms, we developed peptide-based catecholase mimetics with switchable catalytic activity and high selectivity through the co-assembly of nanofibers comprising peptides and copper ions (Cu2+ ). Through careful design and modification of the peptide backbone structure based on the change in the free energy of the system, we identified the peptide with the most effective reversible catalytic activity. Kinase/phosphatase switches were used to control the reversible transition of nanofiber formation and depolymerization, as well as to modulate the active-site microenvironment. Notably, the self-assembly and disassembly processes of nanofibers were simulated using coarse-grained molecular dynamics. Furthermore, theoretical calculations confirmed the coordination of the peptide and Cu2+ , forming a zipper-like four-ligand structure at the catalytically active center of the nanofibers. Additionally, we conducted a comprehensive analysis of the catalytic mechanism. This study opens novel avenues for designing biomimetic enzymes with ordered structures and dynamic catalytic activities.
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Affiliation(s)
- Qing Li
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Jiwei Min
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Jiaxing Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Meital Reches
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yuhe Shen
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
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3
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Dzyhovskyi V, Stokowa-Sołtys K. Divalent metal ion binding to Staphylococcus aureus FeoB transporter regions. J Inorg Biochem 2023; 244:112203. [PMID: 37018851 DOI: 10.1016/j.jinorgbio.2023.112203] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023]
Abstract
Transition metal ions such as iron, copper, zinc, manganese or, nickel are essential in many biological processes. Bacteria have developed a number of mechanisms for their acquisition and transport, in which numerous of proteins and smaller molecules are involved. One of the representatives of these proteins is FeoB, which belongs to the Feo (ferrous ion transporter) family. Although ferrous iron transport system is widespread among microorganisms, it is still poorly described in Gram-positive pathogens, such as Staphylococcus aureus. In this work, combined potentiometric and spectroscopic studies (UV-Vis, CD and EPR) were carried out to determine Cu(II), Fe(II) and Zn(II) binding modes to FeoB fragments (Ac-IDYHKLMK-NH2, Ac-ETSHDKY-NH2, and Ac-SFLHMVGS-NH2). For the first time iron(II) complexes with peptides were characterized by potentiometry. All studied ligands are able to form a variety of thermodynamically stable complexes with transition metal ions. It was concluded that among the studied systems, the most effective metal ion binding is observed for the Ac-ETSHDKY-NH2 peptide. Moreover, comparing preferences of all ligands towards different metal ions, copper(II) complexes are the most stable ones at physiological pH.
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4
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Yu L, Zeng G, Xu J, Han M, Wang Z, Li T, Long M, Wang L, Huang W, Wu Y. Development of Poly(Glycerol Sebacate) and Its Derivatives: A Review of the Progress over the past Two Decades. POLYM REV 2022. [DOI: 10.1080/15583724.2022.2150774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Liu Yu
- Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangdong Provincial Key Laboratory of Digital Medicine and Biomechanics, Department of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guanjie Zeng
- Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangdong Provincial Key Laboratory of Digital Medicine and Biomechanics, Department of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jie Xu
- Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Mingying Han
- Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Zihan Wang
- Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangdong Provincial Key Laboratory of Digital Medicine and Biomechanics, Department of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Ting Li
- Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangdong Provincial Key Laboratory of Digital Medicine and Biomechanics, Department of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Meng Long
- Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangdong Provincial Key Laboratory of Digital Medicine and Biomechanics, Department of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ling Wang
- Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Wenhua Huang
- Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangdong Provincial Key Laboratory of Digital Medicine and Biomechanics, Department of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yaobin Wu
- Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangdong Provincial Key Laboratory of Digital Medicine and Biomechanics, Department of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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5
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Wu B, Hanay SB, Kimmins SD, Cryan SA, Hermida Merino D, Heise A. Ion-Triggered Hydrogels Self-Assembled from Statistical Copolypeptides. ACS Macro Lett 2022; 11:323-328. [PMID: 35575374 PMCID: PMC8928472 DOI: 10.1021/acsmacrolett.1c00774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Statistical copolypeptides
comprising lysine and tyrosine with
unprecedented ion-induced gelation behavior are reported. Copolypeptides
are obtained by one-step N-carboxyanhydride (NCA)
ring-opening polymerization. The gelation mechanism is studied by
in situ SAXS analyses, in addition to optical spectroscopy and transmission
electron microscopy (TEM). It is found that the gelation of these
statistically polymerized polypeptides is due to the formation of
stable intermolecular β-sheet secondary structures induced by
the presence of salt ions as well as the aggregation of an α-helix
between the copolypeptides. This behavior is unique to the statistical
lysine/tyrosine copolypeptides and was not observed in any other amino
acid combination or arrangement. Furthermore, the diffusion and mechanical
properties of these hydrogels can be tuned through tailoring the polypeptide
chain length and ion strength.
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Affiliation(s)
- Bing Wu
- Department of Chemistry, RCSI University of Medicine and Health Sciences, Dublin 2, Ireland
- Dutch-Belgian Beamline (DUBBLE), ESRF - The European Synchrotron Radiation Facility, CS 40220, Grenoble 38043 Cedex 9, France
| | - Saltuk B. Hanay
- Department of Chemistry, RCSI University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Scott D. Kimmins
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Avda. Universidad 330, Curauma, Placilla 2950, Valparaíso, Chile
| | - Sally-Ann Cryan
- School of Pharmacy and Biomolecular Sciences and Tissue Engineering Research Group, RCSI University of Medicine and Health Sciences, Dublin 2, Ireland
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CURAM), RCSI, Dublin 2, Ireland
- AMBER, The SFI Advanced Materials and Bioengineering Research Centre, RCSI, Dublin 2, Ireland
| | - Daniel Hermida Merino
- Dutch-Belgian Beamline (DUBBLE), ESRF - The European Synchrotron Radiation Facility, CS 40220, Grenoble 38043 Cedex 9, France
| | - Andreas Heise
- Department of Chemistry, RCSI University of Medicine and Health Sciences, Dublin 2, Ireland
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CURAM), RCSI, Dublin 2, Ireland
- AMBER, The SFI Advanced Materials and Bioengineering Research Centre, RCSI, Dublin 2, Ireland
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6
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Joseph JA, Reinhardt A, Aguirre A, Chew PY, Russell KO, Espinosa JR, Garaizar A, Collepardo-Guevara R. Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy. NATURE COMPUTATIONAL SCIENCE 2021; 1:732-743. [PMID: 35795820 PMCID: PMC7612994 DOI: 10.1038/s43588-021-00155-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Various physics- and data-driven sequence-dependent protein coarse-grained models have been developed to study biomolecular phase separation and elucidate the dominant physicochemical driving forces. Here, we present Mpipi, a multiscale coarse-grained model that describes almost quantitatively the change in protein critical temperatures as a function of amino-acid sequence. The model is parameterised from both atomistic simulations and bioinformatics data and accounts for the dominant role of π-π and hybrid cation-π/π-π interactions and the much stronger attractive contacts established by arginines than lysines. We provide a comprehensive set of benchmarks for Mpipi and seven other residue-level coarse-grained models against experimental radii of gyration and quantitative in-vitro phase diagrams; Mpipi predictions agree well with experiment on both fronts. Moreover, it can account for protein-RNA interactions, correctly predicts the multiphase behaviour of a charge-matched poly-arginine/poly-lysine/RNA system, and recapitulates experimental LLPS trends for sequence mutations on FUS, DDX4 and LAF-1 proteins.
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Affiliation(s)
- Jerelle A. Joseph
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Anne Aguirre
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Kieran O. Russell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Jorge R. Espinosa
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Adiran Garaizar
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
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7
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Cheng HB, Zhang S, Qi J, Liang XJ, Yoon J. Advances in Application of Azobenzene as a Trigger in Biomedicine: Molecular Design and Spontaneous Assembly. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007290. [PMID: 34028901 DOI: 10.1002/adma.202007290] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Azobenzene is a well-known derivative of stimulus-responsive molecular switches and has shown superior performance as a functional material in biomedical applications. The results of multiple studies have led to the development of light/hypoxia-responsive azobenzene for biomedical use. In recent years, long-wavelength-responsive azobenzene has been developed. Matching the longer wavelength absorption and hypoxia-response characteristics of the azobenzene switch unit to the bio-optical window results in a large and effective stimulus response. In addition, azobenzene has been used as a hypoxia-sensitive connector via biological cleavage under appropriate stimulus conditions. This has resulted in on/off state switching of properties such as pharmacology and fluorescence activity. Herein, recent advances in the design and fabrication of azobenzene as a trigger in biomedicine are summarized.
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Affiliation(s)
- Hong-Bo Cheng
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, 15 North Third Ring Road, Beijing, 100029, P. R. China
| | - Shuchun Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, 15 North Third Ring Road, Beijing, 100029, P. R. China
| | - Ji Qi
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, 15 North Third Ring Road, Beijing, 100029, P. R. China
| | - Xing-Jie Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, No. 11, First North Road, Zhongguancun, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Juyoung Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Korea
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8
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Horsfall AJ, McDougal DP, Scanlon DB, Bruning JB, Abell AD. Approaches to Introduce Helical Structure in Cysteine-Containing Peptides with a Bimane Group. Chembiochem 2021; 22:2711-2720. [PMID: 34107164 DOI: 10.1002/cbic.202100241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Indexed: 01/01/2023]
Abstract
An i-i+4 or i-i+3 bimane-containing linker was introduced into a peptide known to target Estrogen Receptor alpha (ERα), in order to stabilise an α-helical geometry. These macrocycles were studied by CD and NMR to reveal the i-i+4 constrained peptide adopts a 310 -helical structure in solution, and an α-helical conformation on interaction with the ERα coactivator recruitment surface in silico. An acyclic bimane-modified peptide is also helical, when it includes a tryptophan or tyrosine residue; but is significantly less helical with a phenylalanine or alanine residue, which indicates such a bimane modification influences peptide structure in a sequence dependent manner. The fluorescence intensity of the bimane appears influenced by peptide conformation, where helical peptides displayed a fluorescence increase when TFE was added to phosphate buffer, compared to a decrease for less helical peptides. This study presents the bimane as a useful modification to influence peptide structure as an acyclic peptide modification, or as a side-chain constraint to give a macrocycle.
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Affiliation(s)
- Aimee J Horsfall
- ARC Centre of Excellence for Nanoscale Biophotonics (CNBP), University of Adelaide, Adelaide, SA 5005, Australia.,Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia.,The Institute for Photonics & Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA 5005, Australia
| | - Daniel P McDougal
- The Institute for Photonics & Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA 5005, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Denis B Scanlon
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia.,The Institute for Photonics & Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA 5005, Australia
| | - John B Bruning
- The Institute for Photonics & Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA 5005, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Andrew D Abell
- ARC Centre of Excellence for Nanoscale Biophotonics (CNBP), University of Adelaide, Adelaide, SA 5005, Australia.,Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia.,The Institute for Photonics & Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA 5005, Australia
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9
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Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun 2021; 12:1085. [PMID: 33597515 PMCID: PMC7889641 DOI: 10.1038/s41467-021-21181-9] [Citation(s) in RCA: 207] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/08/2021] [Indexed: 01/31/2023] Open
Abstract
Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.
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10
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Krainer G, Welsh TJ, Joseph JA, Espinosa JR, Wittmann S, de Csilléry E, Sridhar A, Toprakcioglu Z, Gudiškytė G, Czekalska MA, Arter WE, Guillén-Boixet J, Franzmann TM, Qamar S, George-Hyslop PS, Hyman AA, Collepardo-Guevara R, Alberti S, Knowles TPJ. Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun 2021; 12:1085. [PMID: 33597515 DOI: 10.1101/2020.05.04.076299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/08/2021] [Indexed: 05/26/2023] Open
Abstract
Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.
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Affiliation(s)
- Georg Krainer
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jerelle A Joseph
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Jorge R Espinosa
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Sina Wittmann
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Ella de Csilléry
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Akshay Sridhar
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Zenon Toprakcioglu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Giedre Gudiškytė
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Magdalena A Czekalska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka, 44/52 01-224, Warsaw, Poland
| | - William E Arter
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jordina Guillén-Boixet
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Titus M Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Seema Qamar
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Peter St George-Hyslop
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
- Division of Neurology, Department of Medicine, University of Toronto and University Health Network, Toronto, Ontario, Canada.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
| | - Rosana Collepardo-Guevara
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany.
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.
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11
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Wang F, Gnewou O, Modlin C, Beltran LC, Xu C, Su Z, Juneja P, Grigoryan G, Egelman EH, Conticello VP. Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials. Nat Commun 2021; 12:407. [PMID: 33462223 PMCID: PMC7814010 DOI: 10.1038/s41467-020-20689-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Charles Modlin
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Leticia C Beltran
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Chunfu Xu
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Puneet Juneja
- The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA. .,The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA.
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12
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Segatta F, Rogers DM, Dyer NT, Guest EE, Li Z, Do H, Nenov A, Garavelli M, Hirst JD. Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides. Molecules 2021; 26:E396. [PMID: 33451152 PMCID: PMC7828623 DOI: 10.3390/molecules26020396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.
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Affiliation(s)
- Francesco Segatta
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - David M. Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Naomi T. Dyer
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Ellen E. Guest
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Zhuo Li
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China;
| | - Hainam Do
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, Ningbo 315100, China
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China;
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
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13
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Araujo NA, Bruix M, Laurents DV. Disorder and partial folding in the regulatory subunit hinge region of Trypanosoma brucei protein kinase A: The C-linker portion inhibits the parasite's protein kinase A. Arch Biochem Biophys 2020; 698:108731. [PMID: 33359563 DOI: 10.1016/j.abb.2020.108731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 11/19/2022]
Abstract
Microbial pathogens, such as Trypanosoma brucei, have an enormous impact on global health and economic systems. Protein kinase A of T. brucei is an attractive drug target as it is an essential enzyme which differs significantly from its human homolog. The hinge region of this protein's regulatory domain is vital for enzymatic function, but its conformation is unknown. Here, the secondary structure of this region has been characterized using NMR and CD spectroscopies. More specifically, three overlapping peptides corresponding to residues T187-I211, G198-Y223 and V220-S245 called peptide 1, peptide 2 and peptide 3, respectively, were studied. The peptide 1 and peptide 2 are chiefly unfolded; only low populations (<10%) of α-helix were detected under the conditions studied. In contrast, the peptide 3 contains a long α-helix whose population is significantly higher; namely, 36% under the conditions studied. Utilizing the dihedral φ and ψ angles calculated on the basis of the NMR data, the conformation of the peptide 3 was calculated and revealed an α-helix spanning residues E230-N241. This α-helix showed amphiphilicity and reversible unfolding and refolding upon heating and cooling. Most fascinating, however, is its capacity to inhibit the activity of the catalytic domain of Trypanosoma equiperdum protein kinase A even though it is quite distinct from the canonical inhibitor motif. Based on this property, we advance that peptoids based on the peptide 3 α-helix could be novel leads for developing anti-trypanosomal therapeutics.
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Affiliation(s)
- Nelson A Araujo
- Departamento de Biología Celular, Universidad Simón Bolívar, Apartado 89.000, Valle de Sartenejas, Baruta, Caracas, 1081-A, Venezuela.
| | - Marta Bruix
- Departamento de Química Física Biológica, Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006, Madrid, Spain
| | - Douglas V Laurents
- Departamento de Química Física Biológica, Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006, Madrid, Spain.
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14
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Zwillinger M, Reddy PS, Wicher B, Mandal PK, Csékei M, Fischer L, Kotschy A, Huc I. Aromatic Foldamer Helices as α-Helix Extended Surface Mimetics. Chemistry 2020; 26:17366-17370. [PMID: 32910480 PMCID: PMC7839445 DOI: 10.1002/chem.202004064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Indexed: 12/15/2022]
Abstract
Helically folded aromatic oligoamide foldamers have a size and geometrical parameters very distinct from those of α-helices and are not obvious candidates for α-helix mimicry. Nevertheless, they offer multiple sites for attaching side chains. It was found that some arrays of side chains at the surface of an aromatic helix make it possible to mimic extended α-helical surfaces. Synthetic methods were developed to produce quinoline monomers suitably functionalized for solid phase synthesis. A dodecamer was prepared. Its crystal structure validated the initial design and showed helix bundling involving the α-helix-like interface. These results open up new uses of aromatic helices to recognize protein surfaces and to program helix bundling in water.
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Affiliation(s)
- Márton Zwillinger
- Servier Research Institute of Medicinal ChemistryZáhony utca 7.Budapest1031Hungary
- Hevesy György PhD School of ChemistryEötvös Loránd UniversityBudapestHungary
| | - Post Sai Reddy
- CNRS, Bordeaux Institut National PolytechniqueCBMN (UMR 5248)IECBUniversité de Bordeaux2 rue Robert Escarpit33600PessacFrance
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
| | - Barbara Wicher
- Department of Chemical Technology of DrugsPoznan University of Medical SciencesGrunwaldzka 660780PoznanPoland
| | - Pradeep K. Mandal
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
| | - Márton Csékei
- Servier Research Institute of Medicinal ChemistryZáhony utca 7.Budapest1031Hungary
| | - Lucile Fischer
- CNRS, Bordeaux Institut National PolytechniqueCBMN (UMR 5248)IECBUniversité de Bordeaux2 rue Robert Escarpit33600PessacFrance
| | - András Kotschy
- Servier Research Institute of Medicinal ChemistryZáhony utca 7.Budapest1031Hungary
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
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15
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Abstract
We present an atomistic force field for the azo-moiety of the photoswitchable FK-11-X peptide. We use the parameters to study the unfolding of the peptide through molecular dynamics simulations. The unfolded ensemble contains many different structures, ranging from a partially unfolded peptide to a fully unfolded structure. The averaged computed far-ultraviolet circular dichroism (CD) spectrum of the set of structures, which was simulated using the newly developed force field, agrees well with experiment. The rate of the simulated unfolding process was estimated to have a time constant of 5.80 ± 0.03 ns from the time evolution of the CD spectrum of the peptide, computed from the backbone conformations sampled over 40 simulated trajectories. Our estimated time constant is faster than, but not inconsistent with, previous experimental estimates from time-resolved infrared and optical rotatory dispersion spectroscopy.
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Affiliation(s)
- Francois Auvray
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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16
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Orabi EA, Davis RL, Lamoureux G. Drude polarizable force field for cation–π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains. J Comput Chem 2019; 41:472-481. [DOI: 10.1002/jcc.26084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/14/2019] [Accepted: 09/16/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Esam A. Orabi
- Department of ChemistryFaculty of Science, Assiut University Assiut 71516 Egypt
- Department of ChemistryUniversity of Manitoba Winnipeg Manitoba R3T 2N2 Canada
| | - Rebecca L. Davis
- Department of ChemistryUniversity of Manitoba Winnipeg Manitoba R3T 2N2 Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Center for Computational and Integrative Biology (CCIB)Rutgers University Camden New Jersey 08102
- Centre for Research in Molecular Modeling (CERMM), Concordia University Montréal Québec H4B 1R6 Canada
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17
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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18
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Bagheri M, Amininasab M, Dathe M. Arginine/Tryptophan-Rich Cyclic α/β-Antimicrobial Peptides: The Roles of Hydrogen Bonding and Hydrophobic/Hydrophilic Solvent-Accessible Surface Areas upon Activity and Membrane Selectivity. Chemistry 2018; 24:14242-14253. [PMID: 29969522 DOI: 10.1002/chem.201802881] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 11/08/2022]
Abstract
The bacterial selectivity of an amphiphilic library of small cyclic α/β-tetra-, α/β-penta-, and α/β-hexapeptides rich in arginine/tryptophan (Arg/Trp) residues, which contains asymmetric backbone configurations and differ in hydrophobicity and alternating d,l-amino acids, was investigated against Bacillus subtilis and Escherichia coli. The structural analyses showed that the peptides tend to form assemblies of different shapes. All-l-peptides, especially the most hydrophobic pentamers, were more strongly anti-B. subtilis. With the exception to cyclo(Phe-d-Trp-β3 hArg-Arg-d-Trp) (Phe=phenylalanine), the peptides had no effects on inner membrane of E. coli, but lyzed the lipopolysaccharide layer according to their activity pattern. The activities adversely changed with a decrease in the number of amide intramolecular hydrogen bonds in assemblies of diastereomeric peptides and the ratio of hydrophobic/hydrophilic solvent-accessible surface areas. The remarkable enhanced entropic contribution for the partitioning of the least conformationally constrained cyclo(Trp-d-Phe-β3 hTrp-Arg-d-Arg) sequence into the membranes supported the strong self-assembly behavior, therefore making the peptide less penetrable through the E. coli outer layer.
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Affiliation(s)
- Mojtaba Bagheri
- Peptide Chemistry Laboratory, Institute of Biochemistry and Biophysics, University of Tehran, 16 Azar Street, 14176-14335, Tehran, Iran
| | - Mehriar Amininasab
- Department of cell and molecular Biology, School of Biology, College of Science, University of, Tehran, Iran
| | - Margitta Dathe
- Leibniz institute of molecular pharmacology (FMP), Robert Roessle Street 10, 13125, Berlin, Germany
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19
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Orabi EA, Lamoureux G. Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution. J Phys Chem B 2018; 122:2251-2260. [PMID: 29397727 DOI: 10.1021/acs.jpcb.7b11983] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cation-π interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH3+ and RN(CH3)3+) to various protein receptors and are likely involved in the blockage of potassium channels by tetramethylammonium (TMA+) and tetraethylammonium (TEA+). Polarizable molecular models are calibrated for NH4+, TMA+, and TEA+ interacting with benzene, toluene, 4-methylphenol, and 3-methylindole (representing aromatic amino acid side chains) based on the ab initio MP2(full)/6-311++G(d,p) properties of the complexes. Whereas the gas-phase affinity of the ions with a given aromatic follows the trend NH4+ > TMA+ > TEA+, molecular dynamics simulations using the polarizable models show a reverse trend in water, likely due to a contribution from the hydrophobic effect. This reversed trend follows the solubility of aromatic hydrocarbons in quaternary ammonium salt solutions, which suggests a role for cation-π interactions in the salting-in of aromatic compounds in solution. Simulations in water show that the complexes possess binding free energies ranging from -1.3 to -3.3 kcal/mol (compared to gas-phase binding energies between -8.5 and -25.0 kcal/mol). Interestingly, whereas the most stable complexes involve TEA+ (the largest ion), the most stable solvent-separated complexes involve TMA+ (the intermediate-size ion).
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Affiliation(s)
- Esam A Orabi
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM), Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM), Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
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20
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Das S, Ben Haj Salah K, Wenger E, Martinez J, Kotarba J, Andreu V, Ruiz N, Savini F, Stella L, Didierjean C, Legrand B, Inguimbert N. Enhancing the Antimicrobial Activity of Alamethicin F50/5 by Incorporating N-terminal Hydrophobic Triazole Substituents. Chemistry 2017; 23:17964-17972. [DOI: 10.1002/chem.201703569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Sanjit Das
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS; Université de Perpignan Via Domitia, Laboratoire d'Excellence « CORAIL » Bâtiment T; 58 avenue P. Alduy 66860 Perpignan France)
| | - Khoubaib Ben Haj Salah
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS; Université de Perpignan Via Domitia, Laboratoire d'Excellence « CORAIL » Bâtiment T; 58 avenue P. Alduy 66860 Perpignan France)
| | - Emmanuel Wenger
- CRM2 (UMR UL-CNRS 7036) Faculté des Sciences et Technologies; Université de Lorraine; 70239 Boulevard des Aiguillettes 54506 Vandoeuvre-lès-Nancy France)
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; Université de Montpellier; 15 avenue Charles Flahault, BP 14491 34093 Montpellier Cedex 5 France
| | | | | | - Nicolas Ruiz
- Laboratoire Mer Molécules Santé.; Université de Nantes, UFR de Sciences pharmaceutiques et biologiques; 9 rue Bias-BP 61112 44035 Nantes France
| | - Filippo Savini
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma, Tor Vergata; Via della Ricerca Scientifica 00133 Roma Italy)
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma, Tor Vergata; Via della Ricerca Scientifica 00133 Roma Italy)
| | - Claude Didierjean
- CRM2 (UMR UL-CNRS 7036) Faculté des Sciences et Technologies; Université de Lorraine; 70239 Boulevard des Aiguillettes 54506 Vandoeuvre-lès-Nancy France)
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; Université de Montpellier; 15 avenue Charles Flahault, BP 14491 34093 Montpellier Cedex 5 France
| | - Nicolas Inguimbert
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS; Université de Perpignan Via Domitia, Laboratoire d'Excellence « CORAIL » Bâtiment T; 58 avenue P. Alduy 66860 Perpignan France)
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21
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Ding X, Wu YL, Gao J, Wells A, Lee K, Wang Y. Tyramine functionalization of poly(glycerol sebacate) increases the elasticity of the polymer. J Mater Chem B 2017; 5:6097-6109. [PMID: 29276605 PMCID: PMC5737705 DOI: 10.1039/c7tb01078h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Poly(glycerol sebacate) (PGS) is an elastomer used widely in tissue engineering studies due to good biocompatibility. Hereby we report a tyramine functionalized PGS called PGS-TA. Tyramine adds a stronger physical bonding capability to PGS-TA. Tensile tests showed that the softness and toughness of the material were similar to PGS. However, PGS-TA demonstrated 16-folds increase of elastic deformations compared to PGS processed under identical conditions. The in vitro studies demonstrated that the viability, and metabolic activity of baboon smooth muscle cells were the same as those on tissue culture polystyrene. Porous subcutaneous implants of PGS-TA substantially degraded in vivo over two weeks, showing good biodegradability and biocompatibility. We expect PGS-TA to be useful for applications in tissues and organs that are subjected to large reversible mechanical deformations.
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Affiliation(s)
- Xiaochu Ding
- Department of Bioengineering and the McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yen-Lin Wu
- Department of Bioengineering and the McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jin Gao
- Department of Bioengineering and the McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Albin Wells
- Allderdice High School, 2409 Shady Ave, Pittsburgh, PA 15217
| | - Keewon Lee
- Department of Bioengineering and the McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yadong Wang
- Department of Bioengineering and the McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Chemical and Petroleum Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Clinical Translational Science Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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22
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Goomber S, Chopra N, Kaur Bedi G, Kaur J. Comparative analysis of point mutations on protein COOH terminal near surface and its hydrophobic core provide insights on thermostability of Bacillus Lipase LipJ. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2017.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Pham K, Miksovska J. Molecular insight of DREAM and presenilin 1 C-terminal fragment interactions. FEBS Lett 2016; 590:1114-22. [PMID: 27009418 DOI: 10.1002/1873-3468.12156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 02/24/2016] [Accepted: 03/21/2016] [Indexed: 12/21/2022]
Abstract
Interactions between downstream regulatory element antagonist modulator (DREAM) and presenilin 1 (PS1) are related to numerous neuronal processes. We demonstrate that association of PS1 carboxyl peptide (residues 445-467, HL9) with DREAM is calcium dependent and stabilized by a cluster of three aromatic residues: F462 and F465 from PS1 and F252 from DREAM. Additional stabilization is provided by residues in a loop connecting α helices 7 and 8 in DREAM and residues of PS1, namely cation-π interactions between R200 in DREAM and F465 in PS1 and the salt bridges formed by R207 in DREAM and D450 and D458 in PS1.
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Affiliation(s)
- Khoa Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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24
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Matyska Liskova P, Fiser R, Macek P, Chmelik J, Sykora J, Bednarova L, Konopasek I, Bumba L. Probing the Ca(2+)-assisted π-π interaction during Ca(2+)-dependent protein folding. SOFT MATTER 2016; 12:531-541. [PMID: 26489523 DOI: 10.1039/c5sm01796c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein folding is governed by a balance of non-covalent interactions, of which cation-π and π-π play important roles. Theoretical calculations revealed a strong cooperativity between cation-π involving alkali and alkaline earth metal ions and π-π interactions, but however, no experimental evidence was provided in this regard. Here, we characterized a Ca(2+)-binding self-processing module (SPM), which mediates a highly-specific Ca(2+)-dependent autocatalytic processing of iron-regulated protein FrpC secreted by the pathogenic Gram-negative bacterium Neisseria meningitidis. The SPM undergoes a Ca(2+)-induced transition from an intrinsically unstructured conformation to the compact protein fold that is ultimately stabilized by the π-π interaction between two unique tryptophan residues arranged in the T-shaped orientation. Moreover, the pair of tryptophans is located in a close vicinity of a calcium-binding site, suggesting the involvement of a Ca(2+)-assisted π-π interaction in the stabilization of the tertiary structure of the SPM. This makes the SPM an excellent model for the investigation of the Ca(2+)-assisted π-π interaction during Ca(2+)-induced protein folding.
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Affiliation(s)
- Petra Matyska Liskova
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 14200 Prague, Czech Republic.
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25
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Abstract
Using structure and sequence based analysis we can engineer proteins to increase their thermal stability.
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Affiliation(s)
- H. Pezeshgi Modarres
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - M. R. Mofrad
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - A. Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory
- Department of Mechanical and Manufacturing Engineering
- University of Calgary
- Calgary
- Canada
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26
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Makwana KM, Mahalakshmi R. Nature of aryl-tyrosine interactions contribute to β-hairpin scaffold stability: NMR evidence for alternate ring geometry. Phys Chem Chem Phys 2016; 17:4220-30. [PMID: 25569770 DOI: 10.1039/c4cp04991h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The specific contribution of the acidic-aromatic β-sheet favouring amino acid tyrosine to the stability of short octapeptide β-hairpin structures is presented here. Solution NMR analysis in near-apolar environments suggests the energetically favourable mode of interaction to be T-shaped face-to-edge (FtE) and that a Trp-Tyr interacting pair is the most stabilizing. Alternate aryl geometries also exist in solution, which readily equilibrate between a preferred π···π conformation to an aromatic-amide conformation, without any change in the backbone structure. While the phenolic ring is readily accommodated at the "edge" of FtE aryl interactions, it exhibits an overall lowered contribution to scaffold stability in the "face" orientation. Such differential tyrosine interactions are key to its dual nature in proteins.
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Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal-462023, India.
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27
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Madhusudan Makwana K, Mahalakshmi R. Implications of aromatic-aromatic interactions: From protein structures to peptide models. Protein Sci 2015; 24:1920-33. [PMID: 26402741 DOI: 10.1002/pro.2814] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 12/11/2022]
Abstract
With increasing structural information on proteins, the opportunity to understand physical forces governing protein folding is also expanding. One of the significant non-covalent forces between the protein side chains is aromatic-aromatic interactions. Aromatic interactions have been widely exploited and thoroughly investigated in the context of folding, stability, molecular recognition, and self-assembly processes. Through this review, we discuss the contribution of aromatic interactions to the activity and stability of thermophilic, mesophilic, and psychrophilic proteins. Being hydrophobic, aromatic amino acids tend to reside in the protein hydrophobic interior or transmembrane segments of proteins. In such positions, it can play a diverse role in soluble and membrane proteins, and in α-helix and β-sheet stabilization. We also highlight here some excellent investigations made using peptide models and several approaches involving aryl-aryl interactions, as an increasingly popular strategy in protein and peptide engineering. A recent survey described the existence of aromatic clusters (trimer, tetramer, pentamer, and higher order assemblies), revealing the self-associating property of aryl groups, even in folded protein structures. The application of this self-assembly of aromatics in the generation of modern bionanomaterials is also discussed.
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Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, India
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Toward understanding driving forces in membrane protein folding. Arch Biochem Biophys 2014; 564:297-313. [DOI: 10.1016/j.abb.2014.07.031] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 12/13/2022]
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29
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Karabencheva-Christova TG, Carlsson U, Balali-Mood K, Black GW, Christov CZ. Conformational effects on the circular dichroism of Human Carbonic Anhydrase II: a multilevel computational study. PLoS One 2013; 8:e56874. [PMID: 23526922 PMCID: PMC3582176 DOI: 10.1371/journal.pone.0056874] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 01/15/2013] [Indexed: 11/25/2022] Open
Abstract
Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions.
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Affiliation(s)
- Tatyana G Karabencheva-Christova
- Department of Applied Sciences, School of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.
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30
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Zheng X, Wu C, Ponder JW, Marshall GR. Molecular dynamics of β-hairpin models of epigenetic recognition motifs. J Am Chem Soc 2012; 134:15970-8. [PMID: 22934656 DOI: 10.1021/ja306803v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The conformations and stabilities of the β-hairpin model peptides of Waters (Riemen, A. J.; Waters, M. L. Biochemistry 2009, 48, 1525; Hughes, R. M.; Benshoff, M. L.; Waters, M. L. Chemistry 2007, 13, 5753) have been experimentally characterized as a function of lysine ε-methylation. These models were developed to explore molecular recognition of known epigenetic recognition motifs. This system offered an opportunity to computationally examine the role of cation-π interactions, desolvation of the ε-methylated ammonium groups, and aromatic/aromatic interactions on the observed differences in NMR spectra. AMOEBA, a second-generation force field (Ponder, J. W.; Wu, C.; Ren, P.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A., Jr.; Head-Gordon, M.; Clark, G. N.; Johnson, M. E.; Head-Gordon, T. J. Phys. Chem. B 2010, 114, 2549), was chosen as it includes both multipole electrostatics and polarizability thought to be essential to accurately characterize such interactions. Independent parametrization of ε-methylated amines was required from which aqueous solvation free energies were estimated and shown to agree with literature values. Molecular dynamics simulations (100 ns) using the derived parameters with model peptides, such as Ac-R-W-V-W-V-N-G-Orn-K(Me)(n)-I-L-Q-NH(2), where n = 0, 1, 2, or 3, were conducted in explicit solvent. Distances between the centers of the indole rings of the two-tryptophan residues, 2 and 4, and the ε-methylated ammonium group on Lys-9 as well as the distance between the N- and C-termini were monitored to estimate the strength and orientation of the cation-π and aromatic/aromatic interactions. In agreement with the experimental data, the stability of the β-hairpin increased significantly with lysine ε-methylation. The ability of MD simulations to reproduce the observed NOEs for the four peptides was further estimated for the monopole-based force fields, AMBER, CHARMM, and OPLSAA. AMOEBA correctly predicted over 80% of the observed NOEs for all 4 peptides, while the three-monopole force fields were 40-50% predictive in only 2 cases and approximately 10% in the other 10 examples. Preliminary analysis suggests that the decreased cost of desolvation of the substituted ammonium group significantly compensated for the reduced cation-π interaction resulting from the increased separation due to steric bulk of the ε-methylated amines.
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Affiliation(s)
- Xiange Zheng
- Department of Chemistry and of Biochemistry, Washington University, St. Louis, Missouri 63105, United States
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31
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32
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Dorff G, Hahn M, Laschewsky A, Lieske A. Optimization of the property profile of poly-L-lactide by synthesis of PLLA-polystyrene-block copolymers. J Appl Polym Sci 2012. [DOI: 10.1002/app.37836] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Brkljača Z, Čondić-Jurkić K, Smith AS, Smith DM. Calculation of the CD Spectrum of a Peptide from Its Conformational Phase Space: The Case of Met-enkephalin and Its Unnatural Analogue. J Chem Theory Comput 2012; 8:1694-705. [PMID: 26593663 DOI: 10.1021/ct200868y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Zlatko Brkljača
- Institute for Theoretical
Physics
and Excellence Cluster: Engineering of Advanced Materials, FA University Erlangen—Nürnberg, Nägelsbachstraße
49b, Erlangen, 91052, Germany
| | - Karmen Čondić-Jurkić
- Institute for Theoretical
Physics
and Excellence Cluster: Engineering of Advanced Materials, FA University Erlangen—Nürnberg, Nägelsbachstraße
49b, Erlangen, 91052, Germany
- Division of Organic Chemistry
and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Ana-Sunčana Smith
- Institute for Theoretical
Physics
and Excellence Cluster: Engineering of Advanced Materials, FA University Erlangen—Nürnberg, Nägelsbachstraße
49b, Erlangen, 91052, Germany
| | - David M. Smith
- Division of Organic Chemistry
and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
- Center for Computational Chemistry, FA University of Erlangen—Nürnberg, Nägelsbachstraße
25, Erlangen, 91052, Germany
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34
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Cavalli S, Robson Marsden H, Albericio F, Kros A. Peptide Self-Assembly. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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35
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Shen YT, Zhu N, Zhang XM, Deng K, Feng W, Yan Q, Lei S, Zhao D, Zeng QD, Wang C. A Foldamer at the Liquid/Graphite Interface: The Effect of Interfacial Interactions, Solvent, Concentration, and Temperature. Chemistry 2011; 17:7061-8. [DOI: 10.1002/chem.201003589] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Indexed: 11/05/2022]
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36
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Contributions of cation–π interactions to the collagen triple helix stability. Arch Biochem Biophys 2011; 508:46-53. [DOI: 10.1016/j.abb.2011.01.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 01/07/2011] [Accepted: 01/12/2011] [Indexed: 11/20/2022]
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37
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de Sousa MM, Munteanu CR, Pazos A, Fonseca NA, Camacho R, Magalhães AL. Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins. J Theor Biol 2010; 271:136-44. [PMID: 21130100 DOI: 10.1016/j.jtbi.2010.11.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 11/03/2010] [Accepted: 11/23/2010] [Indexed: 10/18/2022]
Abstract
A statistical approach has been applied to analyse primary structure patterns at inner positions of α-helices in proteins. A systematic survey was carried out in a recent sample of non-redundant proteins selected from the Protein Data Bank, which were used to analyse α-helix structures for amino acid pairing patterns. Only residues more than three positions apart from both termini of the α-helix were considered as inner. Amino acid pairings i, i+k (k=1, 2, 3, 4, 5), were analysed and the corresponding 20×20 matrices of relative global propensities were constructed. An analysis of (i, i+4, i+8) and (i, i+3, i+4) triplet patterns was also performed. These analysis yielded information on a series of amino acid patterns (pairings and triplets) showing either high or low preference for α-helical motifs and suggested a novel approach to protein alphabet reduction. In addition, it has been shown that the individual amino acid propensities are not enough to define the statistical distribution of these patterns. Global pair propensities also depend on the type of pattern, its composition and orientation in the protein sequence. The data presented should prove useful to obtain and refine useful predictive rules which can further the development and fine-tuning of protein structure prediction algorithms and tools.
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Affiliation(s)
- Miguel M de Sousa
- REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal
| | - Cristian R Munteanu
- REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal; Computer Science Faculty, University of A Coruña, Campus de Elviña S/N, 15071A Coruña, Spain
| | - Alejandro Pazos
- Computer Science Faculty, University of A Coruña, Campus de Elviña S/N, 15071A Coruña, Spain
| | - Nuno A Fonseca
- CRACS-INESC Porto L.A., R. Campo Alegre 1021/1055, 4169-007 Porto, Portugal
| | - Rui Camacho
- LIAAD-INESC-Porto, DEI and FEUP, R. Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - A L Magalhães
- REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal
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38
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Cheng RP, Girinath P, Suzuki Y, Kuo HT, Hsu HC, Wang WR, Yang PA, Gullickson D, Wu CH, Koyack MJ, Chiu HP, Weng YJ, Hart P, Kokona B, Fairman R, Lin TE, Barrett O. Positional Effects on Helical Ala-Based Peptides. Biochemistry 2010; 49:9372-84. [DOI: 10.1021/bi101156j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard P. Cheng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Prashant Girinath
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Yuta Suzuki
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Hsiou-Ting Kuo
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Hao-Chun Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Ren Wang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Po-An Yang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Donald Gullickson
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Cheng-Hsun Wu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Marc J. Koyack
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Hsien-Po Chiu
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Yi-Jen Weng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Pier Hart
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Tzu-En Lin
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Olivia Barrett
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
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39
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Gribbon C, Channon KJ, Zhang W, Banwell EF, Bromley EHC, Chaudhuri JB, Oreffo ROC, Woolfson DN. MagicWand: A Single, Designed Peptide That Assembles to Stable, Ordered α-Helical Fibers. Biochemistry 2008; 47:10365-71. [DOI: 10.1021/bi801072s] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Christopher Gribbon
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Kevin J. Channon
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Weijie Zhang
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Eleanor F. Banwell
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Elizabeth H. C. Bromley
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Julian B. Chaudhuri
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Richard O. C. Oreffo
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
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40
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Kumar A, De S, Samuelson AG, Jemmis ED. Differing Reactivities of Zirconium and Titanium Alkoxides with Phenyl Isocyanate: An Experimental and Computational Study. Organometallics 2008. [DOI: 10.1021/om701004f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akshai Kumar
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Susmita De
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Ashoka G. Samuelson
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Eluvathingal D. Jemmis
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560 012, India
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41
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Fonseca NA, Camacho R, Magalhães AL. Amino acid pairing at the N- and C-termini of helical segments in proteins. Proteins 2008; 70:188-96. [PMID: 17654550 DOI: 10.1002/prot.21525] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A systematic survey was carried out in an unbiased sample of 815 protein chains with a maximum of 20% homology selected from the Protein Data Bank, whose structures were solved at a resolution higher than 1.6 A and with a R-factor lower than 25%. A set of 5556 subsequences with alpha-helix or 3(10)-helix motifs was extracted from the protein chains considered. Global and local propensities were then calculated for all possible amino acid pairs of the type (i, i + 1), (i, i + 2), (i, i + 3), and (i, i + 4), starting at the relevant helical positions N1, N2, N3, C3, C2, C1, and N-int (interior positions), and also at the first nonhelical positions in both termini of the helices, namely, N-cap and C-cap. The statistical analysis of the propensity values has shown that pairing is significantly dependent on the type of the amino acids and on the position of the pair. A few sequences of three and four amino acids were selected and their high prevalence in helices is outlined in this work. The Glu-Lys-Tyr-Pro sequence shows a peculiar distribution in proteins, which may suggest a relevant structural role in alpha-helices when Pro is located at the C-cap position. A bioinformatics tool was developed, which updates automatically and periodically the results and makes them available in a web site.
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Affiliation(s)
- Nuno A Fonseca
- IBMC and LIACC, R. Campo Alegre, 1021/1055, 4169-007 Porto, Portugal
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42
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Soteras I, Orozco M, Luque FJ. Induction effects in metal cation–benzene complexes. Phys Chem Chem Phys 2008; 10:2616-24. [DOI: 10.1039/b719461g] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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43
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Gunasekar SK, Haghpanah JS, Montclare JK. Assembly of bioinspired helical protein fibers. POLYM ADVAN TECHNOL 2008. [DOI: 10.1002/pat.1136] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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44
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Stability and Design of α-Helical Peptides. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2008; 83:1-52. [DOI: 10.1016/s0079-6603(08)00601-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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45
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Rana S, Kundu B, Durani S. A mixed-α,β miniprotein stereochemically reprogrammed to high-binding affinity for acetylcholine. Biopolymers 2007; 87:231-43. [PMID: 17879332 DOI: 10.1002/bip.20829] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The protein-structure space is limited to L configuration in the asymmetric alpha-amino acid structures; the function space, on other hand, seems limitless because of the chemical diversity in the amino acid side chain structures. The chemical diversity in side chain structure may be multiplied beneficially with the stereochemical diversity in main chain structure; thus, de novo protein design may be explored for customizing molecular structures stereochemically and molecular functions chemically. Illustrating de novo design in the structure space of L and D alphabet, canonical all-beta folds of poly-L structure were reprogrammed as bracelet, boat, and canoe-shaped molecules-the "boat" as a receptor-like pocket and the "canoe" as a metal-ion receptor-simply by mutating specific L-amino acid residues to the corresponding D stereochemical structure. Demonstrating customization of molecular shape stereochemically and function chemically, a 15-residue mixed-alpha, beta miniprotein of canonical poly-L structure is now reprogrammed stereochemically as a cup-shaped receptor for acetylcholine via cation-pi interaction with a triad of aromatic side chains placed in mimicry of the acetylcholine-receptor sites both natural and artificial. Evidence from CD, fluorescence, NMR, DSC, ITC, MD, and molecular-docking studies is presented to show that a rationally designed 15-residue mixed-L, D peptide is a cooperatively ordered molecular fold in the stereochemically specified molecular morphology, submicromolar in affinity of acetylcholine and thus an acetylcholine receptor exceptionally small and simple. .
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Affiliation(s)
- Soumendra Rana
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
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46
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Anderson MA, Ogbay B, Arimoto R, Sha W, Kisselev OG, Cistola DP, Marshall GR. Relative strength of cation-pi vs salt-bridge interactions: the Gtalpha(340-350) peptide/rhodopsin system. J Am Chem Soc 2007; 128:7531-41. [PMID: 16756308 DOI: 10.1021/ja058513z] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interactions between cationic and aromatic side chains of amino acid residues, the so-called cation-pi interaction, are thought to contribute to the overall stability of the folded structure of peptides and proteins. The transferred NOE NMR structure of the G(t)alpha(340-350) peptide bound to photoactivated rhodopsin (R*) geometrically suggests a cation-pi interaction stabilizing the structure between the epsilon-amine of Lys341 and the aromatic ring of the C-terminal residue, Phe350. This interaction has been explored by varying substituents on the phenyl ring to alter the electron density of the aromatic ring of Phe350 and observing the impact on binding of the peptide to R*. The results suggest that while a cation-pi interaction geometrically exists in the G(t)alpha(340-350) peptide when bound to R*, its energetic contribution to the stability of the receptor-bound structure is relatively insignificant, as it was not observed experimentally. The presence of an adjacent and competing salt-bridge interaction between the epsilon-amine of Lys341 and the C-terminal carboxylate of Phe350 effectively shields the charge of the ammonium group. Experimental data supporting a significant cation-pi interaction can be regained through a series of Phe350 analogues where the C-terminal carboxyl has been converted to the neutral carboxamide, thus eliminating the shielding salt-bridge. TrNOE NMR experiments confirmed the existence of the cation-pi interaction in the carboxamide analogues. Various literature estimates of the strength of cation-pi interactions, including some that estimate strengths in excess of salt-bridges, are compromised by omission of the relevant anion in the calculations.
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Affiliation(s)
- Matthew A Anderson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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47
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Chakrabarti P, Bhattacharyya R. Geometry of nonbonded interactions involving planar groups in proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2007; 95:83-137. [PMID: 17629549 DOI: 10.1016/j.pbiomolbio.2007.03.016] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 03/18/2007] [Indexed: 11/26/2022]
Abstract
Although hydrophobic interaction is the main contributing factor to the stability of the protein fold, the specificity of the folding process depends on many directional interactions. An analysis has been carried out on the geometry of interaction between planar moieties of ten side chains (Phe, Tyr, Trp, His, Arg, Pro, Asp, Glu, Asn and Gln), the aromatic residues and the sulfide planes (of Met and cystine), and the aromatic residues and the peptide planes within the protein tertiary structures available in the Protein Data Bank. The occurrence of hydrogen bonds and other nonconventional interactions such as C-H...pi, C-H...O, electrophile-nucleophile interactions involving the planar moieties has been elucidated. The specific nature of the interactions constraints many of the residue pairs to occur with a fixed sequence difference, maintaining a sequential order, when located in secondary structural elements, such as alpha-helices and beta-turns. The importance of many of these interactions (for example, aromatic residues interacting with Pro or cystine sulfur atom) is revealed by the higher degree of conservation observed for them in protein structures and binding regions. The planar residues are well represented in the active sites, and the geometry of their interactions does not deviate from the general distribution. The geometrical relationship between interacting residues provides valuable insights into the process of protein folding and would be useful for the design of protein molecules and modulation of their binding properties.
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Affiliation(s)
- Pinak Chakrabarti
- Department of Biochemistry and Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India.
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48
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Berry BW, Elvekrog MM, Tommos C. Environmental modulation of protein cation-pi interactions. J Am Chem Soc 2007; 129:5308-9. [PMID: 17417844 DOI: 10.1021/ja068957a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bruce W Berry
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
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49
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Yang ZY, Wang Y, Wang Y. Study on synthesis, structure, and DNA-binding of lanthanide complexes with 2-carboxylbenzaldehyde thiosemicarbazone. Bioorg Med Chem Lett 2007; 17:2096-101. [PMID: 17317160 DOI: 10.1016/j.bmcl.2006.10.049] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 10/02/2006] [Accepted: 10/21/2006] [Indexed: 11/23/2022]
Abstract
2-Carboxylbenzaldehyde thiosemicarbazone (HL), and its three lanthanide (III) complexes, LnL(3) x 4H(2)O [Ln(III)=La, Sm, Eu], have been synthesized in water. The complexes were characterized by elemental analyses, molar conductivity and IR spectra. The crystal structure of [Sm(2)L(6)(CH(3)OH)(4)] x 7.5CH(3)OH x 0.5H(2)O obtained from methanol solution was determined by X-ray diffraction analysis, crystallized in the triclinic system, space group P-1, Z=1, a=12.217 (2)A, b=14.706 (2)A, c=15.035 (2)A, alpha=111.84(1) degrees , beta=103.47(1) degrees , gamma=104.24(1) degrees , R(1)=0.0290. It has symmetrical (mu-OCO)(2), (mu-O)(2) and disamarium(III) units. The coordination geometry of each Sm(III) ion is a distorted tetradecahedron with nine oxygen atoms. In addition, the DNA-binding properties of the ligand and its complexes have been investigated by absorption, fluorescence, and viscosity measurements. The experimental results indicate that the ligand and the Sm-complex can bind to DNA, but the other two complexes cannot; the binding affinity of the Sm-complex is higher than that of the ligand and the intrinsic binding constant K(b) of the complex is 3.22 x 10(5)M(-1).
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Affiliation(s)
- Zheng-Yin Yang
- College of Chemistry and Chemical Engineering and State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, PR China.
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Abstract
Circular dichroism (CD) is an important technique in the structural characterisation of proteins, and especially for secondary structure determination. The CD of proteins can be calculated from first principles using the so-called matrix method, with an accuracy which is almost quantitative for helical proteins. Thus, for proteins of unknown structure, CD calculations and experimental data can be used in conjunction to aid structure analysis. Linear dichroism (LD) can be calculated using analogous methodology and has been used to establish the relative orientations of subunits in proteins and protein orientation in an environment such as a membrane. However, simple analysis of LD data is not possible, due to overlapping transitions. So coupling the calculations and experiment is an important strategy. In this paper, the use of LD for the determination of protein orientation and how these data can be interpreted with the aid of calculations, are discussed. We review methods for the calculation of CD spectra, focusing on semiempirical and ab initio parameter sets used in the matrix method. Lastly, a new web interface for online CD and LD calculation is presented.
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Affiliation(s)
- Benjamin M Bulheller
- School of Chemistry, University of Nottingham, University Park, Nottingham, UK NG7 2RD
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