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Leth JM, Newcombe EA, Grønnemose AL, Jørgensen JT, Qvist K, Clausen AS, Knudsen LBS, Kjaer A, Kragelund BB, Jørgensen TJD, Ploug M. Targeted imaging of uPAR expression in vivo with cyclic AE105 variants. Sci Rep 2023; 13:17248. [PMID: 37821532 PMCID: PMC10567728 DOI: 10.1038/s41598-023-43934-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/30/2023] [Indexed: 10/13/2023] Open
Abstract
A comprehensive literature reports on the correlation between elevated levels of urokinase-type plasminogen activator receptor (uPAR) and the severity of diseases with chronic inflammation including solid cancers. Molecular imaging is widely used as a non-invasive method to locate disease dissemination via full body scans and to stratify patients for targeted treatment. To date, the only imaging probe targeting uPAR that has reached clinical phase-II testing relies on a high-affinity 9-mer peptide (AE105), and several studies by positron emission tomography (PET) scanning or near-infra red (NIR) fluorescence imaging have validated its utility and specificity in vivo. While our previous studies focused on applying various reporter groups, the current study aims to improve uPAR-targeting properties of AE105. We successfully stabilized the small uPAR-targeting core of AE105 by constraining its conformational landscape by disulfide-mediated cyclization. Importantly, this modification mitigated the penalty on uPAR-affinity typically observed after conjugation to macrocyclic chelators. Cyclization did not impair tumor targeting efficiency of AE105 in vivo as assessed by PET imaging and a trend towards increased tracer uptake was observed. In future studies, we predict that this knowledge will aid development of new fluorescent AE105 derivatives with a view to optical imaging of uPAR to assist precision guided cancer surgery.
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Affiliation(s)
- Julie Maja Leth
- Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, 2200, Copenhagen N, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Estella Anne Newcombe
- Structural Biology and NMR Laboratory, Copenhagen N, Denmark
- REPIN, Copenhagen N, Denmark
- The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Anne Louise Grønnemose
- Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, 2200, Copenhagen N, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen N, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Jesper Tranekjær Jørgensen
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Katrine Qvist
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Anne Skovsbo Clausen
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Line Bruhn Schneider Knudsen
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Andreas Kjaer
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Birthe Brandt Kragelund
- Structural Biology and NMR Laboratory, Copenhagen N, Denmark
- REPIN, Copenhagen N, Denmark
- The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | | | - Michael Ploug
- Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, 2200, Copenhagen N, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen N, Denmark.
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2
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Agrahari A, Lipton M, Chmielewski J. Metal-Promoted Higher-Order Assembly of Disulfide-Stapled Helical Barrels. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2645. [PMID: 37836285 PMCID: PMC10574645 DOI: 10.3390/nano13192645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
Peptide-based helical barrels are a noteworthy building block for hierarchical assembly, with a hydrophobic cavity that can serve as a host for cargo. In this study, disulfide-stapled helical barrels were synthesized containing ligands for metal ions on the hydrophilic face of each amphiphilic peptide helix. The major product of the disulfide-stapling reaction was found to be composed of five amphiphilic peptides, thereby going from a 16-amino-acid peptide to a stapled 80-residue protein in one step. The structure of this pentamer, 5HB1, was optimized in silico, indicating a significant hydrophobic cavity of ~6 Å within a helical barrel. Metal-ion-promoted assembly of the helical barrel building blocks generated higher order assemblies with a three-dimensional (3D) matrix morphology. The matrix was decorated with hydrophobic dyes and His-tagged proteins both before and after assembly, taking advantage of the hydrophobic pocket within the helical barrels and coordination sites within the metal ion-peptide framework. As such, this peptide-based biomaterial has potential for a number of biotechnology applications, including supplying small molecule and protein growth factors during cell and tissue growth within the matrix.
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Affiliation(s)
| | - Mark Lipton
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA;
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA;
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3
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Iyer A, Sidhu A, Subramaniam V. How important is the N-terminal acetylation of alpha-synuclein for its function and aggregation into amyloids? Front Neurosci 2022; 16:1003997. [PMID: 36466161 PMCID: PMC9709446 DOI: 10.3389/fnins.2022.1003997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/26/2022] [Indexed: 08/27/2023] Open
Abstract
N-α-acetylation is a frequently occurring post-translational modification in eukaryotic proteins. It has manifold physiological consequences on the regulation and function of several proteins, with emerging studies suggesting that it is a global regulator of stress responses. For decades, in vitro biochemical investigations into the precise role of the intrinsically disordered protein alpha-synuclein (αS) in the etiology of Parkinson's disease (PD) were performed using non-acetylated αS. The N-terminus of α-synuclein is now unequivocally known to be acetylated in vivo, however, there are many aspects of this post-translational modifications that are not understood well. Is N-α-acetylation of αS a constitutive modification akin to most cellular proteins, or is it spatio-temporally regulated? Is N-α-acetylation of αS relevant to the as yet elusive function of αS? How does the N-α-acetylation of αS influence the aggregation of αS into amyloids? Here, we provide an overview of the current knowledge and discuss prevailing hypotheses on the impact of N-α-acetylation of αS on its conformational, oligomeric, and fibrillar states. The extent to which N-α-acetylation of αS is vital for its function, membrane binding, and aggregation into amyloids is also explored here. We further discuss the overall significance of N-α-acetylation of αS for its functional and pathogenic implications in Lewy body formation and synucleinopathies.
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Affiliation(s)
- Aditya Iyer
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Arshdeep Sidhu
- Nitte University Centre for Science Education and Research, Nitte University (DU), Mangalore, India
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4
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Cardoso P, Glossop H, Meikle TG, Aburto-Medina A, Conn CE, Sarojini V, Valery C. Molecular engineering of antimicrobial peptides: microbial targets, peptide motifs and translation opportunities. Biophys Rev 2021; 13:35-69. [PMID: 33495702 PMCID: PMC7817352 DOI: 10.1007/s12551-021-00784-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
The global public health threat of antimicrobial resistance has led the scientific community to highly engage into research on alternative strategies to the traditional small molecule therapeutics. Here, we review one of the most popular alternatives amongst basic and applied research scientists, synthetic antimicrobial peptides. The ease of peptide chemical synthesis combined with emerging engineering principles and potent broad-spectrum activity, including against multidrug-resistant strains, has motivated intense scientific focus on these compounds for the past decade. This global effort has resulted in significant advances in our understanding of peptide antimicrobial activity at the molecular scale. Recent evidence of molecular targets other than the microbial lipid membrane, and efforts towards consensus antimicrobial peptide motifs, have supported the rise of molecular engineering approaches and design tools, including machine learning. Beyond molecular concepts, supramolecular chemistry has been lately added to the debate; and helped unravel the impact of peptide self-assembly on activity, including on biofilms and secondary targets, while providing new directions in pharmaceutical formulation through taking advantage of peptide self-assembled nanostructures. We argue that these basic research advances constitute a solid basis for promising industry translation of rationally designed synthetic peptide antimicrobials, not only as novel drugs against multidrug-resistant strains but also as components of emerging antimicrobial biomaterials. This perspective is supported by recent developments of innovative peptide-based and peptide-carrier nanobiomaterials that we also review.
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Affiliation(s)
- Priscila Cardoso
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia.,School of Science, RMIT University, Melbourne, Australia
| | - Hugh Glossop
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | | | | | | | - Celine Valery
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
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5
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Bozelli JC, Kamski-Hennekam E, Melacini G, Epand RM. α-Synuclein and neuronal membranes: Conformational flexibilities in health and disease. Chem Phys Lipids 2021; 235:105034. [PMID: 33434528 DOI: 10.1016/j.chemphyslip.2020.105034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 02/08/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease. Currently, PD has no treatment. The neuronal protein α-synuclein (αS) plays an important role in PD. However, the molecular mechanisms governing its physiological and pathological roles are not fully understood. It is becoming widely acknowledged that the biological roles of αS involve interactions with biological membranes. In these biological processes there is a fine-tuned interplay between lipids affecting the properties of αS and αS affecting lipid metabolism, αS binding to membranes, and membrane damage. In this review, the intricate interactions between αS and membranes will be reviewed and a discussion of the relationship between αS and neuronal membrane structural plasticity in health and disease will be made. It is proposed that in healthy neurons the conformational flexibilities of αS and the neuronal membranes are coupled to assist the physiological roles of αS. However, in circumstances where their conformational flexibilities are decreased or uncoupled, there is a shift toward cell toxicity. Strategies to modulate toxic αS-membrane interactions are potential approaches for the development of new therapies for PD. Future work using specific αS molecular species as well as membranes with specific physicochemical properties should widen our understanding of the intricate biological roles of αS which, in turn, would propel the development of new strategies for the treatment of PD.
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Affiliation(s)
- José Carlos Bozelli
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Evelyn Kamski-Hennekam
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada; Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada.
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada.
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6
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Salas RL, Garcia JKDL, Miranda ACR, Rivera WL, Nellas RB, Sabido PMG. Effects of truncation of the peptide chain on the secondary structure and bioactivities of palmitoylated anoplin. Peptides 2018; 104:7-14. [PMID: 29614317 DOI: 10.1016/j.peptides.2018.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 12/29/2022]
Abstract
Anoplin (GLLKRIKTLL-NH2) is of current interest due to its short sequence and specificity towards bacteria. Recent studies on anoplin have shown that truncation and acylation compromises its antimicrobial activity and specificity, respectively. In this study, truncated analogues (pal-ano-9 to pal-ano-5) of palmitoylated anoplin (pal-anoplin) were synthesized to determine the effects of C-truncation on its bioactivities. Moreover, secondary structure of each analogue using circular dichroism (CD) spectroscopy was determined to correlate with bioactivities. Interestingly, pal-anoplin, pal-ano-9 and pal-ano-6 were helical in water, unlike anoplin. In contrast, pal-ano-8, pal-ano-7 and pal-ano-5, with polar amino acid residues at the C-terminus, were random coil in water. Nevertheless, all the peptides folded into helical structures in 30% trifluoroethanol/water (TFE/H2O) except for the shortest analogue pal-ano-5. Hydrophobicity played a significant role in the enhancement of activity against bacteria E. coli and S. aureus as all lipopeptides including the random coil pal-ano-5 were more active than the parent anoplin. Meanwhile, the greatest improvement in activity against the fungus C. albicans was observed for pal-anoplin analogues (pal-ano-9 and pal-ano-6) that were helical in water. Although, hydrophobicity is a major factor in the secondary structure and antimicrobial activity, it appears that the nature of amino acids at the C-terminus also influence folding of lipopeptides in water and its antifungal activity. Moreover, the hemolytic activity of the analogues was found to correlate with hydrophobicity, except for the least hemolytic, pal-ano-5. Since most of the analogues are more potent and shorter than anoplin, they are promising drug candidates for further development.
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Affiliation(s)
- Remmer L Salas
- Institute of Chemistry, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines
| | - Jan Kathryne D L Garcia
- Institute of Chemistry, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines; Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines
| | - Ana Carmela R Miranda
- Institute of Chemistry, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines
| | - Windell L Rivera
- Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines; Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines
| | - Ricky B Nellas
- Institute of Chemistry, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines; Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines
| | - Portia Mahal G Sabido
- Institute of Chemistry, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines; Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines.
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7
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Dörfel MJ, Fang H, Crain J, Klingener M, Weiser J, Lyon GJ. Proteomic and genomic characterization of a yeast model for Ogden syndrome. Yeast 2016; 34:19-37. [PMID: 27668839 PMCID: PMC5248646 DOI: 10.1002/yea.3211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/12/2016] [Accepted: 09/16/2016] [Indexed: 11/10/2022] Open
Abstract
Naa10 is an Nα -terminal acetyltransferase that, in a complex with its auxiliary subunit Naa15, co-translationally acetylates the α-amino group of newly synthetized proteins as they emerge from the ribosome. Roughly 40-50% of the human proteome is acetylated by Naa10, rendering this an enzyme one of the most broad substrate ranges known. Recently, we reported an X-linked disorder of infancy, Ogden syndrome, in two families harbouring a c.109 T > C (p.Ser37Pro) variant in NAA10. In the present study we performed in-depth characterization of a yeast model of Ogden syndrome. Stress tests and proteomic analyses suggest that the S37P mutation disrupts Naa10 function and reduces cellular fitness during heat shock, possibly owing to dysregulation of chaperone expression and accumulation. Microarray and RNA-seq revealed a pseudo-diploid gene expression profile in ΔNaa10 cells, probably responsible for a mating defect. In conclusion, the data presented here further support the disruptive nature of the S37P/Ogden mutation and identify affected cellular processes potentially contributing to the severe phenotype seen in Ogden syndrome. Data are available via GEO under identifier GSE86482 or with ProteomeXchange under identifier PXD004923. © 2016 The Authors. Yeast published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Max J Dörfel
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Han Fang
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jonathan Crain
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Michael Klingener
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jake Weiser
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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8
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De Rosa L, Finetti F, Diana D, Di Stasi R, Auriemma S, Romanelli A, Fattorusso R, Ziche M, Morbidelli L, D’Andrea LD. Miniaturizing VEGF: Peptides mimicking the discontinuous VEGF receptor-binding site modulate the angiogenic response. Sci Rep 2016; 6:31295. [PMID: 27498819 PMCID: PMC4976335 DOI: 10.1038/srep31295] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/15/2016] [Indexed: 12/20/2022] Open
Abstract
The angiogenic properties of VEGF are mediated through the binding of VEGF to its receptor VEGFR2. The VEGF/VEGFR interface is constituted by a discontinuous binding region distributed on both VEGF monomers. We attempted to reproduce this discontinuous binding site by covalently linking into a single molecular entity two VEGF segments involved in receptor recognition. We designed and synthesized by chemical ligation a set of peptides differing in length and flexibility of the molecular linker joining the two VEGF segments. The biological activity of the peptides was characterized in vitro and in vivo showing a VEGF-like activity. The most biologically active mini-VEGF was further analyzed by NMR to determine the atomic details of its interaction with the receptor.
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Affiliation(s)
- Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Federica Finetti
- Dipartimento di Scienze della Vita, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Donatella Diana
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Rossella Di Stasi
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Sara Auriemma
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Alessandra Romanelli
- Dipartimento di Farmacia, Università di Napoli “Federico II”, via Mezzocannone 16, 80134, Napoli, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via A. Vivaldi 43, 81100, Caserta, Italy
| | - Marina Ziche
- Dipartimento di Scienze della Vita, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Lucia Morbidelli
- Dipartimento di Scienze della Vita, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
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9
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Effects of N-terminus modifications on the conformation and permeation activities of the synthetic peptide L1A. Amino Acids 2016; 48:1433-44. [PMID: 26920749 DOI: 10.1007/s00726-016-2196-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/06/2016] [Indexed: 10/22/2022]
Abstract
We investigate the effect of the N-terminus modification of the L1A, a synthetic octadecapeptide, on its helical content, affinity and lytic action in model membranes and on its hemolytic and antibacterial activities. L1A and its acetylated analog displayed a selective antibacterial activity to Gram-negative bacteria without being hemolytic. The covalently linked 2-aminobezoic acid to the N-terminus impaired the antibacterial efficacy and increased hemolysis. Despite their lower net charge (+2), N-terminus modifications resulted in enhanced affinity and improved lytic efficiency in anionic vesicles. The analogs also showed higher helical content and consequently higher amphipathicity in these vesicles. The conformational analysis by molecular dynamics simulations in 30 % of TFE/water showed that the hydrophobic faces of the peptides are in close contact with CF3 groups of TFE while the hydrophilic faces with water molecules. Due to the loss of the amino charge, the N-termini of the analogs are buried in TFE molecules. The analysis of the pair distribution functions, obtained for the center of mass of the charged groups, has evidenced that the state of the N-terminus has influenced the possibility of different ion-pairing. The higher complexity of the bacterial cells compared with anionic vesicles hampers to establish correlations structure-function for the analogs.
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10
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Marine JE, Song S, Liang X, Rudick JG. Synthesis and Self-Assembly of Bundle-Forming α-Helical Peptide-Dendron Hybrids. Biomacromolecules 2016; 17:336-44. [PMID: 26674475 PMCID: PMC4710556 DOI: 10.1021/acs.biomac.5b01452] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Dendronized helix bundle assemblies combine the sequence diversity and folding properties of proteins with the tailored physical properties of dendrimers. Assembly of peptide-dendron hybrids into α-helical bundles encapsulates the helix bundle motif in a dendritic sheath that will allow the functional, protein-like domain to be transplanted to nonbiological environments. A bioorthogonal graft-to synthetic strategy for preparing helix bundle-forming peptide-dendron hybrids is described herein for hybrids 1a, 1b, and 2. Titration experiments monitored by circular dichroism spectroscopy support our self-assembly model for how the peptide-dendron hybrids self-assemble into α-helical bundles with the dendrons on outside of the bundle.
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Affiliation(s)
- Jeannette E. Marine
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Shuang Song
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Xiaoli Liang
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Jonathan G. Rudick
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
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11
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Strategies for Exploring Electrostatic and Nonelectrostatic Contributions to the Interaction of Helical Antimicrobial Peptides with Model Membranes. ADVANCES IN BIOMEMBRANES AND LIPID SELF-ASSEMBLY 2016. [DOI: 10.1016/bs.abl.2016.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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12
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Smith CC, Lin K, Stecula A, Sali A, Shah NP. FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors. Leukemia 2015; 29:2390-2. [PMID: 26108694 PMCID: PMC4675689 DOI: 10.1038/leu.2015.165] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/01/2015] [Accepted: 06/02/2015] [Indexed: 12/04/2022]
Affiliation(s)
- C C Smith
- Division of Hematology/Oncology, University of California, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - K Lin
- Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - A Stecula
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - A Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - N P Shah
- Division of Hematology/Oncology, University of California, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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13
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The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 2015; 567:103-31. [PMID: 25987439 DOI: 10.1016/j.gene.2015.04.085] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/07/2023]
Abstract
N-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40% of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
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14
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Takei T, Tsumoto K, Okonogi A, Kimura A, Kojima S, Yazaki K, Takei T, Ueda T, Miura KI. pH responsiveness of fibrous assemblies of repeat-sequence amphipathic α-helix polypeptides. Protein Sci 2015; 24:883-94. [PMID: 25694229 DOI: 10.1002/pro.2665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 12/24/2022]
Abstract
We reported previously that our designed polypeptide α3 (21 residues), which has three repeats of a seven-amino-acid sequence (LETLAKA)3, forms not only an amphipathic α-helix structure but also long fibrous assemblies in aqueous solution. To address the relationship between the electrical states of the polypeptide and its α-helix and fibrous assembly formation, we characterized mutated polypeptides in which charged amino acid residues of α3 were replaced with Ser. We prepared the following polypeptides: 2Sα3 (LSTLAKA)3, in which all Glu residues were replaced with Ser residues; 6Sα3 (LETLASA)3, in which all Lys residues were replaced with Ser; and 2S6Sα3 (LSTLASA)3; in which all Glu and Lys residues were replaced with Ser. In 0.1M KCl, 2Sα3 formed an α-helix under basic conditions and 6Sα3 formed an α-helix under acid conditions. In 1M KCl, they both formed α-helices under a wide pH range. In addition, 2Sα3 and 6Sα3 formed fibrous assemblies under the same buffer conditions in which they formed α-helices. α-Helix and fibrous assembly formation by these polypeptides was reversible in a pH-dependent manner. In contrast, 2S6Sα3 formed an α-helix under basic conditions in 1M KCl. Taken together, these findings reveal that the charge states of the charged amino acid residues and the charge state of the Leu residue located at the terminus play an important role in α-helix formation.
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Affiliation(s)
- Toshiaki Takei
- Department of Medical Genome Sciences, Graduate School of Frontier, The university of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan; Institute for Biomolecular Science, Gakushuin University, Toshima-ku, Tokyo, Japan
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15
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Vorontsova MA, Maes D, Vekilov PG. Recent advances in the understanding of two-step nucleation of protein crystals. Faraday Discuss 2015; 179:27-40. [DOI: 10.1039/c4fd00217b] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The two-step mechanism of nucleation of crystals in solutions posits that the formation of crystal nuclei occurs within structures of extended lifetimes, in which the nucleating solute is at high concentration. The validity of this mechanism has been demonstrated for proteins, small-molecule organic and inorganic materials, colloids, and polymers. Due to large molecule sizes, proteins are an ideal system to study the details of this nucleation pathway, in particular the formation mechanisms of the nucleation precursors and the associated physico-chemical rules. The precursors of protein crystal nuclei are protein-rich clusters of sizes ∼100 nm that contain 10 000–100 000 molecules and occupy less than 10−3of the total solution volume. Here we demonstrate, using oblique illumination microscopy, the liquid nature of the clusters of the protein lysozyme and reveal their inhomogeneous structure. We test a hypothesis put forth by theory that clusters primarily consist of transient protein oligomers. For this, we explore how varying the strength of the Coulomb interaction affects the cluster characteristics. We find that the cluster’s size is insensitive to variations of pH and ionic strength. In contrast, the addition of urea, a chaotropic agent that leads to protein unfolding, strongly decreases the cluster size. Shear stress, a known protein denaturant, induced by bubbling of the solutions with an inert gas, elicits a similar response. These observations support partial protein unfolding, followed by dimerization, as the mechanism of cluster formation. The amide hydrogen–deuterium exchange, monitored by nuclear magnetic resonance, highlights that lysozyme conformational flexibility is a condition for the formation of the protein-rich clusters and facilitates the nucleation of protein crystals.
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Affiliation(s)
- Maria A. Vorontsova
- Department of Chemical and Biomolecular Engineering
- University of Houston
- Houston
- USA
| | - Dominique Maes
- Structural Biology Brussels
- Vrije Universiteit Brussel
- B-1050 Brussel
- Belgium
| | - Peter G. Vekilov
- Department of Chemical and Biomolecular Engineering
- University of Houston
- Houston
- USA
- Department of Chemistry
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16
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Effect of external pulling forces on the length distribution of peptides. Biochim Biophys Acta Gen Subj 2014; 1850:903-910. [PMID: 25261776 DOI: 10.1016/j.bbagen.2014.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 11/20/2022]
Abstract
BACKGROUND The distribution of the length of a polypeptide, or that of the distance between any two of its atoms, is an important property as it can be analytically or numerically estimated for a number of polymer models. Importantly, it is directly measurable through a number of different experimental techniques. Length distributions can be straightforwardly assessed from molecular dynamics simulation; however, true convergence through full accurate coverage of the length range is difficult to achieve. METHODS The application of external constant force combined with the weighted-histogram analysis method (WHAM) is used to enhance sampling of unlikely 'long' or 'short' conformations and obtain the potential of mean force, while also collecting dynamic properties of the chain under variable tension. RESULTS We demonstrate the utility of constant force to enhance the sampling efficiency and obtain experimentally measurable quantities on a series of short peptides, including charge-rich sequences that are known to be highly helical but whose properties are distinct from those of helical peptides undergoing helix-coil transitions. CONCLUSIONS Force-enhanced sampling enhances the range and accuracy of the length-based potential of mean force of the peptide, in particular those sequences that contain increased numbers of charged residues. GENERAL SIGNIFICANCE This approach allows users to simultaneously probe the force-dependent behaviour of peptides directly, enhance the range and accuracy of the length-based PMF of the peptide and also test the convergence of simulations by comparing the overlap of PMF profiles from different constant forces. This article is part of a special issue entitled Recent developments of molecular dynamics.
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17
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Wolny M, Batchelor M, Knight PJ, Paci E, Dougan L, Peckham M. Stable single α-helices are constant force springs in proteins. J Biol Chem 2014; 289:27825-35. [PMID: 25122759 PMCID: PMC4183817 DOI: 10.1074/jbc.m114.585679] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Single α-helix (SAH) domains are rich in charged residues (Arg, Lys, and Glu) and stable in solution over a wide range of pH and salt concentrations. They are found in many different proteins where they bridge two functional domains. To test the idea that their high stability might enable these proteins to resist unfolding along their length, the properties and unfolding behavior of the predicted SAH domain from myosin-10 were characterized. The expressed and purified SAH domain was highly helical, melted non-cooperatively, and was monomeric as shown by circular dichroism and mass spectrometry as expected for a SAH domain. Single molecule force spectroscopy experiments showed that the SAH domain unfolded at very low forces (<30 pN) without a characteristic unfolding peak. Molecular dynamics simulations showed that the SAH domain unfolds progressively as the length is increased and refolds progressively as the length is reduced. This enables the SAH domain to act as a constant force spring in the mechanically dynamic environment of the cell.
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Affiliation(s)
- Marcin Wolny
- From the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Matthew Batchelor
- From the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Peter J Knight
- From the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Emanuele Paci
- From the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lorna Dougan
- From the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Michelle Peckham
- From the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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18
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Holmes WM, Mannakee BK, Gutenkunst RN, Serio TR. Loss of amino-terminal acetylation suppresses a prion phenotype by modulating global protein folding. Nat Commun 2014; 5:4383. [PMID: 25023910 PMCID: PMC4140192 DOI: 10.1038/ncomms5383] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/13/2014] [Indexed: 01/08/2023] Open
Abstract
N-terminal acetylation is among the most ubiquitous of protein modifications in eukaryotes. While loss of N-terminal acetylation is associated with many abnormalities, the molecular basis of these effects is known for only a few cases, where acetylation of single factors has been linked to binding avidity or metabolic stability. In contrast, the impact of N-terminal acetylation for the majority of the proteome, and its combinatorial contributions to phenotypes, are unknown. Here, by studying the yeast prion [PSI+], an amyloid of the Sup35 protein, we show that loss of N-terminal acetylation promotes general protein misfolding, a redeployment of chaperones to these substrates, and a corresponding stress response. These proteostasis changes, combined with the decreased stability of unacetylated Sup35 amyloid, reduce the size of prion aggregates and reverse their phenotypic consequences. Thus, loss of N-terminal acetylation, and its previously unanticipated role in protein biogenesis, globally resculpts the proteome to create a unique phenotype.
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Affiliation(s)
- William M Holmes
- 1] Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA [2]
| | - Brian K Mannakee
- Graduate Interdisciplinary Program in Statistics, University of Arizona, 1548 East Drachman Street, Tucson, Arizona 85721, USA
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, 1007 East Lowell Street, Tucson, Arizona 85721, USA
| | - Tricia R Serio
- 1] Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA [2]
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19
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Leite NB, Dos Santos Alvares D, de Souza BM, Palma MS, Ruggiero Neto J. Effect of the aspartic acid D2 on the affinity of Polybia-MP1 to anionic lipid vesicles. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:121-30. [PMID: 24595375 DOI: 10.1007/s00249-014-0945-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/05/2014] [Accepted: 02/05/2014] [Indexed: 11/28/2022]
Abstract
Polybia-MP1 (IDWKKLLDAAKQIL-NH2), a helical peptide extracted from the venom of a Brazilian wasp, has broad-spectrum antimicrobial activities without being hemolytic or cytotoxic. This peptide has also displayed anticancer activity against cancer cell cultures. Despite its high selectivity, MP1 has an unusual low net charge (Q = +2). The aspartic residue (D2) in the N-terminal region plays an important role in its affinity and selectivity; its substitution by asparagine (D2N mutant) led to a less selective peptide. Aiming to explore the importance of this residue for the peptides' affinity, we compared the zwitterionic and anionic vesicle adsorption activity of Polybia-MP1 versus its D2N mutant and also mastoparan X (MPX). The adsorption, electrostatic, and conformational free energies were assessed by circular dichroism (CD) and fluorescence titrations using large unilamellar vesicles (LUVs) at the same conditions in association with measurement of the zeta potential of LUVs in the presence of the peptides. The adsorption free energies of the peptides, determined from the partition coefficients, indicated higher affinity of MP1 to anionic vesicles compared with the D2N mutant and MPX. The electrostatic and conformational free energies of MP1 in anionic vesicles are less favorable than those found for the D2N mutant and MPX. Therefore, the highest affinity of MP1 to anionic vesicles is likely due to other energetic contributions. The presence of D2 in MP1 makes these energetic components 1.2 and 1.5 kcal/mol more favorable compared with the D2N mutant and MPX, respectively.
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Affiliation(s)
- Natália Bueno Leite
- Department of Physics, IBILCE, São Paulo State University, UNESP, São José do Rio Preto, SP, Brazil
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20
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Hoffman KW, Romei MG, Londergan CH. A New Raman Spectroscopic Probe of Both the Protonation State and Noncovalent Interactions of Histidine Residues. J Phys Chem A 2013; 117:5987-96. [DOI: 10.1021/jp311815k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kevin W. Hoffman
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United
States
| | - Matthew G. Romei
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United
States
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United
States
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21
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Kang L, Moriarty GM, Woods LA, Ashcroft AE, Radford SE, Baum J. N-terminal acetylation of α-synuclein induces increased transient helical propensity and decreased aggregation rates in the intrinsically disordered monomer. Protein Sci 2012; 21:911-7. [PMID: 22573613 DOI: 10.1002/pro.2088] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 04/27/2012] [Indexed: 12/23/2022]
Abstract
The conformational properties of soluble α-synuclein, the primary protein found in patients with Parkinson's disease, are thought to play a key role in the structural transition to amyloid fibrils. In this work, we report that recombinant 100% N-terminal acetylated α-synuclein purified under mild physiological conditions presents as a primarily monomeric protein, and that the N-terminal acetyl group affects the transient secondary structure and fibril assembly rates of the protein. Residue-specific NMR chemical shift analysis indicates substantial increase in transient helical propensity in the first 9 N-terminal residues, as well as smaller long-range changes in residues 28-31, 43-46, and 50-66: regions in which the three familial mutations currently known to be causative of early onset disease are found. In addition, we show that the N-terminal acetylated protein forms fibrils that are morphologically similar to those formed from nonacetylated α-synuclein, but that their growth rates are slower. Our results highlight that N-terminal acetylation does not form significant numbers of dimers, tetramers, or higher molecular weight species, but does alter the conformational distributions of monomeric α-synuclein species in regions known to be important in metal binding, in association with membranes, and in regions known to affect fibril formation rates.
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Affiliation(s)
- Lijuan Kang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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22
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Liu G, Robbins KJ, Sparks S, Selmani V, Bilides KM, Gomes EE, Lazo ND. Helix-Dipole Effects in Peptide Self-Assembly to Amyloid. Biochemistry 2012; 51:4167-74. [DOI: 10.1021/bi3001616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gai Liu
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
| | - Kevin J. Robbins
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
| | - Samuel Sparks
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
| | - Veli Selmani
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
| | - Kalin M. Bilides
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
| | - Erin E. Gomes
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
| | - Noel D. Lazo
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
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23
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Becucci L, Guryanov I, Maran F, Guidelli R. Effect of a strong interfacial electric field on the orientation of the dipole moment of thiolated aib-oligopeptides tethered to mercury on either the N- or C-terminus. J Am Chem Soc 2010; 132:6194-204. [PMID: 20392067 DOI: 10.1021/ja100486y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Four oligopeptides consisting of a sequence of alpha-aminoisobutyric acid (Aib) residues, thiolated at either the N- or C-terminus by means of a -(CH(2))(2)-SH anchor, were self-assembled on mercury, which is a substrate known to impart a high fluidity to self-assembled monolayers (SAMs). The surface dipole potential of these peptide SAMs was estimated in 0.1 M KCl aqueous solution at a negatively charged electrode, where the interfacial electric field is directed toward the metal. To the best of our knowledge, this is the first estimate of the surface dipole potential of peptide SAMs in aqueous solution. The procedure adopted consisted in measuring the charge involved in the gradual expansion of a peptide-coated mercury drop and then combining the resulting information with an estimate of the charge density experienced by diffuse layer ions. The dipole moment of the tethered thiolated peptides was found to be directed toward the metal, independent of whether they were thiolated at the C- or N-terminus. This result was confirmed by the effect of these SAMs on the kinetics and thermodynamics of the Eu(III)/Eu(II) redox couple. The combined outcome of these studies indicates that a strong interfacial electric field orients the dipole moment of peptide SAMs tethered to mercury, even against their "natural" dipole moment.
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Affiliation(s)
- Lucia Becucci
- Department of Chemistry, Florence University, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy.
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24
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Kuemin M, Schweizer S, Ochsenfeld C, Wennemers H. Effects of Terminal Functional Groups on the Stability of the Polyproline II Structure: A Combined Experimental and Theoretical Study. J Am Chem Soc 2009; 131:15474-82. [DOI: 10.1021/ja906466q] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Michael Kuemin
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland, and Institute for Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen, Germany
| | - Sabine Schweizer
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland, and Institute for Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen, Germany
| | - Christian Ochsenfeld
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland, and Institute for Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen, Germany
| | - Helma Wennemers
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland, and Institute for Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen, Germany
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25
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26
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Evaluation of strategies for improving proteolytic resistance of antimicrobial peptides by using variants of EFK17, an internal segment of LL-37. Antimicrob Agents Chemother 2008; 53:593-602. [PMID: 19029324 DOI: 10.1128/aac.00477-08] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Methods for increasing the proteolytic stability of EFK17 (EFKRIVQRIKDFLRNLV), a new peptide sequence with antimicrobial properties derived from LL-37, were evaluated. EFK17 was modified by four d-enantiomer or tryptophan (W) substitutions at known protease cleavage sites as well as by terminal amidation and acetylation. The peptide variants were studied in terms of proteolytic resistance, antibacterial potency, and cytotoxicity but also in terms their adsorption at model lipid membranes, liposomal leakage generation, and secondary-structure behavior. The W substitutions resulted in a marked reduction in the proteolytic degradation caused by human neutrophil elastase, Staphylococcus aureus aureolysin, and V8 protease but not in the degradation caused by Pseudomonas aeruginosa elastase. For the former two endoproteases, amidation and acetylation of the terminals also reduced proteolytic degradation but only when used in combination with W substitutions. The d-enantiomer substitutions rendered the peptides indigestible by all four proteases; however, those peptides displayed little antimicrobial potency. The W- and end-modified peptides, on the other hand, showed an increased bactericidal potency compared to that of the native peptide sequence, coupled with a moderate cytotoxicity that was largely absent in serum. The bactericidal, cytotoxic, and liposome lytic properties correlated with each other as well as with the amount of peptide adsorbed at the lipid membrane and the extent of helix formation associated with the adsorption. The lytic properties of the W-substituted peptides were less impaired by increased ionic strength, presumably by a combination of W-mediated stabilization of the largely amphiphilic helix conformation and a nonelectrostatic W affinity for the bilayer interface. Overall, W substitutions constitute an interesting means to reduce the proteolytic susceptibility of EFK17 while also improving antimicrobial performance.
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27
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Guerler A, Knapp EW. Novel protein folds and their nonsequential structural analogs. Protein Sci 2008; 17:1374-82. [PMID: 18583523 DOI: 10.1110/ps.035469.108] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Newly determined protein structures are classified to belong to a new fold, if the structures are sufficiently dissimilar from all other so far known protein structures. To analyze structural similarities of proteins, structure alignment tools are used. We demonstrate that the usage of nonsequential structure alignment tools, which neglect the polypeptide chain connectivity, can yield structure alignments with significant similarities between proteins of known three-dimensional structure and newly determined protein structures that possess a new fold. The recently introduced protein structure alignment tool, GANGSTA, is specialized to perform nonsequential alignments with proper assignment of the secondary structure types by focusing on helices and strands only. In the new version, GANGSTA+, the underlying algorithms were completely redesigned, yielding enhanced quality of structure alignments, offering alignment against a larger database of protein structures, and being more efficient. We applied DaliLite, TM-align, and GANGSTA+ on three protein crystal structures considered to be novel folds. Applying GANGSTA+ to these novel folds, we find proteins in the ASTRAL40 database, which possess significant structural similarities, albeit the alignments are nonsequential and in some cases involve secondary structure elements aligned in reverse orientation. A web server is available at http://agknapp.chemie.fu-berlin.de/gplus for pairwise alignment, visualization, and database comparison.
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Affiliation(s)
- Aysam Guerler
- Department of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
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28
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Bryksa BC, MacDonald LD, Patrzykat A, Douglas SE, Mattatall NR. A C-terminal glycine suppresses production of pleurocidin as a fusion peptide in Escherichia coli. Protein Expr Purif 2006; 45:88-98. [PMID: 15935695 DOI: 10.1016/j.pep.2005.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Accepted: 04/19/2005] [Indexed: 11/25/2022]
Abstract
The winter flounder (Pseudopleuronectes americanus) antimicrobial peptide pleurocidin was produced in Escherichia coli using a synthetic gene constructed by PCR. The gene expresses pleurocidin from pET21a fused to the C-terminus of an insoluble carrier peptide. Once expressed, the fusion peptide formed inclusion bodies in the cytoplasm that were collected, solubilized in guanidine-HCl, and chemically cleaved using hydroxylamine at a unique asparaginyl-glycyl dipeptide. This released recombinant pleurocidin (r-pleurocidin), which was purified using ultrafiltration followed by reverse phase chromatography. The r-pleurocidin peptide resolved as a single band (2.7 kDa) when analyzed by Tris-Tricine buffered SDS-PAGE, and its amino acid sequence was confirmed using tandem mass spectrometry. Extending the pleurocidin sequence with a C-terminal glycine (r-pleurocidin-G) suppressed production of the fusion peptide 15-fold. When pleurocidin was extended further to include aspartate (r-pleurocidin-GD), the same effect was observed, and when pleurocidin was extended with aspartate alone, no effect was observed. Expression of fusion peptide containing either r-pleurocidin-G or r-pleurocidin-GD with low concentrations of inductant caused E. coli to enter stationary phase prematurely, but did not affect overall growth rates. A partial production recovery of r-pleurocidin-G was achieved by inducing expression in stationary phase cells. We observed r-pleurocidin-G to have enhanced antimicrobial activity compared with r-pleurocidin, and we propose that this activity interferes with E. coli metabolism during expression. This antimicrobial effect is probably facilitated by residual solubility of the fusion peptide and by a C-terminal cap structure, which stabilizes the r-pleurocidin-G alpha-helix that is thought to be important for activity.
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Affiliation(s)
- Brian C Bryksa
- NRC Institute for Marine Biosciences, National Research Council Canada, Halifax, NS, Canada B3H 3Z1
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29
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Vila JA, Baldoni HA, Scheraga HA. Position dependence of the 13C chemical shifts of alpha-helical model peptides. Fingerprint of the 20 naturally occurring amino acids. Protein Sci 2005; 13:2939-48. [PMID: 15498939 PMCID: PMC2286576 DOI: 10.1110/ps.04930804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The position dependence of the (13)C chemical shifts was investigated at the density functional level for alpha-helical model peptides represented by the sequence Ac-(Ala)(i)-X-(Ala)(j)-NH(2), where X represents any of the 20 naturally occurring amino acids, with 0 < or = i < or = 8 and i + j = 8. Adoption of the locally dense basis approach for the quantum chemical calculations enabled us to reduce the length of the chemical-shift calculations while maintaining good accuracy of the results. For the 20 naturally occurring amino acids in alpha-helices, there is (1) significant variability of the computed (13)C shielding as a function of both the guest residue (X) and the position along the sequence; for example, at the N terminus, the (13)C(alpha) and (13)C(beta) shieldings exhibit a uniform pattern of variation with respect to both the central or the C-terminal positions; (2) good agreement between computed and observed (13)C(alpha) and (13)C(beta) chemical shifts in the interior of the helix, with correlation coefficients of 0.98 and 0.99, respectively; for (13)C(alpha) chemical shifts, computed in the middle of the helix, only five residues, namely Asn, Asp, Ser, Thr, and Leu, exhibit chemical shifts beyond the observed standard deviation; and (3) better agreement for four of these residues (Asn, Asp, Ser, and Thr) only for the computed values of the (13)C(alpha) chemical shifts at the N terminus. The results indicate that (13)C(beta), but not (13)C(beta), chemical shifts are sensitive enough to reflect the propensities of some amino acids for specific positions within an alpha-helix, relative to the N and C termini of peptides and proteins.
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Affiliation(s)
- Jorge A Vila
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
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30
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Kritzer JA, Tirado-Rives J, Hart SA, Lear JD, Jorgensen WL, Schepartz A. Relationship between side chain structure and 14-helix stability of beta3-peptides in water. J Am Chem Soc 2005; 127:167-78. [PMID: 15631466 PMCID: PMC2873033 DOI: 10.1021/ja0459375] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Folded polymers are used in Nature for virtually every vital process. Nonnatural folded polymers, or foldamers, have the potential for similar versatility, and the design and refinement of such molecules is of considerable current interest. Here we report a complete and systematic analysis of the relationship between side chain structure and the 14-helicity of a well-studied class of foldamers, beta(3)-peptides, in water. Our experimental results (1) verify the importance of macrodipole stabilization for maintaining 14-helix structure, (2) provide comprehensive evidence that beta(3)-amino acids branched at the first side chain carbon are 14-helix-stabilizing, (3) suggest a novel role for side chain hydrogen bonding as an additional stabilizing force in beta(3)-peptides containing beta(3)-homoserine or beta(3)-homothreonine, and (4) demonstrate that diverse functionality can be incorporated into a stable 14-helix. Gas- and solution-phase calculations and Monte Carlo simulations recapitulate the experimental trends only in the context of oligomers, yielding insight into the mechanisms behind 14-helix folding. The 14-helix propensities of beta(3)-amino acids differ starkly from the alpha-helix propensities of analogous alpha-amino acids. This contrast informs current models for alpha-helix folding, and suggests that 14-helix folding is governed by different biophysical forces than is alpha-helix folding. The ability to modulate 14-helix structure through side chain choice will assist rational design of 14-helical beta-peptide ligands for macromolecular targets.
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Affiliation(s)
- Joshua A. Kritzer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | | | - Scott A. Hart
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | - James D. Lear
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| | | | - Alanna Schepartz
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8107
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Kritzer JA, Stephens OM, Guarracino DA, Reznik SK, Schepartz A. beta-Peptides as inhibitors of protein-protein interactions. Bioorg Med Chem 2005; 13:11-6. [PMID: 15582447 PMCID: PMC2853017 DOI: 10.1016/j.bmc.2004.09.009] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Accepted: 09/08/2004] [Indexed: 01/10/2023]
Abstract
We became interested several years ago in exploring whether 14-helical beta-peptide foldamers could bind protein surfaces and inhibit protein-protein interactions, and if so, whether their affinities and specificities would compare favorably with those of natural or miniature proteins. This exploration was complicated initially by the absence of a suitable beta-peptide scaffold, one that possessed a well-defined 14-helical structure in water and tolerated the diverse sequence variation required to generate high-affinity protein surface ligands. In this perspective, we describe our approach to the design of adaptable beta-peptide scaffolds with high levels of 14-helix structure in water, track the subsequent development of 14-helical beta-peptide protein-protein interaction inhibitors, and examine the potential of this strategy for targeting other therapeutically important proteins.
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Affiliation(s)
| | - Olen M. Stephens
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | | | - Samuel K. Reznik
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Alanna Schepartz
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
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32
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Blatchly RA, Tew GN. Theoretical Study of Helix Formation in Substituted Phenylene Ethynylene Oligomers. J Org Chem 2003; 68:8780-5. [PMID: 14604344 DOI: 10.1021/jo034827y] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Theoretical investigations of the relative stabilities of helical vs extended forms of phenylene ethynylene oligomers established that MMFF molecular mechanics was more useful than AM1 or DFT for calculating helical structures and for estimating relative energies. At the level of MMFF, theory predicts that for o- or m-oligophenylene ethynylenes, helix formation is enthalpically favored for ester and ether-substituted oligomers. In contrast to simple electron-demand predictions, we predict that the position of substituents can make a substantial difference in the tendency to form helices.
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Affiliation(s)
- Richard A Blatchly
- Chemistry Department, Keene State College, Keene, New Hampshire 03435, USA.
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33
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Hart SA, Bahadoor ABF, Matthews EE, Qiu XJ, Schepartz A. Helix macrodipole control of beta 3 peptide 14-helix stability in water. J Am Chem Soc 2003; 125:4022-3. [PMID: 12670203 DOI: 10.1021/ja029868a] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
beta-Peptides have attracted considerable attention by virtue of their ability to populate helical secondary structures in methanol, even in the absence of stabilizing tertiary interactions. Recent efforts in beta-peptide design have produced few beta3-peptides that form stable 14-helices in water; those that do require stabilizing intramolecular salt bridges on two of three helical faces and therefore possess limited utility as tools in biological research. Here we show that favorable interactions with the 14-helix macrodipole significantly stabilize the 14-helix in water, alleviating the need for multiple salt bridges on two of three helical faces. We also report the previously unrecognized stabilization of 14-helix structure by gamma-branched beta3-amino acids. The most structured molecules we describe are highly heterogeneous at the primary sequence level, containing seven different beta3-amino acids within an 11-residue sequence. These results represent the essential first step toward the design of well-folded 14-helices that explore the interactions between beta3-peptides and biological macromolecules in vitro and in vivo.
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Affiliation(s)
- Scott A Hart
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA
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34
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Santiveri CM, Santoro J, Rico M, Jiménez MA. Thermodynamic analysis of beta-hairpin-forming peptides from the thermal dependence of (1)H NMR chemical shifts. J Am Chem Soc 2002; 124:14903-9. [PMID: 12475331 DOI: 10.1021/ja0278537] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The temperature dependence of the (1)H chemical shifts of six designed peptides previously shown to adopt beta-hairpin structures in aqueous solution has been analyzed in terms of two-state (beta-hairpin left arrow over right arrow coil) equilibrium. The stability of the beta-hairpins formed by these peptides, as derived from their T(m) (midpoint transition temperature) values, parallels in general their ability to adopt those structures as deduced from independent NMR parameters: NOEs, Deltadelta(C)(alpha)(H), Deltadelta(C)(alpha), and Deltadelta(C)(beta) values. The observed T(m) values are dependent on the particular position within the beta-hairpin that is probed, indicating that their folding to a beta-hairpin conformation deviates from a "true" two-state transition. To obtain individual T(m) values for each hairpin region in each peptide, a simplified model of a successive uncoupled two-state equilibrium covering the entire process has been applied. The distribution of T(m) values obtained for the different beta-hairpin regions (turn, strands, backbone, side chains) in the six analyzed peptides reveals a similar pattern. A model for beta-hairpin folding is proposed on the basis of this pattern and the reasonable assumption that regions showing higher T(m) values are the last ones to unfold and, presumably, the first to form. With this assumption, the analysis suggests that turn formation is the first event in beta-hairpin folding. This is consistent with previous results on the essential role of the turn sequence in beta-hairpin folding.
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Affiliation(s)
- Clara M Santiveri
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006-Madrid, Spain
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35
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Kuiper MJ, Fecondo JV, Wong MG. Rational design of alpha-helical antifreeze peptides. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2002; 59:1-8. [PMID: 11906602 DOI: 10.1046/j.1397-002x.2001.00001.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The alanine-rich alpha-helical antifreeze protein from the winter flounder Pseudopleuronectes americanus adsorbs to specific planes of ice guided by an ice lattice match to threonine residues regularly spaced 16.6 A apart. We report here that by redesigning the winter flounder antifreeze peptide to incorporate a 27.1-A spacing between putative 'ice-binding' threonines, the deduced binding alignment of the helical molecule on the ice lattice is changed from the Miller indices directional vector [1102 ] to [2203 ]. Subsequent ice-binding characteristics are altered, including changes in adsorption specificity, decreases in thermal hysteresis activity and the formation of rotated hexagonal bipyramid ice crystal morphology.
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Affiliation(s)
- M J Kuiper
- School of Engineering and Science, Swinburne University of Technology, Hawthorn, Victoria, Australia
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36
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Affiliation(s)
- J Venkatraman
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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37
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Wieprecht T, Rothemund S, Bienert M, Krause E. Role of helix formation for the retention of peptides in reversed-phase high-performance liquid chromatography. J Chromatogr A 2001; 912:1-12. [PMID: 11307972 DOI: 10.1016/s0021-9673(01)00531-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In order to get insight into the role of helix formation for retention in reversed-phase HPLC, we have studied the isocratic retention behavior of amphipathic and non-amphipathic potentially helical model peptides. Plots of the logarithmic capacity factor in absence of organic solvent (ln k0) versus l/T were used to derive the enthalpy, deltaH0, the free energy, deltaG0, the entropy of interaction, deltaS0, and the heat capacity change, deltaCp. Retention of all peptides was accompanied by negative deltaCp revealing that hydrophobic interactions play a large role independent of peptide sequence and secondary structure. deltaH0 was negative for the amphipathic analogs and was attributed mainly to helix formation of these peptides upon interaction with the stationary phase. In contrast, deltaH0 was considerably less exothermic or even endothermic for the non-amphipathic analogs. The differences in helix formation between the individual analogs were quantified on the basis of thermodynamic data of helix formation previously derived for peptides in a hydrophobic environment. Correlation of the helicity with the free energy of stationary phase interaction revealed that helix formation accounts for approximately 40-70% of deltaG0, and is hence in addition to the hydrophobic effect a major driving force of retention.
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Affiliation(s)
- T Wieprecht
- Institute of Molecular Pharmacology, Berlin, Germany
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38
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Kwok SC, Tripet B, Man JH, Chana MS, Lavigne P, Mant CT, Hodges RS. Structural cassette mutagenesis in a de novo designed protein: proof of a novel concept for examining protein folding and stability. Biopolymers 2000; 47:101-23. [PMID: 9692331 DOI: 10.1002/(sici)1097-0282(1998)47:1<101::aid-bip11>3.0.co;2-l] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The solution to the protein folding problem lies in defining the relative energetic contributions of short-range and long-range interactions. In other words, the tendency of a stretch of amino acids to adopt a final secondary structural fold is context dependent. Our approach to this problem is to address whether an amino acid sequence, a "cassette," with a defined secondary structure in the three-dimensional structure of a native protein, can adopt a different conformation when placed into a different protein environment. Thus, we designed de novo a disulfide-bridged two-stranded alpha-helical parallel coiled coil, where each polypeptide chain consisted of 39 residues, as a "cassette holder." The 11-residue cassette would be inserted into the center of each polypeptide chain between the two nucleating alpha-helices to replace the control sequence. This Structural Cassette Mutagenesis model permits the analysis of short-range interactions within the inserted cassette as well as long-range interactions between the nucleating helices and the cassette region. The cassette holder, with a control sequence as the cassette, had a GdnHCl transition midpoint during denaturation of 5.6M. To demonstrate the feasibility of our model, an 11-residue beta-strand cassette from an immunoglobulin fold was inserted. The cassette was fully induced into the alpha-helical conformation with a [GdnHCl]1/2 value of 3.2M. To demonstrate the importance of short-range interactions (beta-sheet/alpha-helical propensities of amino acid side chains) in modulating structure and stability, a series of 1-5 threonine residues (highest beta-sheet propensity) were substituted into the solvent-exposed portions of the cassette in the alpha-helical conformation. Each successive substitution systematically decreased the stability of the coiled coil with peptide T4b (4 Thr residues) having a [GdnHCl]1/2 value of 2.2M. The single substitution of Ile in the hydrophobic core of the cassette with Ala or Thr had the most dramatic effect on protein stability (peptide 120T, [GdnHCl]1/2 value of 1.4M). Though these substitutions were able to modulate stability, they were not able to disrupt the alpha-helical conformation of the cassette, showing the importance of the nucleating alpha-helices on either side of the cassette in controlling conformation of the cassette. We have demonstrated the feasibility of our model protein to accept a beta-strand cassette. The effect of cassettes containing other beta-strands, beta-turns, loops, regions of undefined structure, and helical segments on conformation and stability of our model protein will also be determined.
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Affiliation(s)
- S C Kwok
- Department of Biochemistry, University of Alberta, Edmonton, Canada
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39
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Rivier JE, Porter J, Cervini LA, Lahrichi SL, Kirby DA, Struthers RS, Koerber SC, Rivier CL. Design of monocyclic (1-3) and dicyclic (1-3/4-10) gonadotropin releasing hormone (GnRH) antagonists. J Med Chem 2000; 43:797-806. [PMID: 10715148 DOI: 10.1021/jm9901172] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Careful analysis of the NMR structures of cyclo(4-10)[Ac-Delta(3)Pro(1),DFpa(2),DTrp(3),Asp(4),DNal (6), Dpr(10)]GnRH, dicyclo(4-10/5-8)[Ac-DNal(1),DCpa(2),DTrp(3), Asp(4), Glu(5),DArg(6),Lys(8),Dpr(10)]GnRH, and dicyclo(4-10/5, 5'-8)[Ac-DNal(1),DCpa(2),DPal(3),Asp(4), Glu(5)(Gly),DArg(6),Dbu(8), Dpr(10)]GnRH showed that, in the N-terminal tripeptide, a type II beta-turn around residues 1 and 2 was probable along with a gamma-turn around DTrp(3)/DPal(3). This suggested the possibility of constraining the N-terminus by the introduction of a cyclo(1-3) scaffold. Optimization of ring size and composition led to the discovery of cyclo(1-3)[Ac-DAsp(1),DCpa(2),DLys(3),DNal(6), DAla(10)]GnRH (5, K(i) = 0.82 nM), cyclo(1,1'-3)[Ac-DAsp(1)(Gly), DCpa(2),DOrn(3),DNal(6),DAla(10)]GnRH (13, K(i) = 0.34 nM), cyclo(1, 1'-3)[Ac-DAsp(1)(Gly),DCpa(2),DLys(3),DNal(6),DA la(10)]GnRH (20, K(i) = 0.14 nM), and cyclo(1,1'-3)[Ac-DAsp(1)(betaAla), DCpa(2), DOrn(3),DNal(6),DAla(10)]GnRH (21, K(i) = 0.17 nM), which inhibited ovulation significantly at doses equal to or lower than 25 microgram/rat. These results were particularly unexpected in view of the critical role(s) originally ascribed to the side chains of residues 1 and 3.(1) Other closely related analogues, such as those where the [DAsp(1)(betaAla), DOrn(3)] cycle of 21 was changed to [DOrn(1)(betaAla), DAsp(3)] of cyclo(1,1'-3)[Ac-DOrn(1)(betaAla), DCpa(2),DAsp(3),DNal(6),DAla(10)]GnRH (22, K(i) = 2.2 nM) or where the size of the cycle was conserved and [DAsp(1)(betaAla), DOrn(3)] was replaced by [DGlu(1)(Gly), DOrn(3)] as in cyclo(1, 1'-3)[Ac-DGlu(1)(Gly),DCpa(2),DOrn(3),DNal(6),DA la(10)]GnRH (23, K(i) = 4.2 nM), were approximately 100 and 25 times less potent in vivo, respectively. Analogues with ring sizes of 18 ¿cyclo(1, 1'-3)[Ac-DGlu(1)(Gly),DCpa(2),DLys(3),DNal(6),DA la(10)]GnRH (24)¿ and 19 ¿cyclo(1,1'-3)[Ac-DGlu(1)(betaAla),DCpa(2),DLys( 3),DNal(6), DAla(10)]GnRH (25)¿ atoms were also less potent than 21 with slightly higher K(i) values (1.5 and 2.2 nM, respectively). These results suggested that the N-terminal tripeptide was likely to assume a folded conformation favoring the close proximity of the side chains of residues 1 and 3. The dicyclic analogue dicyclo(1-3/4-10)[Ac-DAsp(1),DCpa(2),DLys(3),Asp (4),DNal(6), Dpr(10)]GnRH (26) was fully active at 500 microgram, with a K(i) value of 1 nM. The in vivo potency of 26 was at least 10-fold less than that of monocyclic cyclo(1-3)[Ac-DAsp(1),DCpa(2),DLys(3),DNal(6), DAla(10)]GnRH (5); this suggested the existence of unfavorable interactions between the now optimized and constrained (1-3) and (4-10) cyclic moieties that must interact as originally hypothesized. Tricyclo(1-3/4-10/5-8)[Ac-DGlu(1),DCpa(2), DLys(3),Asp(4),Glu(5), DNal(6),Lys(8),Dpr(10)] GnRH (27) was inactive at 500 microgram/rat with a corresponding low affinity (K(i) = 4.6 nM) when compared to those of the most potent analogues (K(i) < 0.5 nM).
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Affiliation(s)
- J E Rivier
- The Clayton Foundation Laboratories for Peptide Biology, The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
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Niwa M, Morikawa MA, Higashi N. Controllable Orientation of Helical Poly(L-glutamic acid) Rods through Macrodipole Interaction on Gold Surfaces and Vectorial Electron Transfer. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/(sici)1521-3757(20000303)112:5<990::aid-ange990>3.0.co;2-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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41
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Abstract
Theoretical calculations (Hendsch ZS & Tidor B, 1994, Protein Sci 3:211-226) and experiments (Waldburger CD et al., 1995, Nat Struct Biol 2:122-128; Wimley WC et al., 1996, Proc Natl Acad Sci USA 93:2985-2990) suggest that hydrophobic interactions are more stabilizing than salt bridges in protein folding. The lack of apparent stability benefit for many salt bridges requires an alternative explanation for their occurrence within proteins. To examine the effect of salt bridges on protein structure and stability in more detail, we have developed an energy function for simple cubic lattice polymers based on continuum electrostatic calculations of a representative selection of salt bridges found in known protein crystal structures. There are only three types of residues in the model, with charges of -1, 0, or + 1. We have exhaustively enumerated conformational space and significant regions of sequence space for three-dimensional cubic lattice polymers of length 16. The results demonstrate that, while the more highly charged sequences are less stable, the loss of stability is accompanied by a substantial reduction in the degeneracy of the lowest-energy state. Moreover, the reduction in degeneracy is greater due to charges that pair than for lone charges that remain relatively exposed to solvent. We have also explored and illustrated the use of ion-pairing strategies for rational structural design using model lattice studies.
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Affiliation(s)
- C V Sindelar
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139-4307, USA
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42
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Rivier J, Lahrichi SL, Gulyas J, Erchegyi J, Koerber SC, Craig AG, Corrigan A, Rivier C, Vale W. Minimal-size, constrained corticotropin-releasing factor agonists with i-(i+3) Glu-Lys and Lys-Glu bridges. J Med Chem 1998; 41:2614-20. [PMID: 9651165 DOI: 10.1021/jm980164e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In three earlier publications (Miranda et al. J. Med. Chem. 1994, 37, 1450-1459; 1997, 40, 3651-3658; Gulyas et al. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 10575-10579) we have hypothesized that covalent constraints such as side-chain-to-side-chain lactam rings would stabilize an alpha-helical conformation shown to be important for the recognition and binding of the CRF C-terminus 30 residues, to CRF receptors. These studies led to the discovery of useful CRF antagonists such as alpha-helical CRF (alpha-hel-CRF) and Astressin both in vitro and in vivo. To test the hypothesis that such lactam rings may also be modulating activation of the receptor when introduced at the N-terminus of CRF, we studied the influence of the successive introduction from residues 4 to 14 of a cyclo(i, i+3)[Lysi-Glu(i+3)] and a cyclo(i,i+3)[Glui-Lys(i+3)] bridge on the in vitro potency of the agonist [Ac-Pro4,dPhe12,Nle21,38]hCRF(4-41) and related compounds. We have also introduced the favored cyclo(Glu30-Lys33) substitution found to be remarkable in several families of antagonists (such as Astressin) and in a number of CRF agonists and investigated the role of residues 4-8 on receptor activation using successive deletions. Earlier studies had shown that in both oCRF and alpha-helical CRF, deletion of residues 1-6, 1-7, and 1-8 led to gradual loss of intrinsic activity (IA) (from 50% IA to <10% IA) resulting in alpha-hel-CRF being a potent competitive antagonist. We show that acetylation of the N-terminus of these fragments generally increases potency by a factor of 2-3 with no influence on IA. While cyclo(30-33)[Ac-Leu8,dPhe12,Nle21, Glu30,Lys33,Nle38]hCRF(8-41) (30) is the shortest reported analogue of CRF to be equipotent to CRF (70% IA), the corresponding linear analogue (31) is 120 times less potent (59% IA). Addition of one amino acid at the N-terminus ¿cyclo(30-33)[Ac-Ser7,dPhe12,Nle21, Glu30,Lys33,Nle38]hCRF(7-41) (28)¿ results in a 5-fold increase in agonist potency and full intrinsic activity (113%). The most favored modifications were also introduced in other members of the CRF family including sauvagine (Sau), urotensin (Utn), urocortin (Ucn), and alpha-hel-CRF. Parallel and consistent results were obtained suggesting that the lactam cyclization at residues 29-32 and 30-33 (for the members of the CRF family with 40 and 41 amino acid residues, respectively) will induce (in the shortened agonists) a structural constraint (alpha-helix) that stabilizes a bioactive conformation similar to that shown in the Astressin family of CRF antagonists and that residue 8 (leucine or isoleucine) bears the sole responsibility for activation of the receptor since deletion of that residue leads to potent antagonists (Gulyas et al. Proc. Natl. Acad.Sci. U.S.A. 1995, 92, 10575-10579).
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MESH Headings
- Amino Acid Sequence
- Animals
- Cells, Cultured
- Chromatography, High Pressure Liquid
- Corticotropin-Releasing Hormone/agonists
- Corticotropin-Releasing Hormone/analogs & derivatives
- Corticotropin-Releasing Hormone/chemical synthesis
- Corticotropin-Releasing Hormone/pharmacology
- Electrophoresis, Capillary
- Glutamine/chemistry
- Humans
- Lysine/chemistry
- Mass Spectrometry
- Molecular Sequence Data
- Peptides, Cyclic/chemical synthesis
- Peptides, Cyclic/chemistry
- Peptides, Cyclic/pharmacology
- Pituitary Gland, Anterior/cytology
- Pituitary Gland, Anterior/drug effects
- Pituitary Gland, Anterior/metabolism
- Rats
- Rats, Sprague-Dawley
- Sheep
- Structure-Activity Relationship
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Affiliation(s)
- J Rivier
- The Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
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43
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Marx UC, Adermann K, Bayer P, Meyer M, Forssmann WG, Rösch P. Structure-activity relation of NH2-terminal human parathyroid hormone fragments. J Biol Chem 1998; 273:4308-16. [PMID: 9468478 DOI: 10.1074/jbc.273.8.4308] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Human parathyroid hormone (hPTH) is involved in the regulation of the calcium level in blood. This hormone function is located in the NH2-terminal 34 amino acids of the 84-amino acid peptide hormone and is transduced via the adenylate cyclase and the phosphatidylinositol signaling pathways. It is well known that truncation of the two NH2-terminal amino acids of the hormone leads to complete loss of in vivo normocalcemic function. To correlate loss of calcium level regulatory activity after stepwise NH2-terminal truncation and solution structure, we studied the conformations of fragments hPTH-(2-37), hPTH-(3-37), and hPTH-(4-37) in comparison to hPTH-(1-37) in aqueous buffer solution under near physiological conditions by circular dichroism spectroscopy, two-dimensional nuclear magnetic resonance spectroscopy, and restrained molecular dynamics calculations. All peptides show helical structures and hydrophobic interactions between Leu-15 and Trp-23 that lead to a defined loop region from His-14 to Ser-17. A COOH-terminal helix from Met-18 to at least Leu-28 was found for all peptides. The helical structure in the NH2-terminal part of the peptides was lost in parallel with the NH2-terminal truncation and can be correlated with the loss of calcium regulatory activity.
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Affiliation(s)
- U C Marx
- Lehrstuhl für Biopolymere, Universität Bayreuth, D-95440 Bayreuth, Federal Republic of Germany
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44
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Lauer JL, Fields GB. Design and Use of Synthetic Peptides as Biological Models. Proteins 1998. [DOI: 10.1016/b978-012058785-8/50005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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45
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Abstract
Helix-capping motifs are specific patterns of hydrogen bonding and hydrophobic interactions found at or near the ends of helices in both proteins and peptides. In an alpha-helix, the first four >N-H groups and last four >C=O groups necessarily lack intrahelical hydrogen bonds. Instead, such groups are often capped by alternative hydrogen bond partners. This review enlarges our earlier hypothesis (Presta LG, Rose GD. 1988. Helix signals in proteins. Science 240:1632-1641) to include hydrophobic capping. A hydrophobic interaction that straddles the helix terminus is always associated with hydrogen-bonded capping. From a global survey among proteins of known structure, seven distinct capping motifs are identified-three at the helix N-terminus and four at the C-terminus. The consensus sequence patterns of these seven motifs, together with results from simple molecular modeling, are used to formulate useful rules of thumb for helix termination. Finally, we examine the role of helix capping as a bridge linking the conformation of secondary structure to supersecondary structure.
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Affiliation(s)
- R Aurora
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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46
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DeOliveira DB, Laursen RA. Control of Calcite Crystal Morphology by a Peptide Designed To Bind to a Specific Surface. J Am Chem Soc 1997. [DOI: 10.1021/ja972270w] [Citation(s) in RCA: 204] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel B. DeOliveira
- Contribution from the Department of Chemistry, Boston University, Boston, Massachusetts 02215
| | - Richard A. Laursen
- Contribution from the Department of Chemistry, Boston University, Boston, Massachusetts 02215
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47
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Fleming T, Littlechild J. Sequence and structural comparison of thermophilic phosphoglycerate kinases with a mesophilic equivalent. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART A, PHYSIOLOGY 1997; 118:439-51. [PMID: 9406428 DOI: 10.1016/s0300-9629(97)00005-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The monomeric glycolytic enzyme phosphoglycerate kinase (PGK) has been used as a model system to study protein thermostability. The primary sequence of this enzyme has been elucidated from 47 species to date. Although only 42 amino acids are totally conserved, most of which line the active site cleft, the protein is structurally conserved. This is achieved by making conservative changes to maintain the same secondary and tertiary folds. The crystal structures of 5 PGK enzymes have been solved by X-ray diffraction methods. This paper seeks to use the available information to understand protein thermostability. Although some general mechanisms to increase stability can be determined, different species have adopted a variety of subtle additive changes to achieve greater protein stability. Comparisons have been directly made between the PGK enzyme from yeast, the moderate thermophilic bacterium Bacillus stearothermophilus, the hyperthermophilic bacteria Thermus thermophilus, Thermotoga maritima, and the hyperthermophilic archaea Sulpholobus solfataricus and Methanothermus fervidus.
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Affiliation(s)
- T Fleming
- Department of Chemistry, Exeter University, Devon, U.K
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48
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Gazzara JA, Phillips MC, Lund-Katz S, Palgunachari MN, Segrest JP, Anantharamaiah GM, Snow JW. Interaction of class A amphipathic helical peptides with phospholipid unilamellar vesicles. J Lipid Res 1997. [DOI: 10.1016/s0022-2275(20)37143-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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49
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Kuhlman B, Yang HY, Boice JA, Fairman R, Raleigh DP. An exceptionally stable helix from the ribosomal protein L9: implications for protein folding and stability. J Mol Biol 1997; 270:640-7. [PMID: 9245593 DOI: 10.1006/jmbi.1997.1146] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The ribosomal protein L9 has an unusual structure comprising two compact globular domains connected by a 34 residue alpha-helix. The middle 17 residues of the helix are exposed to solvent while the first seven pack against and form part of the N-terminal domain, and the last ten form part of the C-terminal domain. Here we report results which show that a peptide corresponding to the central helix of L9 is monomeric in aqueous solution and >85% helical at 1 degrees C and 68(+/-7)% helical at 25 degrees C. This is considerably more helical than any other protein fragment studied to date. Another peptide corresponding to the middle 17 residues of the helix is monomeric and is 41(+/-4)% helical at 1 degrees C. Because the central helix has high intrinsic stability the globular N and C-terminal domains will likely be stabilized by their interactions with the helix. Therefore, the stability of the two terminal domains should not be completely independent because both domains gain stability from a shared structural element, the central helix. Also, the ability of the central helix to form native-like structure in isolation highlights a potential role for the helix in the early stages of the folding process.
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Affiliation(s)
- B Kuhlman
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, NY, 11794-3400, USA
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50
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Kohn WD, Kay CM, Hodges RS. Positional dependence of the effects of negatively charged Glu side chains on the stability of two-stranded α-helical coiled-coils. J Pept Sci 1997. [DOI: 10.1002/(sici)1099-1387(199705)3:3<209::aid-psc102>3.0.co;2-s] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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