201
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Senior L, Crump MP, Williams C, Booth PJ, Mann S, Perriman AW, Curnow P. Structure and function of the silicifying peptide R5. J Mater Chem B 2015; 3:2607-2614. [DOI: 10.1039/c4tb01679c] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first detailed description of the structure and function of the silicifying peptide R5.
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Affiliation(s)
- Laura Senior
- School of Biochemistry
- University of Bristol
- UK
- Bristol Centre for Functional Nanomaterials
- University of Bristol
| | | | | | | | | | - Adam W. Perriman
- School of Cellular and Molecular Medicine
- University of Bristol
- UK
| | - Paul Curnow
- School of Biochemistry
- University of Bristol
- UK
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202
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Banerjee PR, Pande A, Shekhtman A, Pande J. Molecular mechanism of the chaperone function of mini-α-crystallin, a 19-residue peptide of human α-crystallin. Biochemistry 2014; 54:505-15. [PMID: 25478825 PMCID: PMC4303307 DOI: 10.1021/bi5014479] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
α-Crystallin
is the archetypical chaperone of the small heat-shock
protein family, all members of which contain the so-called “α-crystallin
domain” (ACD). This domain and the N- and C-terminal extensions
are considered the main functional units in its chaperone function.
Previous studies have shown that a 19-residue fragment of the ACD
of human αA-crystallin called mini-αA-crystallin (MAC)
shows chaperone properties similar to those of the parent protein.
Subsequent studies have confirmed the function of this peptide, but
no studies have addressed the mechanistic basis for the chaperone
function of MAC. Using human γD-crystallin (HGD), a key substrate
protein for parent α-crystallin in the ocular lens, we show
here that MAC not only protects HGD from aggregation during thermal
and chemical unfolding but also binds weakly and reversibly to HGD
(Kd ≈ 200–700 μM)
even when HGD is in the native state. However, at temperatures favoring
the unfolding of HGD, MAC forms a stable complex with HGD similar
to parent α-crystallin. Using nuclear magnetic resonance spectroscopy,
we identify the residues in HGD that are involved in these two modes
of binding and show that MAC protects HGD from aggregation by binding
to Phe 56 and Val 132 at the domain interface of the target protein,
and residues Val 164 to Leu 167 in the core of the C-terminal domain.
Furthermore, we suggest that the low-affinity, reversible binding
of MAC on the surface of HGD in the native state is involved in facilitating
its binding to both the domain interface and core regions during the
early stages of the unfolding of HGD. This work highlights some structural
features of MAC and MAC-like peptides that affect their chaperone
activity and can potentially be manipulated for translational studies.
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Affiliation(s)
- Priya R Banerjee
- Department of Chemistry, Life Sciences, University at Albany, State University of New York , Albany, New York 12222, United States
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203
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Koerber JT, Hornsby MJ, Wells JA. An improved single-chain Fab platform for efficient display and recombinant expression. J Mol Biol 2014; 427:576-86. [PMID: 25481745 DOI: 10.1016/j.jmb.2014.11.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/17/2014] [Accepted: 11/25/2014] [Indexed: 12/13/2022]
Abstract
Antibody phage display libraries combined with high-throughput selections have recently demonstrated tremendous promise to create the next generation of renewable, recombinant antibodies to study proteins and their many post-translational modification states; however, many challenges still remain, such as optimized antibody scaffolds. Recently, a single-chain fragment antigen binding (Fab) (scFab) format, in which the carboxy-terminus of the light chain is linked to the amino-terminus of the heavy chain, was described to potentially combine the high display levels of a single-chain fragment variable with the high stability of purified Fabs. However, this format required removal of the interchain disulfide bond to achieve modest display levels and subsequent bacterial expression resulted in high levels of aggregated scFab, hindering further use of scFabs. Here, we developed an improved scFab format that retains the interchain disulfide bond by increasing the linker length between the light and heavy chains to improve display and bacterial expression levels to 1-3 mg/L. Furthermore, rerouting of the scFab to the co-translational signal recognition particle pathway combined with reengineering of the signal peptide sequence results in display levels 24-fold above the original scFab format and 3-fold above parent Fab levels. This optimized scFab scaffold can be easily reformatted in a single step for expression in a bacterial or mammalian host to produce stable (Tm of 81 °C), predominantly monomeric (>90%) antibodies at a high yield. Ultimately, this new scFab format will advance high-throughput antibody generation platforms to discover the next generation of research and therapeutic antibodies.
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Affiliation(s)
- James T Koerber
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA; Recombinant Antibody Network, University of California, San Francisco, CA, 94158, USA
| | - Michael J Hornsby
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA; Recombinant Antibody Network, University of California, San Francisco, CA, 94158, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA; Recombinant Antibody Network, University of California, San Francisco, CA, 94158, USA.
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204
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Chakraborty S, Rao B, Dandekar A. PAGAL - Properties and corresponding graphics of alpha helical structures in proteins. F1000Res 2014; 3:206. [PMID: 25352981 PMCID: PMC4207245 DOI: 10.12688/f1000research.4952.2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/17/2014] [Indexed: 11/20/2022] Open
Abstract
Alpha helices (AH) are peptide fragments characterized by regular patterns of hydrogen bonding between the carbonyl oxygen and amino nitrogen of residues regularly spaced in sequence, resulting in spiral conformations. Their preponderance in protein structures underlines their importance. Interestingly, AHs are present in most anti-microbial peptides, although they might remain in random-coil conformations depending on the solvent dielectric. For example, the cecropin component of the chimeric anti-microbial protein designed previously by our group comprises of two AHs linked by a short stretch of random coil. These anti-microbial peptides are often amphipathic (quantified by a hydrophobic moment), aligning hydrophobic residues on one surface and charged residues on the others. In the current work, we reproduce previously described computational methods to compute the hydrophobic moment of AHs - and provide open access to the source code (PAGAL). We simultaneously generated input files for TikZ (a package for creating high resolution graphics programmatically) to obtain the Edmundson wheel and showing the direction and magnitude of the hydrophobic moment, and Pymol scripts to generate color coded protein surfaces. Additionally, we have observed an empirical structural property of AHs: the distance between the Cα atoms of the ith and (i+4)th residue is equal to the distance between the carbonyl oxygens of the ith and (i+4)th residue. We validated this using 100 non-homologous high resolution structures from the PISCES database. The source code and manual is available at http://github.com/sanchak/pagal and on http://dx.doi.org/10.5281/zenodo.11136.
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Affiliation(s)
- Sandeep Chakraborty
- Plant Sciences Department, University of California, Davis, 95616, USA ; Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Basuthkar Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Abhaya Dandekar
- Plant Sciences Department, University of California, Davis, 95616, USA
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205
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Gunawan ST, Liang K, Such GK, Johnston APR, Leung MKM, Cui J, Caruso F. Engineering enzyme-cleavable hybrid click capsules with a pH-sheddable coating for intracellular degradation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:4080-4086. [PMID: 25044500 DOI: 10.1002/smll.201400450] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Indexed: 06/03/2023]
Abstract
The engineering of layer-by-layer (LbL) hybrid click capsules that are responsive to biological stimuli is reported. The capsules comprise a pH-sheddable, non cross-linked outer coating that protects enzyme-cleavable inner layers. Upon cellular uptake, the outer coating is released and the capsules are enzymatically degraded. In vitro cell degradation results in rapid capsule degradation (10 min) upon cellular internalization.
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Affiliation(s)
- Sylvia T Gunawan
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
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206
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Vymětal J, Bathula SR, Černý J, Chaloupková R, Žídek L, Sklenář V, Vondrášek J. Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition. Protein Eng Des Sel 2014; 27:463-72. [DOI: 10.1093/protein/gzu046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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207
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A view of the E2-CD81 interface at the binding site of a neutralizing antibody against hepatitis C virus. J Virol 2014; 89:492-501. [PMID: 25339761 DOI: 10.1128/jvi.01661-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED Hepatitis C virus (HCV) glycoprotein E2 is considered a major target for generating neutralizing antibodies against HCV, primarily due to its role of engaging host entry factors, such as CD81, a key cell surface protein associated with HCV entry. Based on a series of biochemical analyses in combination with molecular docking, we present a description of a potential binding interface formed between the E2 protein and CD81. The virus side of this interface includes a hydrophobic helix motif comprised of residues W(437)LAGLF(442), which encompasses the binding site of a neutralizing monoclonal antibody, mAb41. The helical conformation of this motif provides a structural framework for the positioning of residues F442 and Y443, serving as contact points for the interaction with CD81. The cell side of this interface likewise involves a surface-exposed hydrophobic helix, namely, the D-helix of CD81, which coincides with the binding site of 1D6, a monoclonal anti-CD81 antibody known to block HCV entry. Our illustration of this virus-host interface suggests an important role played by the W(437)LAGLF(442) helix of the E2 protein in the hydrophobic interaction with the D-helix of CD81, thereby facilitating our understanding of the mechanism for antibody-mediated neutralization of HCV. IMPORTANCE Characterization of the interface established between a virus and host cells can provide important information that may be used for the control of virus infections. The interface that enables hepatitis C virus (HCV) to infect human liver cells has not been well understood because of the number of cell surface proteins, factors, and conditions found to be associated with the infection process. Based on a series of biochemical analyses in combination with molecular docking, we present such an interface, consisting of two hydrophobic helical structures, from the HCV E2 surface glycoprotein and the CD81 protein, a major host cell receptor recognized by all HCV strains. Our study reveals the critical role played by hydrophobic interactions in the formation of this virus-host interface, thereby contributing to our understanding of the mechanism for antibody-mediated neutralization of HCV.
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208
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Hoffmann F, Vancea I, Kamat SG, Strodel B. Protein structure prediction: assembly of secondary structure elements by basin-hopping. Chemphyschem 2014; 15:3378-90. [PMID: 25056272 DOI: 10.1002/cphc.201402247] [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: 04/15/2014] [Indexed: 12/30/2022]
Abstract
The prediction of protein tertiary structure from primary structure remains a challenging task. One possible approach to this problem is the application of basin-hopping global optimization combined with an all-atom force field. In this work, the efficiency of basin-hopping is improved by introducing an approach that derives tertiary structures from the secondary structure assignments of individual residues. This approach is termed secondary-to-tertiary basin-hopping and benchmarked for three miniproteins: trpzip, trp-cage and ER-10. For each of the three miniproteins, the secondary-to-tertiary basin-hopping approach successfully and reliably predicts their three-dimensional structure. When it is applied to larger proteins, correctly folded structures are obtained. It can be concluded that the assembly of secondary structure elements using basin-hopping is a promising tool for de novo protein structure prediction.
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Affiliation(s)
- Falk Hoffmann
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany)
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209
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Nelson MD, Trojanowski NF, George-Raizen JB, Smith CJ, Yu CC, Fang-Yen C, Raizen DM. The neuropeptide NLP-22 regulates a sleep-like state in Caenorhabditis elegans. Nat Commun 2014; 4:2846. [PMID: 24301180 PMCID: PMC3867200 DOI: 10.1038/ncomms3846] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 10/30/2013] [Indexed: 11/09/2022] Open
Abstract
Neuropeptides play central roles in the regulation of homeostatic behaviors such as sleep and feeding. Caenorhabditis elegans displays sleep-like quiescence of locomotion and feeding during a larval transition stage called lethargus and feeds during active larval and adult stages. Here we show that the neuropeptide NLP-22 is a regulator of Caenorhabditis elegans sleep-like quiescence observed during lethargus. nlp-22 shows cyclical mRNA expression in synchrony with lethargus; it is regulated by LIN-42, an orthologue of the core circadian protein PERIOD; and it is expressed solely in the two RIA interneurons. nlp-22 and the RIA interneurons are required for normal lethargus quiescence, and forced expression of nlp-22 during active stages causes anachronistic locomotion and feeding quiescence. Optogenetic stimulation of RIA interneurons has a movement-promoting effect, demonstrating functional complexity in a single neuron type. Our work defines a quiescence-regulating role for NLP-22 and expands our knowledge of the neural circuitry controlling Caenorhabditis elegans behavioral quiescence.
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Affiliation(s)
- M D Nelson
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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210
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Rapsch K, Bier FF, von Nickisch-Rosenegk M. Rational design of artificial β-strand-forming antimicrobial peptides with biocompatible properties. Mol Pharm 2014; 11:3492-502. [PMID: 25192319 DOI: 10.1021/mp500271c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Because the intensive use of antibiotics has led to a large variety of resistant bacterial strains, therapeutic measures have become increasingly challenging. In order to ensure reliable treatment of diseases, alternative antimicrobial agents need to be explored. In this context, antimicrobial peptides have been discussed as novel bioactive molecules, which, however, may be limited in their applicability due to their high manufacturing costs and poor pharmacokinetic properties. Consequently, the design of artificial antimicrobial peptides featuring two flanking cationic regions and a hydrophobic center is presented. These sequences led to distinct antimicrobial activity on the same order of magnitude as that of naturally occurring reference peptides but with less cytotoxic or cytostatic drawbacks. Furthermore, a deletion and substitution library revealed the minimal sequence requirements. By analysis of the computed 3D structures of these peptides, a single characteristic β-strand was identified. This structural motif was pivotal for antimicrobial activity. Consequently, an optimized peptide sequence with antimicrobial and biocompatible properties was derived, and its application was demonstrated in a mixed culture experiment. Thus, it was shown that the optimized artificial antimicrobial peptide is suitable as a therapeutic agent and may be used as template for the development of new antimicrobial peptides with unique secondary structures.
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Affiliation(s)
- Karsten Rapsch
- Fraunhofer Institute for Biomedical Engineering IBMT , Branch Potsdam, Am Muehlenberg 13, 14476 Potsdam, Germany
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211
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Shen Y, Maupetit J, Derreumaux P, Tufféry P. Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction. J Chem Theory Comput 2014; 10:4745-58. [DOI: 10.1021/ct500592m] [Citation(s) in RCA: 416] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yimin Shen
- INSERM U973, MTi, F-75205 Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Julien Maupetit
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, F-75005 Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, F-75005 Paris, France
- Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Pierre Tufféry
- INSERM U973, MTi, F-75205 Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
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212
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Affiliation(s)
- Zhaoqian Su
- Physics Department, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Cristiano L. Dias
- Physics Department, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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213
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Singh PK, Sharma S, Kumari A, Korpole S. A non-pediocin low molecular weight antimicrobial peptide produced by Pediococcus pentosaceus strain IE-3 shows increased activity under reducing environment. BMC Microbiol 2014; 14:226. [PMID: 25158757 PMCID: PMC4243815 DOI: 10.1186/s12866-014-0226-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 08/18/2014] [Indexed: 11/26/2022] Open
Abstract
Background Species of the genus Pediococcus are known to produce antimicrobial peptides such as pediocin-like bacteriocins that contain YGNGVXC as a conserved motif at their N-terminus. Until now, the molecular weight of various bacteriocins produced by different strains of the genus Pediococcus have been found to vary between 2.7 to 4.6 kD. In the present study, we characterized an antimicrobial peptide produced by P. pentosaceus strain IE-3. Results Antimicrobial peptide was isolated and purified from the supernatant of P. pentosaceus strain IE-3 grown for 48 h using cation exchange chromatography and reversed-phase high-performance liquid chromatography (RP-HPLC) techniques. While MALDI-TOF MS experiments determined the precise molecular mass of the peptide to be 1701.00 Da, the de novo sequence (APVPFSCTRGCLTHLV) of the peptide revealed no similarity with reported pediocins and did not contain the YGNGVXC conserved motif. Unlike pediocin-like bacteriocins, the low molecular weight peptide (LMW) showed resistance to different proteases. Moreover, peptide treated with reducing agent like dithiothreitol (DTT) exhibited increased activity against both Gram-positive and Gram-negative test strains in comparison to native peptide. However, peptide treated with oxidizing agent such as hydrogen peroxide (H2O2) did not show any antimicrobial activity. Conclusion To our knowledge this is the lowest molecular weight peptide produced by members of the genus Pediococcus. The low molecular weight peptide shared amino acid arrangement with N-terminal sequence of Class IIa, pediocin-like bacteriocins and showed increased activity under reducing conditions. Antimicrobial peptides active under reduced conditions are valuable for the preservation of processed foods like meat, dairy and canned foods where low redox potential prevails.
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Affiliation(s)
| | | | | | - Suresh Korpole
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, 160036, Chandigarh, India.
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214
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HCV E2 core structures and mAbs: something is still missing. Drug Discov Today 2014; 19:1964-70. [PMID: 25172800 DOI: 10.1016/j.drudis.2014.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/17/2014] [Accepted: 08/21/2014] [Indexed: 02/07/2023]
Abstract
The lack of structural information on hepatitis C virus (HCV) surface proteins has so far hampered the development of effective vaccines. Recently, two crystallographic structures have described the core portion (E2c) of E2 surface glycoprotein, the primary mediator of HCV entry. Despite the importance of these studies, the E2 overall structure is still unknown and, most importantly, several biochemical and functional studies are in disagreement with E2c structures. Here, the main literature will be discussed and an alternative disulfide bridge pattern will be proposed, based on unpublished human monoclonal antibody reactivity. A modeling strategy aiming at recapitulating the available structural and functional studies of E2 will also be proposed.
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215
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Kar P, Feig M. Recent advances in transferable coarse-grained modeling of proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:143-80. [PMID: 25443957 PMCID: PMC5366245 DOI: 10.1016/bs.apcsb.2014.06.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Computer simulations are indispensable tools for studying the structure and dynamics of biological macromolecules. Biochemical processes occur on different scales of length and time. Atomistic simulations cannot cover the relevant spatiotemporal scales at which the cellular processes occur. To address this challenge, coarse-grained (CG) modeling of the biological systems is employed. Over the last few years, many CG models for proteins continue to be developed. However, many of them are not transferable with respect to different systems and different environments. In this review, we discuss those CG protein models that are transferable and that retain chemical specificity. We restrict ourselves to CG models of soluble proteins only. We also briefly review recent progress made in the multiscale hybrid all-atom/CG simulations of proteins.
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Affiliation(s)
- Parimal Kar
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA; Department of Chemistry, Michigan State University, East Lansing, Michigan, USA.
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216
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Mahdavi M, Keyhanfar M, Jafarian A, Mohabatkar H, Rabbani M. Immunization with a novel chimeric peptide representing B and T cell epitopes from HER2 extracellular domain (HER2 ECD) for breast cancer. Tumour Biol 2014; 35:12049-57. [DOI: 10.1007/s13277-014-2503-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/13/2014] [Indexed: 11/24/2022] Open
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217
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Pichlo M, Bungert-Plümke S, Weyand I, Seifert R, Bönigk W, Strünker T, Kashikar ND, Goodwin N, Müller A, Pelzer P, Van Q, Enderlein J, Klemm C, Krause E, Trötschel C, Poetsch A, Kremmer E, Kaupp UB, Körschen HG, Collienne U. High density and ligand affinity confer ultrasensitive signal detection by a guanylyl cyclase chemoreceptor. J Cell Biol 2014; 206:541-57. [PMID: 25135936 PMCID: PMC4137060 DOI: 10.1083/jcb.201402027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 07/15/2014] [Indexed: 12/28/2022] Open
Abstract
Guanylyl cyclases (GCs), which synthesize the messenger cyclic guanosine 3',5'-monophosphate, control several sensory functions, such as phototransduction, chemosensation, and thermosensation, in many species from worms to mammals. The GC chemoreceptor in sea urchin sperm can decode chemoattractant concentrations with single-molecule sensitivity. The molecular and cellular underpinnings of such ultrasensitivity are not known for any eukaryotic chemoreceptor. In this paper, we show that an exquisitely high density of 3 × 10(5) GC chemoreceptors and subnanomolar ligand affinity provide a high ligand-capture efficacy and render sperm perfect absorbers. The GC activity is terminated within 150 ms by dephosphorylation steps of the receptor, which provides a means for precise control of the GC lifetime and which reduces "molecule noise." Compared with other ultrasensitive sensory systems, the 10-fold signal amplification by the GC receptor is surprisingly low. The hallmarks of this signaling mechanism provide a blueprint for chemical sensing in small compartments, such as olfactory cilia, insect antennae, or even synaptic boutons.
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Affiliation(s)
- Magdalena Pichlo
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
| | - Stefanie Bungert-Plümke
- Marine Biological Laboratory, Woods Hole, MA 02543 Institute of Complex Systems (ICS-4), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ingo Weyand
- Marine Biological Laboratory, Woods Hole, MA 02543 Institute of Complex Systems (ICS-4), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Reinhard Seifert
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
| | - Wolfgang Bönigk
- Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Timo Strünker
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
| | - Nachiket Dilip Kashikar
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543 Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton BN1 9QG, England, UK
| | - Normann Goodwin
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543 Babraham Institute, Cambridge CB22 3AT, England, UK
| | - Astrid Müller
- Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Patric Pelzer
- Marine Biological Laboratory, Woods Hole, MA 02543 Department of Functional Neuroanatomy, Institute of Anatomy and Cell Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Qui Van
- III. Physikalisches Institut, Universität Göttingen, 37077 Göttingen, Germany
| | - Jörg Enderlein
- III. Physikalisches Institut, Universität Göttingen, 37077 Göttingen, Germany
| | - Clementine Klemm
- Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Eberhard Krause
- Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | | | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum. 44801 Bochum, Germany
| | - Elisabeth Kremmer
- Institut für Molekulare Immunologie, Helmholtz-Zentrum München, 81377 München, Germany
| | - U Benjamin Kaupp
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
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Sakib MS, Islam MR, Hasan AKMM, Nabi AHMN. Prediction of epitope-based peptides for the utility of vaccine development from fusion and glycoprotein of nipah virus using in silico approach. Adv Bioinformatics 2014; 2014:402492. [PMID: 25147564 PMCID: PMC4131549 DOI: 10.1155/2014/402492] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/05/2014] [Accepted: 05/11/2014] [Indexed: 01/25/2023] Open
Abstract
This study aims to design epitope-based peptides for the utility of vaccine development by targeting glycoprotein G and envelope protein F of Nipah virus (NiV) that, respectively, facilitate attachment and fusion of NiV with host cells. Using various databases and tools, immune parameters of conserved sequence(s) from G and F proteins of different isolates of NiV were tested to predict probable epitope(s). Binding analyses of the peptides with MHC class-I and class-II molecules, epitope conservancy, population coverage, and linear B cell epitope prediction were analyzed. Predicted peptides interacted with seven or more MHC alleles and illustrated population coverage of more than 99% and 95%, for G and F proteins, respectively. The predicted class-I nonamers, SLIDTSSTI and EWISIVPNF, superimposed on the putative decameric B cell epitopes, were also identified as core sequences of the most probable class-II 15-mer peptides GPKVSLIDTSSTITI and EWISIVPNFILVRNT. These peptides were further validated for their binding to specific HLA alleles using in silico docking technique. Our in silico analysis suggested that the predicted epitopes, either GPKVSLIDTSSTITI or EWISIVPNFILVRNT, could be a better choice as universal vaccine component against NiV irrespective of different isolates which may elicit both humoral and cell-mediated immunity.
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Affiliation(s)
- M. Sadman Sakib
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Md. Rezaul Islam
- International Max Planck Research School for Neurosciences, University of Göttingen, 37077 Göttingen, Germany
| | - A. K. M. Mahbub Hasan
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - A. H. M. Nurun Nabi
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
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219
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Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev 2014; 43:4871-93. [PMID: 24759934 PMCID: PMC4426487 DOI: 10.1039/c4cs00048j] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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220
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Barnea ER, Lubman DM, Liu YH, Absalon-Medina V, Hayrabedyan S, Todorova K, Gilbert RO, Guingab J, Barder TJ. Insight into PreImplantation Factor (PIF*) mechanism for embryo protection and development: target oxidative stress and protein misfolding (PDI and HSP) through essential RIKP [corrected] binding site. PLoS One 2014; 9:e100263. [PMID: 24983882 PMCID: PMC4077574 DOI: 10.1371/journal.pone.0100263] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 05/24/2014] [Indexed: 11/18/2022] Open
Abstract
Background Endogenous PIF, upon which embryo development is dependent, is secreted only by viable mammalian embryos, and absent in non-viable ones. Synthetic PIF (sPIF) administration promotes singly cultured embryos development and protects against their demise caused by embryo-toxic serum. To identify and characterize critical sPIF-embryo protein interactions novel biochemical and bio-analytical methods were specifically devised. Methods FITC-PIF uptake/binding by cultured murine and equine embryos was examined and compared with scrambled FITC-PIF (control). Murine embryo (d10) lysates were fractionated by reversed-phase HPLC, fractions printed onto microarray slides and probed with Biotin-PIF, IDE and Kv1.3 antibodies, using fluorescence detection. sPIF-based affinity column was developed to extract and identify PIF-protein interactions from lysates using peptide mass spectrometry (LC/MS/MS). In silico evaluation examined binding of PIF to critical targets, using mutation analysis. Results PIF directly targets viable cultured embryos as compared with control peptide, which failed to bind. Multistep Biotin-PIF targets were confirmed by single-step PIF-affinity column based isolation. PIF binds protein disulfide isomerases a prolyl-4-hydroxylase β-subunit, (PDI, PDIA4, PDIA6-like) containing the antioxidant thioredoxin domain. PIF also binds protective heat shock proteins (70&90), co-chaperone, BAG-3. Remarkably, PIF targets a common RIPK site in PDI and HSP proteins. Further, single PIF amino acid mutation significantly reduced peptide-protein target bonding. PIF binds promiscuous tubulins, neuron backbones and ACTA-1,2 visceral proteins. Significant anti-IDE, while limited anti-Kv1.3b antibody-binding to Biotin-PIF positive lysates HPLC fractions were documented. Conclusion Collectively, data identifies PIF shared targets on PDI and HSP in the embryo. Such are known to play a critical role in protecting against oxidative stress and protein misfolding. PIF-affinity-column is a novel utilitarian method for small molecule targets direct identification. Data reveals and completes the understanding of mechanisms involved in PIF-induced autotrophic and protective effects on the embryo.
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Affiliation(s)
- Eytan R. Barnea
- Research & Development, SIEP The Society for the Investigation of Early Pregnancy, Cherry Hill, New Jersey, United States of America
- Research & Development, BioIncept, LLC, Cherry Hill, New Jersey, United States of America
- Department of Obstetrics, Gynecology and Reproduction, UMDNJ-Robert Wood Johnson Medical School, Camden, New Jersey, United States of America
- * E-mail:
| | - David M. Lubman
- Department Surgery, University of Michigan Medical Center, Ann Arbor, Michigan, United States of America
| | - Yan-Hui Liu
- Department Surgery, University of Michigan Medical Center, Ann Arbor, Michigan, United States of America
| | - Victor Absalon-Medina
- Reproductive Medicine, Cornell University, College of Veterinary Medicine, Ithaca, New York, United States of America
| | - Soren Hayrabedyan
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Krassimira Todorova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Robert O. Gilbert
- Reproductive Medicine, Cornell University, College of Veterinary Medicine, Ithaca, New York, United States of America
| | - Joy Guingab
- Chemical Biology and Proteomics, Banyan Biomarkers, Alachua, Florida, United States of America
| | - Timothy J. Barder
- Research & Development, Eprogen, Downers Grove, Illinois, United States of America
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221
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Riedl S, Rinner B, Schaider H, Lohner K, Zweytick D. Killing of melanoma cells and their metastases by human lactoferricin derivatives requires interaction with the cancer marker phosphatidylserine. Biometals 2014; 27:981-97. [PMID: 24838743 PMCID: PMC4155172 DOI: 10.1007/s10534-014-9749-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/05/2014] [Indexed: 01/24/2023]
Abstract
Despite favorable advancements in therapy cancer is still not curative in many cases, which is often due to inadequate specificity for tumor cells. In this study derivatives of a short cationic peptide derived from the human host defense peptide lactoferricin were optimized in their selective toxicity towards cancer cells. We proved that the target of these peptides is the negatively charged membrane lipid phosphatidylserine (PS), specifically exposed on the surface of cancer cells. We have studied the membrane interaction of three peptides namely LF11-322, its N-acyl derivative 6-methyloctanoyl-LF11-322 and its retro repeat derivative R(etro)-DIM-P-LF11-322 with liposomes mimicking cancerous and non-cancerous cell membranes composed of PS and phosphatidylcholine (PC), respectively. Calorimetric and permeability studies showed that N-acylation and even more the repeat derivative of LF11-322 leads to strongly improved interaction with the cancer mimic PS, whereas only the N-acyl derivative also slightly affects PC. Tryptophan fluorescence of selective peptide R-DIM-P-LF11-322 revealed specific peptide penetration into the PS membrane interface and circular dichroism showed change of its secondary structure by increase of proportion of β-sheets just in the presence of the cancer mimic. Data correlated with in vitro studies with cell lines of human melanomas, their metastases and melanocytes, revealing R-DIM-P-LF11-322 to exhibit strongly increased specificity for cancer cells. This indicates the need of high affinity to the target PS, a minimum length and net positive charge, an adequate but moderate hydrophobicity, and capability of adoption of a defined structure exclusively in presence of the target membrane for high antitumor activity.
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Affiliation(s)
- Sabrina Riedl
- Biophysics Division, Institute of Molecular Biosciences, University of Graz, Schmiedlstraße 6, 8042, Graz, Austria
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222
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Ryder MP, Wu X, McKelvey GR, McGuire J, Schilke KF. Binding interactions of bacterial lipopolysaccharide and the cationic amphiphilic peptides polymyxin B and WLBU2. Colloids Surf B Biointerfaces 2014; 120:81-7. [PMID: 24905681 DOI: 10.1016/j.colsurfb.2014.05.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 05/01/2014] [Accepted: 05/02/2014] [Indexed: 11/26/2022]
Abstract
Passage of blood through a sorbent device for removal of bacteria and endotoxin by specific binding with immobilized, membrane-active, bactericidal peptides holds promise for treating severe blood infections. Peptide insertion in the target membrane and rapid/strong binding is desirable, while membrane disruption and release of degradation products to the circulating blood is not. Here we describe interactions between bacterial endotoxin (lipopolysaccharide, LPS) and the membrane-active, bactericidal peptides WLBU2 and polymyxin B (PmB). Analysis of the interfacial behavior of mixtures of LPS and peptide using air-water interfacial tensiometry and optical waveguide lightmode spectroscopy strongly suggests insertion of intact LPS vesicles by the peptide WLBU2 without vesicle destabilization. In contrast, dynamic light scattering (DLS) studies show that LPS vesicles appear to undergo peptide-induced destabilization in the presence of PmB. Circular dichroism spectra further confirm that WLBU2, which shows disordered structure in aqueous solution and substantially helical structure in membrane-mimetic environments, is stably located within the LPS membrane in peptide-vesicle mixtures. We therefore expect that presentation of WLBU2 at an interface, if tethered in a fashion which preserves its mobility and solvent accessibility, will enable the capture of bacteria and endotoxin without promoting reintroduction of endotoxin to the circulating blood, thus minimizing adverse clinical outcomes. On the other hand, our results suggest no such favorable outcome of LPS interactions with polymyxin B.
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Affiliation(s)
- Matthew P Ryder
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, United States
| | - Xiangming Wu
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, United States
| | - Greg R McKelvey
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, United States
| | - Joseph McGuire
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, United States
| | - Karl F Schilke
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, United States.
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223
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Saladin A, Rey J, Thévenet P, Zacharias M, Moroy G, Tufféry P. PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces. Nucleic Acids Res 2014; 42:W221-6. [PMID: 24803671 PMCID: PMC4086095 DOI: 10.1093/nar/gku404] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Peptide-protein interactions are important to many processes of life, particularly for signal transmission or regulatory mechanisms. When no information is known about the interaction between a protein and a peptide, it is of interest to propose candidate sites of interaction at the protein surface, to assist the design of biological experiments to probe the interaction, or to serve as a starting point for more focused in silico approaches. PEP-SiteFinder is a tool that will, given the structure of a protein and the sequence of a peptide, identify protein residues predicted to be at peptide-protein interface. PEP-SiteFinder relies on the 3D de novo generation of peptide conformations given its sequence. These conformations then undergo a fast blind rigid docking on the complete protein surface, and we have found, as the result of a benchmark over 41 complexes, that the best poses overlap to some extent the experimental patch of interaction for close to 90% complexes. In addition, PEP-SiteFinder also returns a propensity index we have found informative about the confidence of the prediction. The PEP-SiteFinder web server is available at http://bioserv.rpbs.univ-paris-diderot.fr/PEP-SiteFinder.
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Affiliation(s)
- Adrien Saladin
- INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Julien Rey
- INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France Ressource Parisienne en Bioinformatique Structurale, F-75205 Paris, France
| | - Pierre Thévenet
- INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | | | - Gautier Moroy
- INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Pierre Tufféry
- INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France Ressource Parisienne en Bioinformatique Structurale, F-75205 Paris, France
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224
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Tada S, Timucin E, Kitajima T, Sezerman OU, Ito Y. Direct in vitro selection of titanium-binding epidermal growth factor. Biomaterials 2014; 35:3497-503. [DOI: 10.1016/j.biomaterials.2014.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 01/07/2014] [Indexed: 02/01/2023]
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225
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Li Y, Surya W, Claudine S, Torres J. Structure of a conserved Golgi complex-targeting signal in coronavirus envelope proteins. J Biol Chem 2014; 289:12535-49. [PMID: 24668816 PMCID: PMC4007446 DOI: 10.1074/jbc.m114.560094] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Coronavirus envelope (CoV E) proteins are ∼100-residue polypeptides with at least one channel-forming α-helical transmembrane (TM) domain. The extramembrane C-terminal tail contains a completely conserved proline, at the center of a predicted β-coil-β motif. This hydrophobic motif has been reported to constitute a Golgi-targeting signal or a second TM domain. However, no structural data for this or other extramembrane domains in CoV E proteins is available. Herein, we show that the E protein in the severe acute respiratory syndrome virus has only one TM domain in micelles, whereas the predicted β-coil-β motif forms a short membrane-bound α-helix connected by a disordered loop to the TM domain. However, complementary results suggest that this motif is potentially poised for conformational change or in dynamic exchange with other conformations.
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Affiliation(s)
- Yan Li
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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226
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Malik-Chaudhry HK, Saavedra A, Liao J. A linker strategy for trans-FRET assay to determine activation intermediate of NEDDylation cascade. Biotechnol Bioeng 2014; 111:1288-95. [PMID: 24415255 DOI: 10.1002/bit.25183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 12/27/2013] [Accepted: 01/03/2014] [Indexed: 11/10/2022]
Abstract
Förster resonance energy transfer (FRET) technology has been widely used in biological and biomedical research and is a valuable tool for elucidating molecular interactions in vitro and in vivo. Quantitative FRET analysis is a powerful method for determining biochemical parameters and molecular distances at nanometer levels. Recently, we reported theoretical developments and experimental procedures for determining the dissociation constant, Kd and enzymatic kinetics parameters, Kcat and KM, of protein interactions with the engineered FRET pair, CyPet and YPet. The strong FRET signal from this pair made these developments possible. However, the direct link of fluorescent proteins with proteins of interests may interfere with the folding of some fusion proteins. Here, we report a new protein engineering strategy for improving FRET signals by adding a linker between the fluorescent protein and the targeted protein. This improvement allowed us to follow the covalent conjugation of NEDD8 to its E2 ligase in the presence of E1 and ATP, which was difficult to determine without linker. Three linkers, LAEAAAKEAA, TSGSPGLQEFGT, and LAAALAAA, which are alpha helix or random coil, all significantly improved the FRET signals. Our results show a general methodology for improving trans-FRET signals to effectively determine biochemical reaction intermediates.
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Affiliation(s)
- Harbani Kaur Malik-Chaudhry
- Department of Bioengineering, Center for Bioengineering Research, Bourns College of Engineering, 900 University Avenue, Riverside, California, 92521
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227
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Chandra D, Sankalia N, Arcibal I, Banta S, Cropek D, Karande P. Design of affinity peptides from natural protein ligands: A study of the cardiac troponin complex. Biopolymers 2014; 102:97-106. [DOI: 10.1002/bip.22436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 09/30/2013] [Accepted: 10/15/2013] [Indexed: 01/04/2023]
Affiliation(s)
- Divya Chandra
- Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; Troy NY
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy NY
| | - Nitesh Sankalia
- Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; Troy NY
| | - Imee Arcibal
- U.S. Army Engineer Research and Development Center; Construction Engineering Research Laboratory (CERL); Champaign IL
| | - Scott Banta
- Department of Chemical Engineering; Columbia University; New York NY
| | - Donald Cropek
- U.S. Army Engineer Research and Development Center; Construction Engineering Research Laboratory (CERL); Champaign IL
| | - Pankaj Karande
- Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; Troy NY
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy NY
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228
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Li M, Chang S, Yang L, Shi J, McFarland K, Yang X, Moller A, Wang C, Zou X, Chi C, Cui J. Conopeptide Vt3.1 preferentially inhibits BK potassium channels containing β4 subunits via electrostatic interactions. J Biol Chem 2014; 289:4735-42. [PMID: 24398688 DOI: 10.1074/jbc.m113.535898] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BK channel β subunits (β1-β4) modulate the function of channels formed by slo1 subunits to produce tissue-specific phenotypes. The molecular mechanism of how the homologous β subunits differentially alter BK channel functions and the role of different BK channel functions in various physiologic processes remain unclear. By studying channels expressed in Xenopus laevis oocytes, we show a novel disulfide-cross-linked dimer conopeptide, Vt3.1 that preferentially inhibits BK channels containing the β4 subunit, which is most abundantly expressed in brain and important for neuronal functions. Vt3.1 inhibits the currents by a maximum of 71%, shifts the G-V relation by 45 mV approximately half-saturation concentrations, and alters both open and closed time of single channel activities, indicating that the toxin alters voltage dependence of the channel. Vt3.1 contains basic residues and inhibits voltage-dependent activation by electrostatic interactions with acidic residues in the extracellular loops of the slo1 and β4 subunits. These results suggest a large interaction surface between the slo1 subunit of BK channels and the β4 subunit, providing structural insight into the molecular interactions between slo1 and β4 subunits. The results also suggest that Vt3.1 is an excellent tool for studying β subunit modulation of BK channels and for understanding the physiological roles of BK channels in neurophysiology.
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Affiliation(s)
- Min Li
- From the Institute of Protein Research, Tongji University, Shanghai 200092, China
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229
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Chung MK, Grigoryan H, Iavarone AT, Rappaport SM. Antibody Enrichment and Mass Spectrometry of Albumin-Cys34 Adducts. Chem Res Toxicol 2013; 27:400-7. [DOI: 10.1021/tx400337k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ming-Kei Chung
- Center
for Exposure Biology, School of Public Health, University of California, Berkeley, California 94720, United States
| | - Hasmik Grigoryan
- Center
for Exposure Biology, School of Public Health, University of California, Berkeley, California 94720, United States
| | - Anthony T. Iavarone
- Department
of Chemistry and QB3 Institute, University of California, Berkeley, California 94720, United States
| | - Stephen M. Rappaport
- Center
for Exposure Biology, School of Public Health, University of California, Berkeley, California 94720, United States
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230
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Schulz F, Lutz D, Rusche N, Bastús NG, Stieben M, Höltig M, Grüner F, Weller H, Schachner M, Vossmeyer T, Loers G. Gold nanoparticles functionalized with a fragment of the neural cell adhesion molecule L1 stimulate L1-mediated functions. NANOSCALE 2013; 5:10605-10617. [PMID: 24056775 DOI: 10.1039/c3nr02707d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The neural cell adhesion molecule L1 is involved in nervous system development and promotes regeneration in animal models of acute and chronic injury of the adult nervous system. To translate these conducive functions into therapeutic approaches, a 22-mer peptide that encompasses a minimal and functional L1 sequence of the third fibronectin type III domain of murine L1 was identified and conjugated to gold nanoparticles (AuNPs) to obtain constructs that interact homophilically with the extracellular domain of L1 and trigger the cognate beneficial L1-mediated functions. Covalent conjugation was achieved by reacting mixtures of two cysteine-terminated forms of this L1 peptide and thiolated poly(ethylene) glycol (PEG) ligands (~2.1 kDa) with citrate stabilized AuNPs of two different sizes (~14 and 40 nm in diameter). By varying the ratio of the L1 peptide-PEG mixtures, an optimized layer composition was achieved that resulted in the expected homophilic interaction of the AuNPs. These AuNPs were stable as tested over a time period of 30 days in artificial cerebrospinal fluid and interacted with the extracellular domain of L1 on neurons and Schwann cells, as could be shown by using cells from wild-type and L1-deficient mice. In vitro, the L1-derivatized particles promoted neurite outgrowth and survival of neurons from the central and peripheral nervous system and stimulated Schwann cell process formation and proliferation. These observations raise the hope that, in combination with other therapeutic approaches, L1 peptide-functionalized AuNPs may become a useful tool to ameliorate the deficits resulting from acute and chronic injuries of the mammalian nervous system.
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Affiliation(s)
- Florian Schulz
- Institut für Physikalische Chemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany.
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231
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Zhao W, Jin L, Yuan H, Tan Z, Zhou C, Li LS, Ma L. Targeting human embryonic stem cells with quantum dot-conjugated phages. Sci Rep 2013; 3:3134. [PMID: 24190250 PMCID: PMC3817438 DOI: 10.1038/srep03134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 10/15/2013] [Indexed: 12/11/2022] Open
Abstract
Targeting embryonic stem cells (ESCs) is important for ESC labeling, drug delivery and cell fate control. In this study, we identified twenty-two phage clones that bind specifically to the hESC cell line X-01, which was derived from human blastocysts of Chinese origin. One phage (H178), which displays the sequence VGGEAWSSPTDL, showed higher binding affinity to hESCs than to a monkey ES cell line (RS366.4) and two mouse ES cell lines (R1 and E14). Using quantum dots (QDs) conjugated to the H178 phage, we demonstrate that the phage can specifically bind to hESCs in vitro. Our results suggest a possible interaction between the selected peptide and the stem cell extracellular matrix (ECM). The selection method described here allows rapid and efficient screening of unique phage clones and targeting cells. The phages displaying peptides identified by this study have potential applications for cargo delivery and receptor studies.
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Affiliation(s)
- Wenxiu Zhao
- Division of Life Science & Health, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
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232
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Fine mapping of a linear epitope on EDIII of Japanese encephalitis virus using a novel neutralizing monoclonal antibody. Virus Res 2013; 179:133-9. [PMID: 24184444 DOI: 10.1016/j.virusres.2013.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 10/24/2013] [Accepted: 10/24/2013] [Indexed: 01/12/2023]
Abstract
The domain III (EDIII) of the envelope protein of Japanese encephalitis virus (JEV) is proposed to play an essential role in JEV replication and infection; it is involved in binding to host receptors and contains specific epitopes that elicit neutralizing antibodies. However, most previous studies have not provided detailed molecular information about the functional epitopes on JEV EDIII protein. In this study, we described a monoclonal antibody (mAb 2B4) we produced and characterized by IFA, PRNT, ELISA and Western blot analyses. The results showed that mAb 2B4 was specific to JEV EDIII protein and possessed high neutralization activity against JEV in vitro. Furthermore, we found that the motif, (394)HHWH(397), was the minimal unit of the linear epitope recognized by mAb 2B4 through screening a phage-displayed random 12-mer peptide library. Using sequence alignment analysis it was found that this motif was highly conserved among JEV strains and was present in West Nile Virus (WNV). Indeed, ELISA data showed that this epitope could be recognized by both JEV-positive swine serum and WNV-positive swine serum. Notably, this linear epitope was highly hydrophilic and was located within the terminal end of a β-pleated sheet of EDIII. An analysis of the spatial conformation supported the possibility of inducing specific antibodies to this epitope. Taken together, we identified (394)HHWH(397) as an EDIII-specific linear epitope recognized by mAb 2B4, which would be beneficial for studying the pathogenic mechanism of JEV; and mAb 2B4 was also a potential diagnostic and therapeutic reagent.
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Manijeh M, Mehrnaz K, Violaine M, Hassan M, Abbas J, Mohammad R. In silico Design of Discontinuous Peptides Representative of B and T-cell Epitopes from HER2-ECD as Potential Novel Cancer Peptide Vaccines. Asian Pac J Cancer Prev 2013; 14:5973-81. [DOI: 10.7314/apjcp.2013.14.10.5973] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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234
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Gupta UK, Mahanta S, Paul S. In silico design of small peptide-based Hsp90 inhibitor: a novel anticancer agent. Med Hypotheses 2013; 81:853-61. [PMID: 24018284 DOI: 10.1016/j.mehy.2013.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 08/11/2013] [Indexed: 12/14/2022]
Abstract
BACKGROUND Breast cancer is a common disease found among women and has been a serious issue for last two decades. Although various kinds of heat shock proteins (Hsp's) have strong implications in cancer, heat shock protein 90 alpha (Hsp90α) has attracted highest attention for the cause and therapy of breast cancer. It regulates approximately 200 numbers of proteins known as client proteins including large number of oncoproteins found to be upregulated in many cancer cells. Therefore, inhibition of Hsp90α is a common therapeutic approach pursued in many cancers. However, Hsp90α inhibitors both natural and chemical, reported so far are plagued with problems related to toxicity, bioavailability and solubility including geldanamycin, the most common Hsp90α inhibitor. Therefore, search for a suitable Hsp90α inhibitor is an urgent need. HYPOTHESIS Here we hypothesize that Hsp organizing protein (HOP) helps in the interaction of Hsp90α with Hsp70, which is the key to appropriate chaperonin function of Hsp90α and therefore, inhibiting such interaction might lead to the disruption of Hsp90α-client protein complex, which in turn destabilize and degrade client proteins. We further hypothesize that considering the residues involved in the reaction we can design novel peptide based Hsp90α inhibitor. EXPERIMENTAL DESIGN In our present in silico investigation, we hypothesized that the chaperone function of Hsp90α requires the complex formation with HOP and co-chaperones Hsp70, Hsp40. We performed the docking interaction between Hsp90α and HOP. Based on the key residues involved in the interaction between Hsp90α and HOP, we designed ten peptides having twelve amino acids each. We docked the designed peptides with Hsp90α using docking software Hex 6.1 and the peptide with the highest binding energy value was identified. Using the online FOLDAMYLOID program, we assessed their amyloidogenic propensity. Amylodegenic properties were also considered and based on that five different peptides were again redesigned. Several modifications incorporated onto the peptide led to the design of five different peptides. RESULTS The peptide with the lowest amyloidogenic properties and highest binding energy for Hsp90α was the criteria laid for selection as an Hsp90α-inhibitor. Its potential to bind Hsp90α and disrupt Hsp90α-HOP complex was subsequently investigated using both wild as well as mutant p53 as a client protein. CONCLUSION The predicted binding energy values showed that our designed novel peptide demonstrated strong binding affinity for Hsp90α. Subsequently, the binding affinity of Hsp90α for mutant p53 was shown to be reduced substantially indicating a strong inhibitory potential of the designed peptide PEP73 (INSAYKLKYARG) for Hsp90α.
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Affiliation(s)
- Uday Kumar Gupta
- Structural Biology and Nanomedicine Laboratory, Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, Orissa 769 008, India
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235
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Wang X, Li Q, Davies M. Development of antibody arrays for monoclonal antibody Higher Order Structure analysis. Front Pharmacol 2013; 4:103. [PMID: 23970865 PMCID: PMC3748713 DOI: 10.3389/fphar.2013.00103] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 07/31/2013] [Indexed: 11/17/2022] Open
Abstract
Antibody arrays were developed to probe a monoclonal antibody's three-dimensional structure (3-D structure). Peptides with overlapping regions were designed to cover the whole mAb light chain and heavy chain, respectively, and used to generate polyclonal antibodies after the conjugation of the peptides to a carrier protein, KLH. It was shown that good peptide specificity was achieved from the antibodies generated. Using more than 30 different polyclonal antibodies to measure the surface epitope distribution, it was shown that the mAb antibody array can detect epitope exposure as low as 0.1% of defined mAb populations. This ELISA-based analysis of mAb epitope exposure can be considered as a measurement of “conformational impurity” in biologics development, similar to the analysis of other product-related impurities such as different forms of glycosylation, deamidation, and oxidation. This analysis of “conformational impurity” could provide valuable information on the mAb conformational comparability for biosimilar mAbs as well as novel mAbs, especially in the area of protein immunogenicity. Furthermore, stability studies indicated that there are several conformational “hot spots” in many mAbs tested, especially in the hinge region. This antibody array technology can be used for novel mAb Higher Order Structure (HOS) analysis during process and formulation development. Another important area of application is for biosimilar mAb development where the innovator molecule and biosimilar molecule could be compared based on their systemic “fingerprint” from the 30 plus antibodies.
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Affiliation(s)
- Xing Wang
- Array Bridge Inc. St. Louis, MO, USA
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236
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Sanchita, Chauhan R, Soni G, Sudhamalla B, Sharma A. Docking and molecular dynamics studies of peptide inhibitors of ornithine decarboxylase: a rate-limiting enzyme for the metabolism ofFusarium solani. J Biomol Struct Dyn 2013; 31:874-87. [DOI: 10.1080/07391102.2012.718526] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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237
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Guo T, Yang J, Zeng L, Wang H, Tong Q, Li X. Does there exist an intrinsic relationship between the flexibility and self-assembly of pepfactants? MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.817673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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238
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Stepwise identification of potent antimicrobial peptides from human genome. Biosystems 2013; 113:1-8. [DOI: 10.1016/j.biosystems.2013.03.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 03/18/2013] [Accepted: 03/31/2013] [Indexed: 11/23/2022]
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239
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Ramani V, Madhusoodhanan R, Kosanke S, Awasthi S. A TLR4-interacting SPA4 peptide inhibits LPS-induced lung inflammation. Innate Immun 2013; 19:596-610. [PMID: 23475791 DOI: 10.1177/1753425912474851] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The interaction between surfactant protein-A (SP-A) and TLR4 is important for host defense. We have recently identified an SPA4 peptide region from the interface of SP-A-TLR4 complex. Here, we studied the involvement of the SPA4 peptide region in SP-A-TLR4 interaction using a two-hybrid system, and biological effects of SPA4 peptide in cell systems and a mouse model. HEK293 cells were transfected with plasmid DNAs encoding SP-A or a SP-A-mutant lacking SPA4 peptide region and TLR4. Luciferase activity was measured as the end-point of SP-A-TLR4 interaction. NF-κB activity was also assessed simultaneously. Next, the dendritic cells or mice were challenged with Escherichia coli-derived LPS and treated with SPA4 peptide. Endotoxic shock-like symptoms and inflammatory parameters (TNF-α, NF-κB, leukocyte influx) were assessed. Our results reveal that the SPA4 peptide region contributes to the SP-A-TLR4 interaction and inhibits the LPS-induced NF-κB activity and TNF-α. We also observed that the SPA4 peptide inhibits LPS-induced expression of TNF-α, nuclear localization of NF-κB-p65 and cell influx, and alleviates the endotoxic shock-like symptoms in a mouse model. Our results suggest that the anti-inflammatory activity of the SPA4 peptide through its binding to TLR4 can be of therapeutic benefit.
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Affiliation(s)
- Vijay Ramani
- 1Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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240
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Hoffmann F, Strodel B. Protein structure prediction using global optimization by basin-hopping with NMR shift restraints. J Chem Phys 2013; 138:025102. [PMID: 23320726 DOI: 10.1063/1.4773406] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Computational methods that utilize chemical shifts to produce protein structures at atomic resolution have recently been introduced. In the current work, we exploit chemical shifts by combining the basin-hopping approach to global optimization with chemical shift restraints using a penalty function. For three peptides, we demonstrate that this approach allows us to find near-native structures from fully extended structures within 10,000 basin-hopping steps. The effect of adding chemical shift restraints is that the α and β secondary structure elements form within 1000 basin-hopping steps, after which the orientation of the secondary structure elements, which produces the tertiary contacts, is driven by the underlying protein force field. We further show that our chemical shift-restraint BH approach also works for incomplete chemical shift assignments, where the information from only one chemical shift type is considered. For the proper implementation of chemical shift restraints in the basin-hopping approach, we determined the optimal weight of the chemical shift penalty energy with respect to the CHARMM force field in conjunction with the FACTS solvation model employed in this study. In order to speed up the local energy minimization procedure, we developed a function, which continuously decreases the width of the chemical shift penalty function as the minimization progresses. We conclude that the basin-hopping approach with chemical shift restraints is a promising method for protein structure prediction.
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Affiliation(s)
- Falk Hoffmann
- Institute of Complex Systems: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
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241
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242
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Abstract
Coarse-grained models for protein folding and aggregation are used to explore large dimension scales and timescales that are inaccessible to all-atom models in explicit aqueous solution. Combined with enhanced configuration search methods, these simplified models with various levels of granularity offer the possibility to determine equilibrium structures, compare folding kinetics and thermodynamics with experiments for single proteins and understand the dynamic assembly of amyloid proteins leading to neurodegenerative diseases. I shall describe recent progress in developing such models, and discuss their potentials and limitations in probing the folding and misfolding of proteins with computer simulations.
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243
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Andrews AL, Nordgren IK, Campbell-Harding G, Holloway JW, Holgate ST, Davies DE, Tavassoli A. The association of the cytoplasmic domains of interleukin 4 receptor alpha and interleukin 13 receptor alpha 2 regulates interleukin 4 signaling. MOLECULAR BIOSYSTEMS 2013; 9:3009-14. [DOI: 10.1039/c3mb70298g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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244
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Use of fast conformational sampling to improve the characterization of VEGF A–peptide interactions. J Theor Biol 2013; 317:293-300. [DOI: 10.1016/j.jtbi.2012.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 10/12/2012] [Accepted: 10/15/2012] [Indexed: 01/25/2023]
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245
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Tian F, Wu J, Huang N, Guo T, Mao C. The critical aggregation concentration of peptide surfactants is predictable from dynamic hydrophobic property. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2012; 24:89-101. [PMID: 23171122 DOI: 10.1080/1062936x.2012.742134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Peptide surfactants are a kind of newly emerged functional materials, which have a variety of applications such as building nanoarchitecture, stabilizing membrane proteins and controlling drug release. In the present study, we report the modelling and prediction of critical aggregation concentration (CAC), an important parameter that characterizes the self-assembling behaviour of peptide surfactants through the use of statistical modelling and quantitative structure-property relationship (QSPR) approaches. In order to accurately describe the structural and physicochemical properties of the highly flexible peptide molecules, a new method called molecular dynamics-based hydrophobic cross-field (MD-HCF) is proposed to capture both the hydrophobic profile and dynamic feature of 32 surface-activity, structure-known peptides. A number of statistical models are then developed using partial least squares (PLS) regression with or without improvement by genetic algorithm (GA). We demonstrate that MD-HCF performs much better than the widely used CODESSA method in both its predictability and interpretability. We also highlight the importance of dynamic hydrophobic property in accurate prediction and reasonable explanation of peptide self-assembling behaviour in solution, albeit which is exhaustive to compute compared with those derived directly from peptide static structure. To the best of our knowledge, this study is the first to computationally model and predict the self-assembling behaviour of peptide surfactants.
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Affiliation(s)
- F Tian
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
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246
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Lu Y, Wei G, Derreumaux P. Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: insights from coarse-grained simulations. J Chem Phys 2012; 137:025101. [PMID: 22803563 DOI: 10.1063/1.4732761] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Characterizing the early formed oligomeric intermediates of amyloid peptides is of particular interest due to their links with neurodegenerative diseases. Here we study the NNQQ peptide, known to display parallel β-strands in amyloid fibrils by x-ray microcrystallography, and investigate the structural, thermodynamical, and dynamical properties of 20 NNQQ peptides using molecular dynamics and replica exchange molecular dynamics simulations coupled to a coarse-grained force field. All simulations are initiated from randomized and fully dispersed monomeric conformations. Our simulations reveal that the phase transition is characterized by a change in the oligomer and β-sheet size distributions and the percentage of mixed parallel/antiparallel β-strands when the sheets are formed. At all temperatures, however, the fraction of parallel β-strands remains low, though there are many association/fragmentation events. This work and a growing body of computational studies provide strong evidence that the critical nucleus goes beyond 20 chains and reordering of the β-strands occurs in larger oligomers.
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Affiliation(s)
- Yan Lu
- State Key Laboratory of Surface Physics, and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China
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247
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Human mitochondrial holocytochrome c synthase's heme binding, maturation determinants, and complex formation with cytochrome c. Proc Natl Acad Sci U S A 2012; 110:E788-97. [PMID: 23150584 DOI: 10.1073/pnas.1213897109] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Proper functioning of the mitochondrion requires the orchestrated assembly of respiratory complexes with their cofactors. Cytochrome c, an essential electron carrier in mitochondria and a critical component of the apoptotic pathway, contains a heme cofactor covalently attached to the protein at a conserved CXXCH motif. Although it has been known for more than two decades that heme attachment requires the mitochondrial protein holocytochrome c synthase (HCCS), the mechanism remained unknown. We purified membrane-bound human HCCS with endogenous heme and in complex with its cognate human apocytochrome c. Spectroscopic analyses of HCCS alone and complexes of HCCS with site-directed variants of cytochrome c revealed the fundamental steps of heme attachment and maturation. A conserved histidine in HCCS (His154) provided the key ligand to the heme iron. Formation of the HCCS:heme complex served as the platform for interaction with apocytochrome c. Heme was the central molecule mediating contact between HCCS and apocytochrome c. A conserved histidine in apocytochrome c (His19 of CXXCH) supplied the second axial ligand to heme in the trapped HCCS:heme:cytochrome c complex. We also examined the substrate specificity of human HCCS and converted a bacterial cytochrome c into a robust substrate for the HCCS. The results allow us to describe the molecular mechanisms underlying the HCCS reaction.
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248
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Berges R, Balzeau J, Takahashi M, Prevost C, Eyer J. Structure-function analysis of the glioma targeting NFL-TBS.40-63 peptide corresponding to the tubulin-binding site on the light neurofilament subunit. PLoS One 2012; 7:e49436. [PMID: 23152907 PMCID: PMC3494675 DOI: 10.1371/journal.pone.0049436] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 10/08/2012] [Indexed: 11/23/2022] Open
Abstract
We previously reported that a 24 amino acid peptide (NFL-TBS.40-63) corresponding to the tubulin-binding site located on the light neurofilament subunit, selectively enters in glioblastoma cells where it disrupts their microtubule network and inhibits their proliferation. Here, we analyzed the structure-function relationships using an alanine-scanning strategy, in order to identify residues essential for these biological activities. We showed that the majority of modified peptides present a decreased or total loss to penetrate in these cells, or to alter microtubules. Correspondingly, circular dichroism measurements showed that this peptide forms either β-sheet or α-helix structures according to the solvent and that alanine substitution modified or destabilized the structure, in relation with changes in the biological activities. Moreover, substitution of serine residues by phosphoserine or aspartic acid concomitantly decreased the cell penetrating activity and the structure stability. These results indicate the importance of structure for the activities, including selectivity to glioblastoma cells of this peptide, and its regulation by phosphorylation.
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Affiliation(s)
| | | | | | | | - Joel Eyer
- Laboratoire de Neurobiologie & Transgenèse, UPRES EA 3143, INSERM, Centre Hospitalier Universitaire, Angers, France
- * E-mail:
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249
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Olsson N, Wallin S, James P, Borrebaeck CAK, Wingren C. Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties. Protein Sci 2012; 21:1897-910. [PMID: 23034898 DOI: 10.1002/pro.2173] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 09/26/2012] [Indexed: 01/25/2023]
Abstract
Protein-peptide interactions are a common occurrence and essential for numerous cellular processes, and frequently explored in broad applications within biology, medicine, and proteomics. Therefore, understanding the molecular mechanism(s) of protein-peptide recognition, specificity, and binding interactions will be essential. In this study, we report the first detailed analysis of antibody-peptide interaction characteristics, by combining large-scale experimental peptide binding data with the structural analysis of eight human recombinant antibodies and numerous peptides, targeting tryptic mammalian and eukaryote proteomes. The results consistently revealed that promiscuous peptide-binding interactions, that is, both specific and degenerate binding, were exhibited by all antibodies, and the discovery was corroborated by orthogonal data, indicating that this might be a general phenomenon for low-affinity antibody-peptide interactions. The molecular mechanism for the degenerate peptide-binding specificity appeared to be executed through the use of 2-3 semi-conserved anchor residues in the C-terminal part of the peptides, in analogue to the mechanism utilized by the major histocompatibility complex-peptide complexes. In the long-term, this knowledge will be instrumental for advancing our fundamental understanding of protein-peptide interactions, as well as for designing, generating, and applying peptide specific antibodies, or peptide-binding proteins in general, in various biotechnical and medical applications.
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Affiliation(s)
- Niclas Olsson
- Department of Immunotechnology, Lund University, Lund, Sweden
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250
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Zandawala M. Calcitonin-like diuretic hormones in insects. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 42:816-825. [PMID: 22820711 DOI: 10.1016/j.ibmb.2012.06.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 06/19/2012] [Accepted: 06/24/2012] [Indexed: 06/01/2023]
Abstract
Insect neuropeptides control various biological processes including growth, development, homeostasis and reproduction. The calcitonin-like diuretic hormone (CT/DH) is one such neuropeptide that has been shown to affect salt and water transport by Malpighian tubules of several insects. With an increase in the number of sequenced insect genomes, CT/DHs have been predicted in several insect species, making it easier to characterize the gene encoding this hormone and determine its function in the species in question. This mini review summarizes the current knowledge on insect CT/DHs, focusing on mRNA and peptide structures, distribution patterns, physiological roles, and receptors in insects.
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Affiliation(s)
- Meet Zandawala
- Department of Biology, University of Toronto Mississauga, Room 3016A/B, William Davis Building, 3359 Mississauga Road N., Mississauga, ON, Canada L5L 1C6.
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