51
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Gkikas M, Haataja JS, Seitsonen J, Ruokolainen J, Ikkala O, Iatrou H, Houbenov N. Extended Self-Assembled Long Periodicity and Zig-Zag Domains from Helix–Helix Diblock Copolymer Poly(γ-benzyl-l-glutamate)-block-poly(O-benzyl-l-hydroxyproline). Biomacromolecules 2014; 15:3923-30. [DOI: 10.1021/bm5009734] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Manos Gkikas
- University of Athens, Department of Chemistry, Panepistimiopolis, Zografou, 15771 Athens, Greece
- Molecular
Materials, Department of Applied Physics, Aalto University School of Science and Technology (previously Helsinki University of Technology), P.O. Box 15100, FIN-00076 Aalto, Espoo, Finland
| | - Johannes S. Haataja
- Molecular
Materials, Department of Applied Physics, Aalto University School of Science and Technology (previously Helsinki University of Technology), P.O. Box 15100, FIN-00076 Aalto, Espoo, Finland
| | - Jani Seitsonen
- Molecular
Materials, Department of Applied Physics, Aalto University School of Science and Technology (previously Helsinki University of Technology), P.O. Box 15100, FIN-00076 Aalto, Espoo, Finland
- Nanomicroscopy
Center, Aalto University School of Science and Technology, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland
| | - Janne Ruokolainen
- Molecular
Materials, Department of Applied Physics, Aalto University School of Science and Technology (previously Helsinki University of Technology), P.O. Box 15100, FIN-00076 Aalto, Espoo, Finland
- Nanomicroscopy
Center, Aalto University School of Science and Technology, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland
| | - Olli Ikkala
- Molecular
Materials, Department of Applied Physics, Aalto University School of Science and Technology (previously Helsinki University of Technology), P.O. Box 15100, FIN-00076 Aalto, Espoo, Finland
| | - Hermis Iatrou
- University of Athens, Department of Chemistry, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Nikolay Houbenov
- Molecular
Materials, Department of Applied Physics, Aalto University School of Science and Technology (previously Helsinki University of Technology), P.O. Box 15100, FIN-00076 Aalto, Espoo, Finland
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Abstract
Dynamin is a large GTPase that mediates plasma membrane fission during clathrin-mediated endocytosis. Dynamin assembles into polymers on the necks of budding membranes in cells and has been shown to undergo GTP-dependent conformational changes that lead to membrane fission in vitro. Recent efforts have shed new light on the mechanisms of dynamin-mediated fission, yet exactly how dynamin performs this function in vivo is still not fully understood. Dynamin interacts with a number of proteins during the endocytic process. These interactions are mediated by the C-terminal proline-rich domain (PRD) of dynamin binding to SH3 domain-containing proteins. Three of these dynamin-binding partners (intersectin, amphiphysin and endophilin) have been shown to play important roles in the clathrin-mediated endocytosis process. They promote dynamin-mediated plasma membrane fission by regulating three important sequential steps in the process: recruitment of dynamin to sites of endocytosis; assembly of dynamin into a functional fission complex at the necks of clathrin-coated pits (CCPs); and regulation of dynamin-stimulated GTPase activity, a key requirement for fission.
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53
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Bogdanov B, Zhao X, Robinson DB, Ren J. Electron capture dissociation studies of the fragmentation patterns of doubly protonated and mixed protonated-sodiated peptoids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1202-1216. [PMID: 24845348 DOI: 10.1007/s13361-014-0869-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 02/09/2014] [Accepted: 02/14/2014] [Indexed: 06/03/2023]
Abstract
The fragmentation patterns of a group of doubly protonated ([P + 2H](2+)) and mixed protonated-sodiated ([P + H + Na](2+)) peptide-mimicking oligomers, known as peptoids, have been studied using electron capturing dissociation (ECD) tandem mass spectrometry techniques. For all the peptoids studied, the primary backbone fragmentation occurred at the N-Cα bonds. The N-terminal fragment ions, the C-ions (protonated) and the C'-ions (sodiated) were observed universally for all the peptoids regardless of the types of charge carrier. The C-terminal ions varied depending on the type of charge carrier. The doubly protonated peptoids with at least one basic residue located at a position other than the N-terminus fragmented by producing the Z(•)-series of ions. In addition, most doubly protonated peptoids also produced the Y-series of ions with notable abundances. The mixed protonated-sodiated peptoids fragmented by yielding the Z(•)'-series of ions in addition to the C'-series. Chelation between the sodium cation and the amide groups of the peptoid chain might be an important factor that could stabilize both the N-terminal and the C-terminal fragment ions. Regardless of the types of the charge carrier, one notable fragmentation for all the peptoids was the elimination of a benzylic radical from the odd-electron positive ions of the protonated peptoids ([P + 2H](•+)) and the sodiated peptoids ([P + H + Na](•+)). The study showed potential utility of using the ECD technique for sequencing of peptoid libraries generated by combinatorial chemistry.
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Affiliation(s)
- Bogdan Bogdanov
- Department of Chemistry, University of the Pacific, Stockton, CA, 95211, USA
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54
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Zeller F, Zacharias M. Evaluation of Generalized Born Model Accuracy for Absolute Binding Free Energy Calculations. J Phys Chem B 2014; 118:7467-7474. [DOI: 10.1021/jp5015934] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fabian Zeller
- Physik-Department
T38, Technische Universität München, James-Franck-Str. 1, Garching 85748, Germany
| | - Martin Zacharias
- Physik-Department
T38, Technische Universität München, James-Franck-Str. 1, Garching 85748, Germany
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55
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Renfrew PD, Craven TW, Butterfoss G, Kirshenbaum K, Bonneau R. A rotamer library to enable modeling and design of peptoid foldamers. J Am Chem Soc 2014; 136:8772-82. [PMID: 24823488 PMCID: PMC4227732 DOI: 10.1021/ja503776z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Indexed: 01/08/2023]
Abstract
Peptoids are a family of synthetic oligomers composed of N-substituted glycine units. Along with other "foldamer" systems, peptoid oligomer sequences can be predictably designed to form a variety of stable secondary structures. It is not yet evident if foldamer design can be extended to reliably create tertiary structure features that mimic more complex biomolecular folds and functions. Computational modeling and prediction of peptoid conformations will likely play a critical role in enabling complex biomimetic designs. We introduce a computational approach to provide accurate conformational and energetic parameters for peptoid side chains needed for successful modeling and design. We find that peptoids can be described by a "rotamer" treatment, similar to that established for proteins, in which the peptoid side chains display rotational isomerism to populate discrete regions of the conformational landscape. Because of the insufficient number of solved peptoid structures, we have calculated the relative energies of side-chain conformational states to provide a backbone-dependent (BBD) rotamer library for a set of 54 different peptoid side chains. We evaluated two rotamer library development methods that employ quantum mechanics (QM) and/or molecular mechanics (MM) energy calculations to identify side-chain rotamers. We show by comparison to experimental peptoid structures that both methods provide an accurate prediction of peptoid side chain placements in folded peptoid oligomers and at protein interfaces. We have incorporated our peptoid rotamer libraries into ROSETTA, a molecular design package previously validated in the context of protein design and structure prediction.
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Affiliation(s)
- P. Douglas Renfrew
- Center for Genomics and
Systems Biology, Department
of Biology, Department of Chemistry, and Courant Institute of Mathematical
Sciences, Computer Science Department, New
York University, New York, New York 10003, United States
| | - Timothy W. Craven
- Center for Genomics and
Systems Biology, Department
of Biology, Department of Chemistry, and Courant Institute of Mathematical
Sciences, Computer Science Department, New
York University, New York, New York 10003, United States
| | - Glenn
L. Butterfoss
- Center
for Genomics and Systems Biology, New York
University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kent Kirshenbaum
- Center for Genomics and
Systems Biology, Department
of Biology, Department of Chemistry, and Courant Institute of Mathematical
Sciences, Computer Science Department, New
York University, New York, New York 10003, United States
| | - Richard Bonneau
- Center for Genomics and
Systems Biology, Department
of Biology, Department of Chemistry, and Courant Institute of Mathematical
Sciences, Computer Science Department, New
York University, New York, New York 10003, United States
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56
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Bandyopadhyay C, Valiya-Veettil M, Dutta D, Chakraborty S, Chandran B. CIB1 synergizes with EphrinA2 to regulate Kaposi's sarcoma-associated herpesvirus macropinocytic entry in human microvascular dermal endothelial cells. PLoS Pathog 2014; 10:e1003941. [PMID: 24550731 PMCID: PMC3923796 DOI: 10.1371/journal.ppat.1003941] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/08/2014] [Indexed: 11/19/2022] Open
Abstract
KSHV envelope glycoproteins interact with cell surface heparan sulfate and integrins, and activate FAK, Src, PI3-K, c-Cbl, and Rho-GTPase signal molecules in human microvascular dermal endothelial (HMVEC-d) cells. c-Cbl mediates the translocation of virus bound α3β1 and αVβ3 integrins into lipid rafts (LRs), where KSHV interacts and activates EphrinA2 (EphA2). EphA2 associates with c-Cbl-myosin IIA and augmented KSHV-induced Src and PI3-K signals in LRs, leading to bleb formation and macropinocytosis of KSHV. To identify the factor(s) coordinating the EphA2-signal complex, the role of CIB1 (calcium and integrin binding protein-1) associated with integrin signaling was analyzed. CIB1 knockdown did not affect KSHV binding to HMVEC-d cells but significantly reduced its entry and gene expression. In contrast, CIB1 overexpression increased KSHV entry in 293 cells. Single virus particle infection and trafficking during HMVEC-d cell entry was examined by utilizing DiI (envelope) and BrdU (viral DNA) labeled virus. CIB1 was associated with KSHV in membrane blebs and in Rab5 positive macropinocytic vesicles. CIB1 knockdown abrogated virus induced blebs, macropinocytosis and virus association with the Rab5 macropinosome. Infection increased the association of CIB1 with LRs, and CIB1 was associated with EphA2 and KSHV entry associated signal molecules such as Src, PI3-K, and c-Cbl. CIB1 knockdown significantly reduced the infection induced EphA2, Src and Erk1/2 activation. Mass spectrometry revealed the simultaneous association of CIB1 and EphA2 with the actin cytoskeleton modulating myosin IIA and alpha-actinin 4 molecules, and CIB1 knockdown reduced EphA2's association with myosin IIA and alpha-actinin 4. Collectively, these studies revealed for the first time that CIB1 plays a role in virus entry and macropinocytosis, and suggested that KSHV utilizes CIB1 as one of the key molecule(s) to coordinate and sustain the EphA2 mediated signaling involved in its entry, and CIB1 is an attractive therapeutic target to block KSHV infection.
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Affiliation(s)
- Chirosree Bandyopadhyay
- H. M. Bligh Cancer Research Laboratories, Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Mohanan Valiya-Veettil
- H. M. Bligh Cancer Research Laboratories, Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Dipanjan Dutta
- H. M. Bligh Cancer Research Laboratories, Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Sayan Chakraborty
- H. M. Bligh Cancer Research Laboratories, Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Bala Chandran
- H. M. Bligh Cancer Research Laboratories, Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
- * E-mail:
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57
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Ramirez MA, Chen Z. Synthesis of an intein-mediated artificial protein hydrogel. J Vis Exp 2014:e51202. [PMID: 24514743 DOI: 10.3791/51202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We present the synthesis of a highly stable protein hydrogel mediated by a split-intein-catalyzed protein trans-splicing reaction. The building blocks of this hydrogel are two protein block-copolymers each containing a subunit of a trimeric protein that serves as a crosslinker and one half of a split intein. A highly hydrophilic random coil is inserted into one of the block-copolymers for water retention. Mixing of the two protein block copolymers triggers an intein trans-splicing reaction, yielding a polypeptide unit with crosslinkers at either end that rapidly self-assembles into a hydrogel. This hydrogel is very stable under both acidic and basic conditions, at temperatures up to 50 °C, and in organic solvents. The hydrogel rapidly reforms after shear-induced rupture. Incorporation of a "docking station peptide" into the hydrogel building block enables convenient incorporation of "docking protein"-tagged target proteins. The hydrogel is compatible with tissue culture growth media, supports the diffusion of 20 kDa molecules, and enables the immobilization of bioactive globular proteins. The application of the intein-mediated protein hydrogel as an organic-solvent-compatible biocatalyst was demonstrated by encapsulating the horseradish peroxidase enzyme and corroborating its activity.
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Affiliation(s)
- Miguel A Ramirez
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station
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58
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He P, Wu W, Wang HD, Liao KL, Zhang W, Lv FL, Yang K. Why ligand cross-reactivity is high within peptide recognition domain families? A case study on human c-Src SH3 domain. J Theor Biol 2014; 340:30-7. [DOI: 10.1016/j.jtbi.2013.08.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/26/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
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59
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Fuxe K, Borroto-Escuela DO, Romero-Fernandez W, Palkovits M, Tarakanov AO, Ciruela F, Agnati LF. Moonlighting proteins and protein-protein interactions as neurotherapeutic targets in the G protein-coupled receptor field. Neuropsychopharmacology 2014; 39:131-55. [PMID: 24105074 PMCID: PMC3857668 DOI: 10.1038/npp.2013.242] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 07/04/2013] [Accepted: 07/05/2013] [Indexed: 12/28/2022]
Abstract
There is serious interest in understanding the dynamics of the receptor-receptor and receptor-protein interactions in space and time and their integration in GPCR heteroreceptor complexes of the CNS. Moonlighting proteins are special multifunctional proteins because they perform multiple autonomous, often unrelated, functions without partitioning into different protein domains. Moonlighting through receptor oligomerization can be operationally defined as an allosteric receptor-receptor interaction, which leads to novel functions of at least one receptor protomer. GPCR-mediated signaling is a more complicated process than previously described as every GPCR and GPCR heteroreceptor complex requires a set of G protein interacting proteins, which interacts with the receptor in an orchestrated spatio-temporal fashion. GPCR heteroreceptor complexes with allosteric receptor-receptor interactions operating through the receptor interface have become major integrative centers at the molecular level and their receptor protomers act as moonlighting proteins. The GPCR heteroreceptor complexes in the CNS have become exciting new targets for neurotherapeutics in Parkinson's disease, schizophrenia, drug addiction, and anxiety and depression opening a new field in neuropsychopharmacology.
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Affiliation(s)
- Kjell Fuxe
- Department of Neuroscience, Karolinska Institutet,, Stockholm, Sweden
| | | | | | - Miklós Palkovits
- Department of Anatomy, Histology and Embryology, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Alexander O Tarakanov
- Russian Academy of Sciences, St. Petersburg Institute for Informatics and Automation, Saint Petersburg, Russia
| | - Francisco Ciruela
- Facultat de Medicina, Departament de Patologia i Terapèutica Experimental IDIBELL-Universitat de Barcelona, L'Hospitalet de Llobregat, Unitat de Farmacologia, Barcelona, Spain
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60
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Buratto J, Colombo C, Stupfel M, Dawson SJ, Dolain C, Langlois d'Estaintot B, Fischer L, Granier T, Laguerre M, Gallois B, Huc I. Structure of a Complex Formed by a Protein and a Helical Aromatic Oligoamide Foldamer at 2.1 Å Resolution. Angew Chem Int Ed Engl 2013; 53:883-7. [DOI: 10.1002/anie.201309160] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Indexed: 11/06/2022]
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61
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Buratto J, Colombo C, Stupfel M, Dawson SJ, Dolain C, Langlois d'Estaintot B, Fischer L, Granier T, Laguerre M, Gallois B, Huc I. Structure of a Complex Formed by a Protein and a Helical Aromatic Oligoamide Foldamer at 2.1 Å Resolution. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201309160] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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62
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Gorske BC, Nelson RC, Bowden ZS, Kufe TA, Childs AM. “Bridged” n→π* Interactions Can Stabilize Peptoid Helices. J Org Chem 2013; 78:11172-83. [DOI: 10.1021/jo4014113] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Benjamin C. Gorske
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
| | - Ryan C. Nelson
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
| | - Zara S. Bowden
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
| | - Turner A. Kufe
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
| | - Adam M. Childs
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
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63
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Axelsen LN, Calloe K, Holstein-Rathlou NH, Nielsen MS. Managing the complexity of communication: regulation of gap junctions by post-translational modification. Front Pharmacol 2013; 4:130. [PMID: 24155720 PMCID: PMC3804956 DOI: 10.3389/fphar.2013.00130] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 09/30/2013] [Indexed: 12/21/2022] Open
Abstract
Gap junctions are comprised of connexins that form cell-to-cell channels which couple neighboring cells to accommodate the exchange of information. The need for communication does, however, change over time and therefore must be tightly controlled. Although the regulation of connexin protein expression by transcription and translation is of great importance, the trafficking, channel activity and degradation are also under tight control. The function of connexins can be regulated by several post translational modifications, which affect numerous parameters; including number of channels, open probability, single channel conductance or selectivity. The most extensively investigated post translational modifications are phosphorylations, which have been documented in all mammalian connexins. Besides phosphorylations, some connexins are known to be ubiquitinated, SUMOylated, nitrosylated, hydroxylated, acetylated, methylated, and γ-carboxyglutamated. The aim of the present review is to summarize our current knowledge of post translational regulation of the connexin family of proteins.
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Affiliation(s)
- Lene N Axelsen
- Department of Biomedical Sciences and The Danish National Research Foundation Centre for Cardiac Arrhythmia, Faculty of Health and Medical Sciences, University of Copenhagen Copenhagen, Denmark
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64
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Singhamahapatra A, Sahoo L, Loganathan D. Clickable Glycopeptoids for Synthesis of Glycopeptide Mimic. J Org Chem 2013; 78:10329-36. [DOI: 10.1021/jo401720s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Anadi Singhamahapatra
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Laxminarayan Sahoo
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
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65
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Li Z, Lavergne T, Malyshev DA, Zimmermann J, Adhikary R, Dhami K, Ordoukhanian P, Sun Z, Xiang J, Romesberg FE. Site-specifically arraying small molecules or proteins on DNA using an expanded genetic alphabet. Chemistry 2013; 19:14205-14209. [PMID: 24026962 DOI: 10.1002/chem.201302496] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Indexed: 12/20/2022]
Abstract
A class of replicable unnatural DNA base pairs formed between d5SICS and either dMMO2, dDMO, or dNaM were developed. To explore the use of these pairs to produce site-specifically labeled DNA, the synthesis of a variety of derivatives bearing propynyl groups, an analysis of their polymerase-mediated replication, and subsequent site-specific modification of the amplified DNA by Click chemistry is reported. With the d5SICS scaffold a propynyl ether linker is accommodated better than its aliphatic analogue, but not as well as the protected propargyl amine linker explored previously. It was also found that with the dMMO2 and dDMO analogues, the dMMO2 position para to the glycosidic linkage is best suited for linker attachment and that although aliphatic and ether-based linkers are similarly accommodated, the direct attachment of an ethynyl group to the nucleobase core is most well tolerated. To demonstrate the utility of these analogues, a variety of them were used to site-selectively attach a biotin tag to the amplified DNA. Finally, we use d5SICS(CO) -dNaM to couple one or two proteins to amplified DNA, with the double labeled product visualized by atomic force microscopy. The ability to encode the spatial relationships of arrayed molecules in PCR amplifiable DNA should have important applications, ranging from SELEX with functionalities not naturally present in DNA to the production, and perhaps "evolution" of nanomaterials.
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Affiliation(s)
- Zhengtao Li
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Thomas Lavergne
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Denis A Malyshev
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Jörg Zimmermann
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Ramkrishna Adhikary
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Kirandeep Dhami
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Phillip Ordoukhanian
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Zhelin Sun
- Department of Electrical and Computer Engineering 9500 Gilman Drive University of California, San Diego La Jolla, CA 92093
| | - Jie Xiang
- Department of Electrical and Computer Engineering 9500 Gilman Drive University of California, San Diego La Jolla, CA 92093
| | - Floyd E Romesberg
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
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66
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Adhikary R, Zimmermann J, Liu J, Dawson PE, Romesberg FE. Experimental characterization of electrostatic and conformational heterogeneity in an SH3 domain. J Phys Chem B 2013; 117:13082-9. [PMID: 23834285 DOI: 10.1021/jp402772x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electrostatic and conformational heterogeneity make central contributions to protein function, but their experimental characterization requires a combination of spatial and temporal resolution that is challenging to achieve. Src homology 3 (SH3) domains mediate protein-protein interactions, and NMR studies have demonstrated that most possess conformational heterogeneity, which could be critical for their function. Here, we use the IR absorptions of carbon-deuterium (C-D) bonds site-selectively incorporated throughout the N-terminal SH3 domain from the murine adapter protein Crk-II to characterize its different microenvironments with high spatial and temporal resolution. The C-D absorptions are only differentiated in the folded state of the protein where they show evidence of significant environmental heterogeneity. However, the spectra of the folded state are independent of temperature, and upon thermal denaturation the protein undergoes a single, global unfolding transition. While some evidence of conformational heterogeneity is found within the peptide backbone, the majority of the environmental heterogeneity appears to result from electrostatics.
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Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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67
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Sun J, Zuckermann RN. Peptoid polymers: a highly designable bioinspired material. ACS NANO 2013; 7:4715-32. [PMID: 23721608 DOI: 10.1021/nn4015714] [Citation(s) in RCA: 307] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Bioinspired polymeric materials are attracting increasing attention due to significant advantages over their natural counterparts: the ability to precisely tune their structures over a broad range of chemical and physical properties, increased stability, and improved processability. Polypeptoids, a promising class of bioinspired polymer based on a N-substituted glycine backbone, have a number of unique properties that bridge the material gap between proteins and bulk polymers. Peptoids combine the sequence specificity of biopolymers with the simpler intra/intermolecular interactions and robustness of traditional synthetic polymers. They are highly designable because hundreds of chemically diverse side chains can be introduced from simple building blocks. Peptoid polymers can be prepared by two distinct synthetic techniques offering access to two material subclasses: (1) automated solid-phase synthesis which enables precision sequence control and near absolute monodispersity up to chain lengths of ~50 monomers, and (2) a classical polymerization approach which allows access to higher molecular weights and larger-scale yields, but with less control over length and sequence. This combination of facile synthetic approaches makes polypeptoids a highly tunable, rapid polymer prototyping platform to investigate new materials that are intermediate between proteins and bulk polymers, in both their structure and their properties. In this paper, we review the methods to synthesize peptoid polymers and their applications in biomedicine and nanoscience, as both sequence-specific materials and as bulk polymers.
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Affiliation(s)
- Jing Sun
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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68
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Polyproline-II Helix in Proteins: Structure and Function. J Mol Biol 2013; 425:2100-32. [DOI: 10.1016/j.jmb.2013.03.018] [Citation(s) in RCA: 363] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/28/2013] [Accepted: 03/11/2013] [Indexed: 12/31/2022]
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69
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Ramirez M, Guan D, Ugaz V, Chen Z. Intein-triggered artificial protein hydrogels that support the immobilization of bioactive proteins. J Am Chem Soc 2013; 135:5290-3. [PMID: 23509910 DOI: 10.1021/ja401075s] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein hydrogels have important applications in tissue engineering, drug delivery, and biofabrication. We present the development of a novel self-assembling protein hydrogel triggered by mixing two soluble protein block copolymers, each containing one half of a split intein. Mixing these building blocks initiates an intein trans-splicing reaction that yields a hydrogel that is highly stable over a wide range of pH (6-10) and temperature (4-50 °C), instantaneously recovers its mechanical properties after shear-induced breakdown, and is compatible with both aqueous and organic solvents. Incorporating a "docking station" peptide into the hydrogel building blocks enables simple and stable immobilization of docking protein-fused bioactive proteins in the hydrogel. This intein-triggered protein hydrogel technology opens new avenues for both in vitro metabolic pathway construction and functional/biocompatible tissue engineering scaffolds and provides a convenient platform for immobilizing enzymes in industrial biocatalysis.
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Affiliation(s)
- Miguel Ramirez
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
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70
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Shi B, Zuo G, Xiu P, Zhou R. Binding Preference of Carbon Nanotube Over Proline-Rich Motif Ligand on SH3-Domain: A Comparison with Different Force Fields. J Phys Chem B 2013; 117:3541-7. [DOI: 10.1021/jp312423y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Biyun Shi
- Bio-X Lab, Department of Physics, Zhejiang University, Hangzhou 310027, People’s
Republic of China
| | - Guanghong Zuo
- Shanghai
Institute of Applied
Physics, Chinese Academy of Sciences, P.O.
Box 800-204, Shanghai 201800, People’s Republic of China
- T-Life Research Center, Department
of Physics, Fudan University, Shanghai
200433, People’s Republic of China
| | - Peng Xiu
- Soft Matter Research Center
and Department of Engineering Mechanics, Zhejiang University, Hangzhou, 310027, People’s Republic of China
| | - Ruhong Zhou
- Soft Matter Research Center
and Department of Engineering Mechanics, Zhejiang University, Hangzhou, 310027, People’s Republic of China
- Computational Biology Center,
IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
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71
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Abstract
Peptoids (N-substituted glycines) are mimics of α-peptides in which the side chains are attached to the backbone N (α) -amide nitrogen instead of the C (α) -atom. Peptoids hold promise as therapeutics since they often retain the biological activity of the parent peptide and are stable to proteases. In recent years, peptoids have attracted attention as new potential antibiotics against multiresistant bacteria. Here we describe the submonomer solid-phase synthesis of an antimicrobial peptoid, H-Nmbn-Nlys-Nlys-Nnap-Nbut-Nmbn-Nlys-NH2.
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Affiliation(s)
- Paul R Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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72
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Secondary structure, a missing component of sequence-based minimotif definitions. PLoS One 2012; 7:e49957. [PMID: 23236358 PMCID: PMC3517595 DOI: 10.1371/journal.pone.0049957] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 10/15/2012] [Indexed: 12/27/2022] Open
Abstract
Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis of occurrences of minimotifs in structured and disordered regions of proteins, and review of the literature support a new model for minimotif definitions that includes sequence, structure, and function.
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73
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Zhang J, Fan J, Tian Q, Song Z, Zhang JF, Chen Y. Characterization of two distinct modes of endophilin in clathrin-mediated endocytosis. Cell Signal 2012; 24:2043-50. [DOI: 10.1016/j.cellsig.2012.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 05/24/2012] [Accepted: 06/16/2012] [Indexed: 10/28/2022]
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74
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Olsen CA, Montero A, Leman LJ, Ghadiri MR. Macrocyclic peptoid-Peptide hybrids as inhibitors of class I histone deacetylases. ACS Med Chem Lett 2012; 3:749-53. [PMID: 24900543 DOI: 10.1021/ml300162r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 08/07/2012] [Indexed: 01/04/2023] Open
Abstract
We report the design, synthesis, and biological evaluation of the first macrocyclic peptoid-containing histone deacetylase (HDAC) inhibitors. The compounds selectively inhibit human class I HDAC isoforms in vitro, with no inhibition of the tubulin deacetylase activity associated with class IIb HDAC6 in cultured Jurkat cells. Compared to the natural product apicidin (1), one inhibitor (compound 10) showed equivalent potency against K-562 cells, but was more cytoselective across a panel of cancer cell lines.
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Affiliation(s)
- Christian A. Olsen
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - Ana Montero
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - Luke J. Leman
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - M. Reza Ghadiri
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
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75
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SH3 domains: modules of protein-protein interactions. Biophys Rev 2012; 5:29-39. [PMID: 28510178 DOI: 10.1007/s12551-012-0081-z] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/29/2012] [Indexed: 01/01/2023] Open
Abstract
Src homology 3 (SH3) domains are involved in the regulation of important cellular pathways, such as cell proliferation, migration and cytoskeletal modifications. Recognition of polyproline and a number of noncanonical sequences by SH3 domains has been extensively studied by crystallography, nuclear magnetic resonance and other methods. High-affinity peptides that bind SH3 domains are used in drug development as candidates for anticancer treatment. This review summarizes the latest achievements in deciphering structural determinants of SH3 function.
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76
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Liu F, Park JE, Qian WJ, Lim D, Scharow A, Berg T, Yaffe MB, Lee KS, Burke TR. Peptoid-Peptide hybrid ligands targeting the polo box domain of polo-like kinase 1. Chembiochem 2012; 13:1291-6. [PMID: 22570300 PMCID: PMC4536914 DOI: 10.1002/cbic.201200206] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Indexed: 11/10/2022]
Abstract
We replaced the amino terminal Pro residue of the Plk1 polo-box-domain-binding pentapeptide (PLHSpT) with a library of N-alkyl-Gly "peptoids", and identified long-chain tethered phenyl moieties giving greater than two-orders-of-magnitude affinity enhancement. Further simplification by replacing the peptoid residue with appropriate amides gave low-nanomolar affinity N-acylated tetrapeptides. Binding of the N-terminal long-chain phenyl extension was demonstrated by X-ray co-crystal data.
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Affiliation(s)
- Fa Liu
- Chemical Biology Laboratory, Frederick National Lab, NCI, NIH, Frederick, MD 21702 (USA), Fax: (+1) 301-846-6033
| | - Jung-Eun Park
- Laboratory of Metabolism, National Cancer Institute, NIH, Bethesda, MD 20892 (USA)
| | - Wen-Jian Qian
- Chemical Biology Laboratory, Frederick National Lab, NCI, NIH, Frederick, MD 21702 (USA), Fax: (+1) 301-846-6033
| | - Dan Lim
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (USA)
| | - Andrej Scharow
- Institute of Organic Chemistry, University of Leipzig, 04103 Leipzig (Germany)
| | - Thorsten Berg
- Institute of Organic Chemistry, University of Leipzig, 04103 Leipzig (Germany)
| | - Michael B. Yaffe
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (USA)
| | - Kyung S. Lee
- Laboratory of Metabolism, National Cancer Institute, NIH, Bethesda, MD 20892 (USA)
| | - Terrence R. Burke
- Chemical Biology Laboratory, Frederick National Lab, NCI, NIH, Frederick, MD 21702 (USA), Fax: (+1) 301-846-6033
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77
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Interfacial water molecules in SH3 interactions: Getting the full picture on polyproline recognition by protein-protein interaction domains. FEBS Lett 2012; 586:2619-30. [DOI: 10.1016/j.febslet.2012.04.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/27/2012] [Accepted: 04/30/2012] [Indexed: 01/16/2023]
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78
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Antony J, Grimme S. Fully ab initio protein-ligand interaction energies with dispersion corrected density functional theory. J Comput Chem 2012; 33:1730-9. [PMID: 22570225 DOI: 10.1002/jcc.23004] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/10/2012] [Accepted: 04/11/2012] [Indexed: 01/31/2023]
Abstract
Dispersion corrected density functional theory (DFT-D3) is used for fully ab initio protein-ligand (PL) interaction energy calculation via molecular fractionation with conjugated caps (MFCC) and applied to PL complexes from the PDB comprising 3680, 1798, and 1060 atoms. Molecular fragments with n amino acids instead of one in the original MFCC approach are considered, thereby allowing for estimating the three-body and higher many-body terms. n > 1 is recommended both in terms of accuracy and efficiency of MFCC. For neutral protein side-chains, the computed PL interaction energy is visibly independent of the fragment length n. The MFCC fractionation error is determined by comparison to a full-system calculation for the 1060 atoms containing PL complex. For charged amino acid side-chains, the variation of the MFCC result with n is increased. For these systems, using a continuum solvation model with a dielectricity constant typical for protein environments (ϵ = 4) reduces both the variation with n and improves the stability of the DFT calculations considerably. The PL interaction energies for two typical complexes obtained ab initio for the first time are found to be rather large (-30 and -54 kcal/mol).
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Affiliation(s)
- Jens Antony
- Universität Münster, Organisch-Chemisches Institut, Germany
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79
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Abstract
Peptoid oligomers were initially developed as part of a larger basic research effort to accelerate the drug-discovery process in the biotech/biopharma industry. Their ease of synthesis, stability, and structural similarity to polypeptides made them ideal candidates for the combinatorial discovery of novel peptidomimetic drug candidates. Diverse libraries of short peptoid oligomers provided one of the first demonstrations in the mid-1990s that high-affinity ligands to pharmaceutically relevant receptors could be discovered from combinatorial libraries of synthetic compounds. The solid-phase submonomer method of peptoid synthesis was so efficient and general that it soon became possible to explore the properties of longer polypeptoid chains in a variety of areas beyond drug discovery (e.g., diagnostics, drug delivery, and materials science). Exploration into protein-mimetic materials soon followed, with the fundamental goal of folding a non-natural sequence-specific heteropolymer into defined secondary or tertiary structures. This effort first yielded the peptoid helix and much later the peptoid sheet, both of which are secondary-structure mimetics that are close relatives to their natural counterparts. These crucial discoveries have brought us closer to building proteinlike structure and function from a non-natural polymer and have provided great insight into the rules governing polymer and protein folding. The accessibility of peptoid synthesis to chemists and nonchemists alike, along with a lack of information-rich non-natural polymers available to study, has led to a rapid growth in the field of peptoid science by many new investigators. This work provides an overview of the initial discovery and early developments in the peptoid field.
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Affiliation(s)
- Ronald N Zuckermann
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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80
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Balakrishnan S, Scheuermann MJ, Zondlo NJ. Arginine mimetics using α-guanidino acids: introduction of functional groups and stereochemistry adjacent to recognition guanidiniums in peptides. Chembiochem 2012; 13:259-70. [PMID: 22213184 PMCID: PMC3712784 DOI: 10.1002/cbic.201100638] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Indexed: 01/19/2023]
Abstract
Arginine residues are broadly employed for specific biomolecular recognition, including in protein-protein, protein-DNA, and protein-RNA interactions. Arginine recognition commonly exploits the potential for bidentate electrostatic and hydrogen-bonding interactions. However, in arginine residues, the guanidinium functional group is located at the terminus of a flexible hydrocarbon side chain, which lacks the functionality to contribute to specific arginine-mediated recognition and may entropically disfavor binding. In order to enhance the potential for specificity and affinity in arginine-mediated molecular recognition, we have developed an approach to the synthesis of peptides that incorporates an α-guanidino acid as a novel arginine mimetic. α-Guanidino acids, derived from α-amino acids, with guanidinylation of the amino group, were incorporated stereospecifically into peptides on solid phase via coupling of an Fmoc amino acid to diaminopropionic acid (Dap), Fmoc deprotection, guanidinylation of the amine on solid phase, and deprotection, generating a peptide containing an α-functionalized arginine mimetic. This approach was examined by incorporating arginine mimetics into ligands for the Src, Grb, and Crk SH3 domains at the site of the key recognition arginine. Protein binding was examined for peptides containing guanidino acids derived from Gly, L-Val, L-Phe, L-Trp, D-Val, D-Phe, and D-Trp. We demonstrate that paralogue specificity and target site affinity may be modulated with the use of α-guanidino acid-derived arginine mimetics, generating peptides that exhibit enhanced Src specificity by selection against Grb and peptides that reverse the specificity of the native peptide ligand, with enhancements in Src target specificity of up to 15-fold (1.6 kcal mol(-1)).
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Affiliation(s)
- Shalini Balakrishnan
- Department of Chemistry and Biochemistry University of Delaware Newark, Delaware 19716 (USA)
| | - Michael J. Scheuermann
- Department of Chemistry and Biochemistry University of Delaware Newark, Delaware 19716 (USA)
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry University of Delaware Newark, Delaware 19716 (USA)
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81
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Suppiah S, Mousa HA, Tzeng WP, Matthews JD, Frey TK. Binding of cellular p32 protein to the rubella virus P150 replicase protein via PxxPxR motifs. J Gen Virol 2012; 93:807-816. [PMID: 22238231 DOI: 10.1099/vir.0.038901-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A proline-rich region (PRR) within the rubella virus (RUBV) P150 replicase protein that contains three SH3 domain-binding motifs (PxxPxR) was investigated for its ability to bind cell proteins. Pull-down experiments using a glutathione S-transferase-PRR fusion revealed PxxPxR motif-specific binding with human p32 protein (gC1qR), which could be mediated by either of the first two motifs. This finding was of interest because p32 protein also binds to the RUBV capsid protein. Binding of p32 to P150 was confirmed and was abolished by mutation of the first two motifs. When mutations in the first two motifs were introduced into a RUBV cDNA infectious clone, virus replication was significantly impaired. However, virus RNA synthesis was found to be unaffected, and subsequent immunofluorescence analysis of RUBV-infected cells revealed co-localization of p32 and P150 but little overlap of p32 with RNA replication complexes, indicating that p32 does not participate directly in virus RNA synthesis. Thus, the role of p32 in RUBV replication remains unresolved.
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Affiliation(s)
- Suganthi Suppiah
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Heather A Mousa
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Wen-Pin Tzeng
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Jason D Matthews
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Teryl K Frey
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
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82
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Millward SW, Henning RK, Kwong GA, Pitram S, Agnew HD, Deyle KM, Nag A, Hein J, Lee SS, Lim J, Pfeilsticker JA, Sharpless KB, Heath JR. Iterative in situ click chemistry assembles a branched capture agent and allosteric inhibitor for Akt1. J Am Chem Soc 2011; 133:18280-8. [PMID: 21962254 DOI: 10.1021/ja2064389] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We describe the use of iterative in situ click chemistry to design an Akt-specific branched peptide triligand that is a drop-in replacement for monoclonal antibodies in multiple biochemical assays. Each peptide module in the branched structure makes unique contributions to affinity and/or specificity resulting in a 200 nM affinity ligand that efficiently immunoprecipitates Akt from cancer cell lysates and labels Akt in fixed cells. Our use of a small molecule to preinhibit Akt prior to screening resulted in low micromolar inhibitory potency and an allosteric mode of inhibition, which is evidenced through a series of competitive enzyme kinetic assays. To demonstrate the efficiency and selectivity of the protein-templated in situ click reaction, we developed a novel QPCR-based methodology that enabled a quantitative assessment of its yield. These results point to the potential for iterative in situ click chemistry to generate potent, synthetically accessible antibody replacements with novel inhibitory properties.
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Affiliation(s)
- Steven W Millward
- Nanosystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, MC-127-72, California Institute of Technology, Pasadena, California 91125, United States
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83
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The C2 domain protein Cts1 functions in the calcineurin signaling circuit during high-temperature stress responses in Cryptococcus neoformans. EUKARYOTIC CELL 2011; 10:1714-23. [PMID: 22002655 DOI: 10.1128/ec.05148-11] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Calcineurin is a conserved calcium/calmodulin-dependent serine/threonine-specific protein phosphatase that acts in cell stress responses. Calcineurin is essential for growth at 37°C and for virulence of the human fungal pathogen Cryptococcus neoformans, but its substrates remain unknown. The C2 domain-containing, phospholipid-binding protein Cts1 was previously identified as a multicopy suppressor of a calcineurin mutation in C. neoformans. Here we further characterize the function of Cts1 and the links between Cts1 and calcineurin. GFP-Cts1 localizes to cytoplasmic puncta and colocalizes with the endosomal marker FM4-64. The cts1Δ mutant shows a distinct FM4-64 staining pattern, suggesting involvement of Cts1 in endocytic trafficking. In large budded cells, GFP-Cts1 localizes transiently at the mother bud neck, as a single ring that undergoes contraction. mCherry-Cts1 colocalizes with the GFP-tagged calcineurin catalytic subunit Cna1 at sites of mRNA processing at 37°C, suggesting that Cts1 and calcineurin function coordinately during thermal stress. GFP-Cts1 exhibits slower electrophoretic mobility for cells grown at 37°C than for cells grown at 24°C, and the shift to a higher molecular weight is more pronounced in the presence of the calcineurin inhibitor FK506. In vitro treatment with calf intestinal alkaline phosphatase (CIP) restores faster electrophoretic mobility to GFP-Cts1, suggesting that Cts1 is phosphorylated at 37°C and may be dephosphorylated in a calcineurin-dependent manner. mCherry-Cts1 also coimmunoprecipitates with GFP-Cna1, with greater complex formation at 37°C than at 24°C. Taken together, these findings support potential roles for Cts1 in endocytic trafficking, mRNA processing, and cytokinesis and suggest that Cts1 is a substrate of calcineurin during high-temperature stress responses.
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84
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Leithe E, Sirnes S, Fykerud T, Kjenseth A, Rivedal E. Endocytosis and post-endocytic sorting of connexins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1870-9. [PMID: 21996040 DOI: 10.1016/j.bbamem.2011.09.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 09/19/2011] [Accepted: 09/28/2011] [Indexed: 12/15/2022]
Abstract
The connexins constitute a family of integral membrane proteins that form intercellular channels, enabling adjacent cells in solid tissues to directly exchange ions and small molecules. These channels assemble into distinct plasma membrane domains known as gap junctions. Gap junction intercellular communication plays critical roles in numerous cellular processes, including control of cell growth and differentiation, maintenance of tissue homeostasis and embryonic development. Gap junctions are dynamic plasma membrane domains, and there is increasing evidence that modulation of endocytosis and post-endocytic trafficking of connexins are important mechanisms for regulating the level of functional gap junctions at the plasma membrane. The emerging picture is that multiple pathways exist for endocytosis and sorting of connexins to lysosomes, and that these pathways are differentially regulated in response to physiological and pathophysiological stimuli. Recent studies suggest that endocytosis and lysosomal degradation of connexins is controlled by a complex interplay between phosphorylation and ubiquitination. This review summarizes recent progress in understanding the molecular mechanisms involved in endocytosis and post-endocytic sorting of connexins, and the relevance of these processes to the regulation of gap junction intercellular communication under normal and pathophysiological conditions. This article is part of a Special Issue entitled: The Communicating junctions, composition, structure and characteristics.
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Affiliation(s)
- Edward Leithe
- Department of Cancer Prevention, Oslo University Hospital, Oslo, Norway
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85
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Huang ML, Shin SBY, Benson MA, Torres VJ, Kirshenbaum K. A Comparison of Linear and Cyclic Peptoid Oligomers as Potent Antimicrobial Agents. ChemMedChem 2011; 7:114-22. [DOI: 10.1002/cmdc.201100358] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 09/08/2011] [Indexed: 01/02/2023]
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86
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Simister PC, Feller SM. Order and disorder in large multi-site docking proteins of the Gab family--implications for signalling complex formation and inhibitor design strategies. MOLECULAR BIOSYSTEMS 2011; 8:33-46. [PMID: 21935523 DOI: 10.1039/c1mb05272a] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Large multi-site docking (LMD) proteins of the Gab, IRS, FRS, DOK and Cas families consist of one or two folded N-terminal domains, followed by a predominantly disordered C-terminal extension. Their primary function is to provide a docking platform for signalling molecules (including PI3K, PLC, Grb2, Crk, RasGAP, SHP2) in intracellular signal transmission from activated cell-surface receptors, to which they become coupled. A detailed analysis of the structural nature and intrinsic disorder propensity of LMD proteins, with Gab proteins as specific examples, is presented. By primary sequence analysis and literature review the varying levels of disorder and hidden order are predicted, revealing properties and a physical architecture that help to explain their biological function and characteristics, common for network hub proteins. The virulence factor, CagA, from Helicobacter pylori is able to mimic Gab function once injected by this human pathogen into stomach epithelial cells. Its predicted differential structure is compared to Gab1 with respect to its functional mimicry. Lastly, we discuss how LMD proteins, in particular Gab1 and Gab2, and their protein partners, such as SH2 and SH3 domain-containing adaptors like Grb2, might qualify for future anti-cancer strategies in developing protein-protein interaction (PPI) inhibitors towards binary interactors consisting of an intrinsically disordered epitope and a structured domain surface.
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Affiliation(s)
- Philip C Simister
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
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87
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Liu R, Jiang B, Yu H, Chaput JC. Generating DNA synbodies from previously discovered peptides. Chembiochem 2011; 12:1813-7. [PMID: 21692159 PMCID: PMC3390916 DOI: 10.1002/cbic.201100284] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Indexed: 12/31/2022]
Affiliation(s)
- Rui Liu
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5301, Fax: (+1) (480) 727-6947
| | - Bing Jiang
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5301, Fax: (+1) (480) 727-6947
| | - Hanyang Yu
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5301, Fax: (+1) (480) 727-6947
| | - John C. Chaput
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5301, Fax: (+1) (480) 727-6947
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88
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Liskamp RMJ, Rijkers DTS, Kruijtzer JAW, Kemmink J. Peptides and proteins as a continuing exciting source of inspiration for peptidomimetics. Chembiochem 2011; 12:1626-53. [PMID: 21751324 DOI: 10.1002/cbic.201000717] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Indexed: 12/17/2022]
Abstract
Despite their enormous diversity in biological function and structure, peptides and proteins are endowed with properties that have induced and stimulated the development of peptidomimetics. Clearly, peptides can be considered as the "stem" of a phylogenetic molecular development tree from which branches of oligomeric peptidomimetics such as peptoids, peptidosulfonamides, urea peptidomimetics, as well as β-peptides have sprouted. It is still a challenge to efficiently synthesize these oligomeric species, and study their structural and biological properties. Combining peptides and peptidomimetics led to the emergence of peptide-peptidomimetic hybrids in which one or more (proteinogenic) amino acid residues have been replaced with these mimetic residues. In scan-like approaches, the influence of these replacements on biological activity can then be studied, to evaluate to what extent a peptide can be transformed into a peptidomimetic structure while maintaining, or even improving, its biological properties. A central issue, especially with the smaller peptides, is the lack of secondary structure. Important approaches to control secondary structure include the introduction of α,α-disubstituted amino acids, or (di)peptidomimetic structures such as the Freidinger lactam. Apart from intra-amino acid constraints, inter-amino acid constraints for formation of a diversity of cyclic peptides have shaped a thick branch. Apart from the classical disulfide bridges, the repertoire has been extended to include sulfide and triazole bridges as well as the single-, double- and even triple-bond replacements, accessible by the extremely versatile ring-closing alkene/alkyne metathesis approaches. The latter approach is now the method of choice for the secondary structure that presents the greatest challenge for structural stabilization: the α-helix.
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Affiliation(s)
- Rob M J Liskamp
- Medicinal Chemistry and Chemical Biology, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands.
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89
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Kim SE, Liu F, Im YJ, Stephen AG, Fivash MJ, Waheed AA, Freed EO, Fisher RJ, Hurley JH, Burke TR. Elucidation of New Binding Interactions with the Tumor Susceptibility Gene 101 (Tsg101) Protein Using Modified HIV-1 Gag-p6 Derived Peptide Ligands. ACS Med Chem Lett 2011; 2:337-341. [PMID: 21643473 DOI: 10.1021/ml1002579] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Targeting protein-protein interactions is gaining greater recognition as an attractive approach to therapeutic development. An example of this may be found with the human cellular protein encoded by the tumor susceptibility gene 101 (Tsg101), where interaction with the p6 C-terminal domain of the nascent viral Gag protein is required for HIV-1 particle budding and release. This association of Gag with Tsg101 is highly dependent on a "Pro-Thr-Ala-Pro" ("PTAP") peptide sequence within the p6 protein. Although p6-derived peptides offer potential starting points for developing Tsg101-binding inhibitors, the affinities of canonical peptides are outside the useful range (K(d) values greater than 50 μM). Reported herein are crystal structures of Tsg101 in complex with two structurally-modified PTAP-derived peptides. This data define new regions of ligand interaction not previously identified with canonical peptide sequences. This information could be highly useful in the design of Tsg101-binding antagonists.
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Affiliation(s)
- Sung-Eun Kim
- Chemical Biology Laboratory, Molecular, Discovery Program, CCR, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Fa Liu
- Chemical Biology Laboratory, Molecular, Discovery Program, CCR, NCI-Frederick, Frederick, Maryland 21702, United States
| | | | | | - Matthew J. Fivash
- Data Management Systems, Inc., NCI-Frederick, Frederick, Maryland 21702, United States
| | - Abdul A. Waheed
- HIV Drug Resistance Program, CCR, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Eric O. Freed
- HIV Drug Resistance Program, CCR, NCI-Frederick, Frederick, Maryland 21702, United States
| | | | | | - Terrence R. Burke
- Chemical Biology Laboratory, Molecular, Discovery Program, CCR, NCI-Frederick, Frederick, Maryland 21702, United States
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90
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Horenkamp FA, Breuer S, Schulte A, Lülf S, Weyand M, Saksela K, Geyer M. Conformation of the dileucine-based sorting motif in HIV-1 Nef revealed by intermolecular domain assembly. Traffic 2011; 12:867-77. [PMID: 21477083 DOI: 10.1111/j.1600-0854.2011.01205.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The human immunodeficiency virus 1 (HIV-1) Nef protein is a pathogenicity factor required for effective progression to AIDS, which modulates host cell signaling pathways and T-cell receptor internalization. We have determined the crystal structure of Nef, allele SF2, in complex with an engineered SH3 domain of human Hck showing unnaturally tight binding and inhibitory potential toward Nef. This complex provides the most complete Nef structure described today, and explains the structural basis of the high affinity of this interaction. Intriguingly, the 33-residue C-terminal flexible loop is resolved in the structure by its interactions with a highly conserved hydrophobic groove on the core domain of an adjacent Nef molecule. The loop mediates the interaction of Nef with the cellular adaptor protein machinery for the stimulated internalization of surface receptors. The endocytic dileucine-based sorting motif is exposed at the tip of the acidic loop, giving the myristoylated Nef protein a distinctly dipolar character. The intermolecular domain assembly of Nef provides insights into a possible regulation mechanism for cargo trafficking.
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Affiliation(s)
- Florian A Horenkamp
- Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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91
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Yam AY, Wang X, Gao CM, Connolly MD, Zuckermann RN, Bleu T, Hall J, Fedynyshyn JP, Allauzen S, Peretz D, Salisbury CM. A Universal Method for Detection of Amyloidogenic Misfolded Proteins. Biochemistry 2011; 50:4322-9. [DOI: 10.1021/bi200215j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alice Y. Yam
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Xuemei Wang
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Carol Man Gao
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Michael D. Connolly
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Ronald N. Zuckermann
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Thieu Bleu
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - John Hall
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Joseph P. Fedynyshyn
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Sophie Allauzen
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - David Peretz
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
| | - Cleo M. Salisbury
- Novartis Vaccines and Diagnostics, Inc., 4560 Horton St, Emeryville, California 94608, United States
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92
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Zheng CY, Seabold GK, Horak M, Petralia RS. MAGUKs, synaptic development, and synaptic plasticity. Neuroscientist 2011; 17:493-512. [PMID: 21498811 DOI: 10.1177/1073858410386384] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
MAGUKs are proteins that act as key scaffolds in surface complexes containing receptors, adhesion proteins, and various signaling molecules. These complexes evolved prior to the appearance of multicellular animals and play key roles in cell-cell intercommunication. A major example of this is the neuronal synapse, which contains several presynaptic and postsynaptic MAGUKs including PSD-95, SAP102, SAP97, PSD-93, CASK, and MAGIs. Here, they play roles in both synaptic development and in later synaptic plasticity events. During development, MAGUKs help to organize the postsynaptic density via associations with other scaffolding proteins, such as Shank, and the actin cytoskeleton. They affect the clustering of glutamate receptors and other receptors, and these associations change with development. MAGUKs are involved in long-term potentiation and depression (e.g., via their phosphorylation by kinases and phosphorylation of other proteins associated with MAGUKs). Importantly, synapse development and function are dependent on the kind of MAGUK present. For example, SAP102 shows high mobility and is present in early synaptic development. Later, much of SAP102 is replaced by PSD-95, a more stable synaptic MAGUK; this is associated with changes in glutamate receptor types that are characteristic of synaptic maturation.
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Affiliation(s)
- Chan-Ying Zheng
- National Institute on Deafness and Other Communication Disorders/National Institutes of Health, Bethesda, MD 20892-8027, USA
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93
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Park M, Jardetzky TS, Barron AE. NMEGylation: A novel modification to enhance the bioavailability of therapeutic peptides. Biopolymers 2011; 96:688-93. [DOI: 10.1002/bip.21607] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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94
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Kondo T, Yokomine K, Nakagawa A, Sakagami Y. Analogs of the CLV3 peptide: synthesis and structure-activity relationships focused on proline residues. PLANT & CELL PHYSIOLOGY 2011; 52:30-6. [PMID: 20926417 PMCID: PMC3023850 DOI: 10.1093/pcp/pcq146] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
CLAVATA3 (CLV3) is a plant peptide hormone in which the proline residues are post-translationally hydroxylated and glycosylated. CLV3 plays a key role in controlling the stem cell mass in the shoot meristem of Arabidopsis thaliana. In a previous report, we identified a dodecapeptide (MCLV3) from CLV3-overexpressing Arabidopsis calli; MCLV3 was the smallest functional peptide derived from the CLV3 precursor. Here, we designed a series of MCLV3 analogs in which proline residues were substituted with proline derivatives or N-substituted glycines (peptoids). Peptoid substitution at Pro9 decreased bioactivity without affecting specific binding to the CLV1-related protein in cauliflower membrane. These findings suggest that peptoid-substituted peptides would be lead compounds for developing potential agonists and antagonists of CLV3.
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Affiliation(s)
- Tatsuhiko Kondo
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
- These authors contributed equally to this work
| | - Kenjiro Yokomine
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
- These authors contributed equally to this work
| | - Aya Nakagawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
| | - Youji Sakagami
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
- *Corresponding author: E-mail, ; Fax, +81-52-789-4118
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95
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Recognition of tandem PxxP motifs as a unique Src homology 3-binding mode triggers pathogen-driven actin assembly. Proc Natl Acad Sci U S A 2010; 107:21743-8. [PMID: 21098279 DOI: 10.1073/pnas.1010243107] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Src homology 3 (SH3) domains are globular protein interaction modules that regulate cell behavior. The classic SH3 ligand-binding site accommodates a hydrophobic PxxP motif and a positively charged specificity-determining residue. We have determined the NMR structure of insulin receptor tyrosine kinase substrate (IRTKS) SH3 domain in complex with a repeat from Escherichia coli-secreted protein F-like protein encoded on prophage U (EspF(U)), a translocated effector of enterohemorrhagic E. coli that commandeers the mammalian actin assembly machinery. EspF(U)-IRTKS interaction is among the highest affinity natural SH3 ligands. Our complex structure reveals a unique type of SH3 interaction based on recognition of tandem PxxP motifs in the ligand. Strikingly, the specificity pocket of IRTKS SH3 has evolved to accommodate a polyproline type II helical peptide analogously to docking of the canonical PxxP by the conserved IRTKS SH3 proline-binding pockets. This cooperative binding explains the high-affinity SH3 interaction and is required for EspF(U)-IRTKS interaction in mammalian cells as well as the formation of localized actin "pedestals" beneath bound bacteria. Importantly, tandem PxxP motifs are also found in mammalian ligands and have been shown to contribute to IRTKS SH3 recognition similarly.
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96
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Hong S, Chung T, Kim D. SH3 domain-peptide binding energy calculations based on structural ensemble and multiple peptide templates. PLoS One 2010; 5:e12654. [PMID: 20856816 PMCID: PMC2939891 DOI: 10.1371/journal.pone.0012654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 08/16/2010] [Indexed: 11/26/2022] Open
Abstract
SH3 domains mediate signal transduction by recognizing short peptides. Understanding of the driving forces in peptide recognitions will help us to predict the binding specificity of the domain-peptide recognition and to understand the molecular interaction networks of cells. However, accurate calculation of the binding energy is a tough challenge. In this study, we propose three ideas for improving our ability to predict the binding energy between SH3 domains and peptides: (1) utilizing the structural ensembles sampled from a molecular dynamics simulation trajectory, (2) utilizing multiple peptide templates, and (3) optimizing the sequence-structure mapping. We tested these three ideas on ten previously studied SH3 domains for which SPOT analysis data were available. The results indicate that calculating binding energy using the structural ensemble was most effective, clearly increasing the prediction accuracy, while the second and third ideas tended to give better binding energy predictions. We applied our method to the five SH3 targets in DREAM4 Challenge and selected the best performing method.
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Affiliation(s)
- Seungpyo Hong
- Department of Bio and Brain Engineering, KAIST, Daejeon, South Korea
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97
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Alvarez JL, Petzhold D, Pankonien I, Behlke J, Kouno M, Vassort G, Morano I, Haase H. Ahnak1 modulates L-type Ca2+ channel inactivation of rodent cardiomyocytes. Pflugers Arch 2010; 460:719-30. [DOI: 10.1007/s00424-010-0853-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/28/2010] [Accepted: 06/02/2010] [Indexed: 01/21/2023]
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98
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Abstract
Peptidomimetic oligomers and foldamers have received considerable attention for over a decade, with beta-peptides and the so-called peptoids (N-alkylglycine oligomers) representing prominent examples of such architectures. Lately, hybrid or mixed backbones consisting of both alpha- and beta-amino acids (alpha/beta-peptides) have been investigated in some detail as well. The present Minireview is a survey of the literature concerning hybrid structures of alpha-amino acids and peptoids, including beta-peptoids (N-alkyl-beta-alanine oligomers), and is intended to give an overview of this area of research within the field of peptidomimetic science.
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Affiliation(s)
- Christian A Olsen
- Department of Medicinal Chemistry, University of Copenhagen, Universitetsparken 2, Copenhagen, 2100 Denmark.
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99
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Havrylov S, Redowicz MJ, Buchman VL. Emerging roles of Ruk/CIN85 in vesicle-mediated transport, adhesion, migration and malignancy. Traffic 2010; 11:721-31. [PMID: 20331533 DOI: 10.1111/j.1600-0854.2010.01061.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Ruk/CIN85 is an adaptor protein. Similar to many other proteins of this type, Ruk/CIN85 is known to take part in multiple cellular processes including signal transduction, vesicle-mediated transport, cytoskeleton remodelling, programmed cell death and viral infection. Recent studies have also revealed the potential importance of Ruk/CIN85 in cancer cell invasiveness. In this review we summarize the various roles of this protein as well as the potential contribution of Ruk/CIN85 to malignancy and the invasiveness of cancer cells. In the last section of the paper we also speculate on the utility of Ruk/CIN85 as a target for novel anti-cancer therapies.
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Affiliation(s)
- Serhiy Havrylov
- Nencki Institute of Experimental Biology, Pasteura 3 Street, 02-093 Warsaw, Poland
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100
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Seo J, Michaelian N, Owens SC, Dashner ST, Wong AJ, Barron AE, Carrasco MR. Chemoselective and microwave-assisted synthesis of glycopeptoids. Org Lett 2010; 11:5210-3. [PMID: 19905028 DOI: 10.1021/ol9021468] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemoselective glycosylation of N-alkylaminooxy side chains with unprotected reducing sugars has proven useful for the synthesis of glycopeptides. Herein, we extend the N-alkylaminooxy strategy to the synthesis of glycopeptoids. A N-methylaminooxy submonomer was efficiently synthesized and incorporated into peptoids. Glycosylation of the peptoids proceeded chemoselectively and site-specifically at the N-methylaminooxy moieties. Employing microwave irradiation significantly increased the degree of glycosylation and shortened the reaction times.
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Affiliation(s)
- Jiwon Seo
- Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, California 94305-5440, USA
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