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Duran T, Naik S, Sharifi L, DiLuzio WR, Chanda A, Chaudhuri B. Studying the ssDNA loaded adeno-associated virus aggregation using coarse-grained molecular dynamics simulations. Int J Pharm 2024; 655:123985. [PMID: 38484860 DOI: 10.1016/j.ijpharm.2024.123985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
The aggregation of adeno-associated viral (AAV) capsids in an aqueous environment was investigated via coarse-grained molecular dynamics (CG-MD) simulations. The primary driving force and mechanism of the aggregation were investigated with or without single-strand DNA (ssDNA) loaded at various process temperatures. Capsid aggregation appeared to involve multiple residue interactions (i.e., hydrophobic, polar and charged residues) leading to complex protein aggregation. In addition, two aggregation mechanisms (i.e., the fivefold face-to-face contact and the edge-to-edge contact) were identified from this study. The ssDNA with its asymmetric structure could be the reason for destabilizing protein subunits and enhancing the interaction between the charged residues, and further result in the non-reversible face-to-face contact. At higher temperature, the capsid structure was found to be unstable with the significant size expansion of the loaded ssDNA which could be attributed to reduced number of intramolecular hydrogen bonds, the increased conformational deviations of protein subunits and the higher residue fluctuations. The CG-MD model was further validated with previous experimental and simulation data, including the full capsid size measurement and the capsid internal pressure. Thus, a good understanding of AAV capsid aggregation, instability and the role of ssDNA were revealed by applying the developed computational model.
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Affiliation(s)
- Tibo Duran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
| | - Shivangi Naik
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
| | - Leila Sharifi
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
| | - Willow R DiLuzio
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
| | - Arani Chanda
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
| | - Bodhisattwa Chaudhuri
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA; Institute of Material Sciences (IMS), University of Connecticut, Storrs, CT, USA.
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2
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Potok P, Kola A, Valensin D, Capdevila M, Potocki S. Copper Forms a PPII Helix-Like Structure with the Catalytic Domains of Bacterial Zinc Metalloproteases. Inorg Chem 2023; 62:18425-18439. [PMID: 37909295 PMCID: PMC10647932 DOI: 10.1021/acs.inorgchem.3c02391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 11/03/2023]
Abstract
The rapid spread of antibiotic-resistant bacteria continuously raises concerns about the future ineffectiveness of current antimicrobial treatments against infectious diseases. To address this problem, new therapeutic strategies and antimicrobial drugs with unique modes of action are urgently needed. Inhibition of metalloproteases, bacterial virulence factors, is a promising target for the development of antibacterial treatments. In this study, the interaction among Zn(II), Cu(II), and the metal-binding domains of two metalloproteases, AprA (Pseudomonas aureginosa) and CpaA (Acinetobacter baumanii), was investigated. The objective was to determine the coordination sphere of Zn(II) with a peptide model of two zinc-dependent metalloproteases. Additionally, the study explored the formation of Cu(II) complexes with the domains, as Cu(II) has been shown to inhibit metalloproteases. The third aim was to understand the role of nonbinding amino acids in stabilizing the metal complexes formed by these proteases. This work identified specific coordination patterns (HExxHxxxxxH) for both Zn(II) and Cu(II) complexes, with AprA and CpaA exhibiting a higher affinity for Cu(II) compared to Zn(II). The study also found that the CpaA domain has greater stability for both Zn(II) and Cu(II) complexes compared to AprA. The nonbinding amino acids of CpaA surrounding the metal ion contribute to the increased thermodynamic stability of the metal-peptide complex through various intramolecular interactions. These interactions can also influence the secondary structures of the peptides. The presence of certain amino acids, such as tyrosine, arginine, and glutamic acid, and their interactions contribute to the stability and, only in the case of Cu(II) complexes, the formation of a rare protein structure called a left-handed polyproline II helix (PPII), which is known to play a role in the stability and function of various proteins. These findings provide valuable insights into the coordination chemistry of bacterial metalloproteases and expand our understanding of potential mechanisms for inhibiting these enzymes.
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Affiliation(s)
- Paulina Potok
- Faculty
of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Arian Kola
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Daniela Valensin
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Merce Capdevila
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Sławomir Potocki
- Faculty
of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
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3
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Hazra MK, Gilron Y, Levy Y. Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction. J Mol Biol 2023; 435:168196. [PMID: 37442414 DOI: 10.1016/j.jmb.2023.168196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Intrinsically disordered proteins (IDPs) adopt a wide array of different conformations that can be constrained by the presence of proline residues, which are frequently found in IDPs. To assess the effects of proline, we designed a series of peptides that differ with respect to the number of prolines in the sequence and their organization. Using high-resolution atomistic molecular dynamics simulations, we found that accounting for whether the proline residues are clustered or isolated contributed significantly to explaining deviations in the experimentally-determined gyration radii of IDPs from the values expected based on the Flory scaling-law. By contrast, total proline content makes smaller contribution to explaining the effect of prolines on IDP conformation. Proline residues exhibit opposing effects depending on their organizational pattern in the IDP sequence. Clustered prolines (i.e., prolines with ≤2 intervening non-proline residues) result in expanded peptide conformations whereas isolated prolines (i.e., prolines with >2 intervening non-proline residues) impose compacted conformations. Clustered prolines were estimated to induce an expansion of ∼20% in IDP dimension (via formation of PPII structural elements) whereas isolated prolines were estimated to induce a compaction of ∼10% in IDP dimension (via the formation of backbone turns). This dual role of prolines provides a mechanism for conformational switching that does not rely on the kinetically much slower isomerization of cis proline to the trans form. Bioinformatic analysis demonstrates high populations of both isolated and clustered prolines and implementing them in coarse-grained molecular dynamics models illustrates that they improve the characterization of the conformational ensembles of IDPs.
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Affiliation(s)
- Milan Kumar Hazra
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Gilron
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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4
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Meirson T, Bomze D, Schueler-Furman O, Stemmer SM, Markel G. Systemic structural analysis of alterations reveals a common structural basis of driver mutations in cancer. NAR Cancer 2023; 5:zcac040. [PMID: 36683915 PMCID: PMC9846427 DOI: 10.1093/narcan/zcac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/17/2022] [Accepted: 12/04/2022] [Indexed: 01/19/2023] Open
Abstract
A major effort in cancer research is to organize the complexities of the disease into fundamental traits. Despite conceptual progress in the last decades and the synthesis of hallmark features, no organizing principles governing cancer beyond cellular features exist. We analyzed experimentally determined structures harboring the most significant and prevalent driver missense mutations in human cancer, covering 73% (n = 168178) of the Catalog of Somatic Mutation in Cancer tumor samples (COSMIC). The results reveal that a single structural element-κ-helix (polyproline II helix)-lies at the core of driver point mutations, with significant enrichment in all major anatomical sites, suggesting that a small number of molecular traits are shared by most and perhaps all types of cancer. Thus, we uncovered the lowest possible level of organization at which carcinogenesis takes place at the protein level. This framework provides an initial scheme for a mechanistic understanding underlying the development of tumors and pinpoints key vulnerabilities.
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Affiliation(s)
- Tomer Meirson
- Davidoff Cancer Center, Rabin Medical Center-Beilinson Hospital, Petah Tikva, 49100, Israel
| | - David Bomze
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Salomon M Stemmer
- Davidoff Cancer Center, Rabin Medical Center-Beilinson Hospital, Petah Tikva, 49100, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Gal Markel
- Davidoff Cancer Center, Rabin Medical Center-Beilinson Hospital, Petah Tikva, 49100, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, 6997801, Israel
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Bahraminejad E, Paliwal D, Sunde M, Holt C, Carver JA, Thorn DC. Amyloid fibril formation by α S1- and β-casein implies that fibril formation is a general property of casein proteins. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140854. [PMID: 36087849 DOI: 10.1016/j.bbapap.2022.140854] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Caseins are a diverse family of intrinsically disordered proteins present in the milks of all mammals. A property common to two cow paralogues, αS2- and κ-casein, is their propensity in vitro to form amyloid fibrils, the highly ordered protein aggregates associated with many age-related, including neurological, diseases. In this study, we explored whether amyloid fibril-forming propensity is a general feature of casein proteins by examining the other cow caseins (αS1 and β) as well as β-caseins from camel and goat. Small-angle X-ray scattering measurements indicated that cow αS1- and β-casein formed large spherical aggregates at neutral pH and 20°C. Upon incubation at 65°C, αS1- and β-casein underwent conversion to amyloid fibrils over the course of ten days, as shown by thioflavin T binding, transmission electron microscopy, and X-ray fibre diffraction. At the lower temperature of 37°C where fibril formation was more limited, camel β-casein exhibited a greater fibril-forming propensity than its cow or goat orthologues. Limited proteolysis of cow and camel β-casein fibrils and analysis by mass spectrometry indicated a common amyloidogenic sequence in the proline, glutamine-rich, C-terminal region of β-casein. These findings highlight the persistence of amyloidogenic sequences within caseins, which likely contribute to their functional, heterotypic self-assembly; in all mammalian milks, at least two caseins coalesce to form casein micelles, implying that caseins diversified partly to avoid dysfunctional amyloid fibril formation.
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Affiliation(s)
- Elmira Bahraminejad
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Devashi Paliwal
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Margaret Sunde
- School of Medical Sciences, Faculty of Medicine and Health, and Sydney Nano, The University of Sydney, Sydney, NSW 2006, Australia
| | - Carl Holt
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - John A Carver
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - David C Thorn
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia.
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Patarroyo ME, Bermudez A, Alba MP, Patarroyo MA, Suarez C, Aza-Conde J, Moreno-Vranich A, Vanegas M. Stereo electronic principles for selecting fully-protective, chemically-synthesised malaria vaccines. Front Immunol 2022; 13:926680. [DOI: 10.3389/fimmu.2022.926680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Major histocompatibility class II molecule-peptide-T-cell receptor (MHCII-p-TCR) complex-mediated antigen presentation for a minimal subunit-based, multi-epitope, multistage, chemically-synthesised antimalarial vaccine is essential for inducing an appropriate immune response. Deep understanding of this MHCII-p-TCR complex’s stereo-electronic characteristics is fundamental for vaccine development. This review encapsulates the main principles for achieving such epitopes’ perfect fit into MHC-II human (HLADRβ̞1*) or Aotus (Aona DR) molecules. The enormous relevance of several amino acids’ physico-chemical characteristics is analysed in-depth, as is data regarding a 26.5 ± 2.5Å distance between the farthest atoms fitting into HLA-DRβ1* structures’ Pockets 1 to 9, the role of polyproline II-like (PPIIL) structures having their O and N backbone atoms orientated for establishing H-bonds with specific HLA-DRβ1*-peptide binding region (PBR) residues. The importance of residues having specific charge and orientation towards the TCR for inducing appropriate immune activation, amino acids’ role and that of structures interfering with PPIIL formation and other principles are demonstrated which have to be taken into account when designing immune, protection-inducing peptide structures (IMPIPS) against diseases scourging humankind, malaria being one of them.
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7
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Quantitative multivalent binding model of the structure, size distribution and composition of the casein micelles of cow milk. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2021.105292] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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8
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Meirson T, Bomze D, Markel G. Structural basis of SARS-CoV-2 spike protein induced by ACE2. Bioinformatics 2021; 37:929-936. [PMID: 32818261 PMCID: PMC7558967 DOI: 10.1093/bioinformatics/btaa744] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/20/2020] [Accepted: 08/14/2020] [Indexed: 12/24/2022] Open
Abstract
Motivation The recent emergence of the novel SARS-coronavirus 2 (SARS-CoV-2) and its international
spread pose a global health emergency. The spike (S) glycoprotein binds ACE2 and
promotes SARS-CoV-2 entry into host cells. The trimeric S protein binds the receptor
using the receptor-binding domain (RBD) causing conformational changes in S protein that
allow priming by host cell proteases. Unraveling the dynamic structural features used by
SARS-CoV-2 for entry might provide insights into viral transmission and reveal novel
therapeutic targets. Using structures determined by X-ray crystallography and cryo-EM,
we performed structural analysis and atomic comparisons of the different conformational
states adopted by the SARS-CoV-2-RBD. Results Here, we determined the key structural components induced by the receptor and
characterized their intramolecular interactions. We show that κ-helix (polyproline-II)
is a predominant structure in the binding interface and in facilitating the conversion
to the active form of the S protein. We demonstrate a series of conversions between
switch-like κ-helix and β-strand, and conformational variations in a set of short
α-helices which affect the hinge region. These conformational changes lead to an
alternating pattern in conserved disulfide bond configurations positioned at the hinge,
indicating a possible disulfide exchange, an important allosteric switch implicated in
viral entry of various viruses, including HIV and murine coronavirus. The structural
information presented herein enables to inspect and understand the important dynamic
features of SARS-CoV-2-RBD and propose a novel potential therapeutic strategy to block
viral entry. Overall, this study provides guidance for the design and optimization of
structure-based intervention strategies that target SARS-CoV-2. Availability We have implemented the proposed methods in an R package freely available at https://github.com/Grantlab/bio3d Supplementary information Supplementary data are
available at Bioinformatics online.
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Affiliation(s)
- Tomer Meirson
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Ramat-Gan 526260, Israel.,The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | | | - Gal Markel
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Ramat-Gan 526260, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
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9
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Holt C. A quantitative calcium phosphate nanocluster model of the casein micelle: the average size, size distribution and surface properties. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:847-866. [PMID: 33866398 DOI: 10.1007/s00249-021-01533-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/22/2021] [Accepted: 03/28/2021] [Indexed: 10/21/2022]
Abstract
Caseins (αS1, αS2, β and κ) are the main protein fraction of bovine milk. Together with nanoclusters of amorphous calcium phosphate (CaP) and divalent cations, they combine to form a polydisperse distribution of particles called casein micelles. A casein micelle model is proposed which is consistent with the way in which intrinsically disordered proteins interact through predominantly polar, short, linear, motifs. Using the model, an expression is derived for the size distribution of casein micelles formed when caseins bind to the CaP nanoclusters and the complexes further associate with each other and the remaining mixture of free caseins. The result is a refined coat-core model in which the core is formed mainly by the nanocluster complexes and the coat is formed exclusively by the free caseins. Example calculations of the size distribution and surface composition of an average bovine milk are compared with experiment. The average size, size distribution and surface composition of the micelles is shown to depend on the affinity of the nanocluster complexes for each other in competition with their affinity for free caseins, and on the concentrations of free caseins, calcium ions and other salts in the continuous phase.
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Affiliation(s)
- Carl Holt
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK.
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10
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Duran T, Minatovicz B, Bai J, Shin D, Mohammadiarani H, Chaudhuri B. Molecular Dynamics Simulation to Uncover the Mechanisms of Protein Instability During Freezing. J Pharm Sci 2021; 110:2457-2471. [PMID: 33421436 DOI: 10.1016/j.xphs.2021.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/07/2020] [Accepted: 01/03/2021] [Indexed: 11/19/2022]
Abstract
Freezing is a common process applied in the pharmaceutical industry to store and transport biotherapeutics. Herewith, multi-scale molecular dynamics simulations of Lactate dehydrogenase (LDH) protein in phosphate buffer with/without ice formation performed to uncover the still poorly understood mechanisms and molecular details of protein destabilization upon freezing. Both fast and slow ice growing conditions were simulated at 243 K from one or two-side of the simulation box, respectively. The rate of ice formation at all-atom simulations was crucial to LDH stability, as faster freezing rates resulted in enhanced structural stability maintained by a higher number of intramolecular hydrogen bonds, less flexible protein's residues, lower solvent accessibility and greater structural compactness. Further, protein aggregation investigated by coarse-grained simulations was verified to be initiated by extended protein structures and retained by electrostatic interactions of the salt bridges between charged residues and hydrogen bonds between polar residues of the protein. Lastly, the study of free energy of dissociation through steered molecular dynamics simulation revealed LDH was destabilized by the solvation of the hydrophobic core and the loss of hydrophobic interactions. For the first time, experimentally validated molecular simulations revealed the detailed mechanisms of LDH destabilization upon ice formation and cryoconcentration of solutes.
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Affiliation(s)
- Tibo Duran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA
| | - Bruna Minatovicz
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA
| | - Jun Bai
- Department of Computer Sciences and Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Dongkwan Shin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA
| | - Hossein Mohammadiarani
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA
| | - Bodhisattwa Chaudhuri
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA; Institute of Material Sciences (IMS), University of Connecticut, Storrs, CT, USA; Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA.
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11
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Thorn DC, Bahraminejad E, Grosas AB, Koudelka T, Hoffmann P, Mata JP, Devlin GL, Sunde M, Ecroyd H, Holt C, Carver JA. Native disulphide-linked dimers facilitate amyloid fibril formation by bovine milk α S2-casein. Biophys Chem 2020; 270:106530. [PMID: 33545456 DOI: 10.1016/j.bpc.2020.106530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/12/2020] [Accepted: 12/12/2020] [Indexed: 12/22/2022]
Abstract
Bovine milk αS2-casein, an intrinsically disordered protein, readily forms amyloid fibrils in vitro and is implicated in the formation of amyloid fibril deposits in mammary tissue. Its two cysteine residues participate in the formation of either intra- or intermolecular disulphide bonds, generating monomer and dimer species. X-ray solution scattering measurements indicated that both forms of the protein adopt large, spherical oligomers at 20 °C. Upon incubation at 37 °C, the disulphide-linked dimer showed a significantly greater propensity to form amyloid fibrils than its monomeric counterpart. Thioflavin T fluorescence, circular dichroism and infrared spectra were consistent with one or both of the dimer isomers (in a parallel or antiparallel arrangement) being predisposed toward an ordered, amyloid-like structure. Limited proteolysis experiments indicated that the region from Ala81 to Lys113 is incorporated into the fibril core, implying that this region, which is predicted by several algorithms to be amyloidogenic, initiates fibril formation of αS2-casein. The partial conservation of the cysteine motif and the frequent occurrence of disulphide-linked dimers in mammalian milks despite the associated risk of mammary amyloidosis, suggest that the dimeric conformation of αS2-casein is a functional, yet amyloidogenic, structure.
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Affiliation(s)
- David C Thorn
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Elmira Bahraminejad
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Aidan B Grosas
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Tomas Koudelka
- Institute of Experimental Medicine, University of Kiel, Kiel 24105, Germany
| | - Peter Hoffmann
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Jitendra P Mata
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Glyn L Devlin
- Victorian Health and Human Services Building Authority, Melbourne, Victoria 3000, Australia
| | - Margaret Sunde
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW 2006, Australia
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Carl Holt
- Institute of Molecular, Cell & Systems Biology, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - John A Carver
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia.
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12
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Pignataro MF, Herrera MG, Dodero VI. Evaluation of Peptide/Protein Self-Assembly and Aggregation by Spectroscopic Methods. Molecules 2020; 25:E4854. [PMID: 33096797 PMCID: PMC7587993 DOI: 10.3390/molecules25204854] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
The self-assembly of proteins is an essential process for a variety of cellular functions including cell respiration, mobility and division. On the other hand, protein or peptide misfolding and aggregation is related to the development of Parkinson's disease and Alzheimer's disease, among other aggregopathies. As a consequence, significant research efforts are directed towards the understanding of this process. In this review, we are focused on the use of UV-Visible Absorption Spectroscopy, Fluorescence Spectroscopy and Circular Dichroism to evaluate the self-organization of proteins and peptides in solution. These spectroscopic techniques are commonly available in most chemistry and biochemistry research laboratories, and together they are a powerful approach for initial as well as routine evaluation of protein and peptide self-assembly and aggregation under different environmental stimulus. Furthermore, these spectroscopic techniques are even suitable for studying complex systems like those in the food industry or pharmaceutical formulations, providing an overall idea of the folding, self-assembly, and aggregation processes, which is challenging to obtain with high-resolution methods. Here, we compiled and discussed selected examples, together with our results and those that helped us better to understand the process of protein and peptide aggregation. We put particular emphasis on the basic description of the methods as well as on the experimental considerations needed to obtain meaningful information, to help those who are just getting into this exciting area of research. Moreover, this review is particularly useful to those out of the field who would like to improve reproducibility in their cellular and biomedical experiments, especially while working with peptide and protein systems as an external stimulus. Our final aim is to show the power of these low-resolution techniques to improve our understanding of the self-assembly of peptides and proteins and translate this fundamental knowledge in biomedical research or food applications.
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Affiliation(s)
- María Florencia Pignataro
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
| | - María Georgina Herrera
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Verónica Isabel Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
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13
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Meirson T, Bomze D, Markel G, Samson AO. κ-helix and the helical lock and key model: a pivotal way of looking at polyproline II. Bioinformatics 2020; 36:3726-3732. [DOI: 10.1093/bioinformatics/btaa186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/11/2020] [Accepted: 03/12/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
Motivation
Polyproline II (PPII) is a common conformation, comparable to α-helix and β-sheet. PPII, recently termed with a more generic name—κ-helix, adopts a left-handed structure with 3-fold rotational symmetry. Lately, a new type of binding mechanism—the helical lock and key model was introduced in SH3-domain complexes, where the interaction is characterized by a sliding helical pattern. However, whether this binding mechanism is unique only to SH3 domains is unreported.
Results
Here, we show that the helical binding pattern is a universal feature of the κ-helix conformation, present within all the major target families—SH3, WW, profilin, MHC-II, EVH1 and GYF domains. Based on a geometric analysis of 255 experimentally solved structures, we found that they are characterized by a distinctive rotational angle along the helical axis. Furthermore, we found that the range of helical pitch varies between different protein domains or peptide orientations and that the interaction is also represented by a rotational displacement mimicking helical motion. The discovery of rotational interactions as a mechanism, reveals a new dimension in the realm of protein–protein interactions, which introduces a new layer of information encoded by the helical conformation. Due to the extensive involvement of the conformation in functional interactions, we anticipate our model to expand the current molecular understanding of the relationship between protein structure and function.
Availability and implementation
We have implemented the proposed methods in an R package freely available at https://github.com/Grantlab/bio3d.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tomer Meirson
- Drug Discovery Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Ramat-Gan 526260, Israel
| | - David Bomze
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gal Markel
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Ramat-Gan 526260, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Abraham O Samson
- Drug Discovery Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
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Trichet M, Lappano R, Belnou M, Salazar Vazquez LS, Alves I, Ravault D, Sagan S, Khemtemourian L, Maggiolini M, Jacquot Y. Interaction of the Anti-Proliferative GPER Inverse Agonist ERα17p with the Breast Cancer Cell Plasma Membrane: From Biophysics to Biology. Cells 2020; 9:E447. [PMID: 32075246 PMCID: PMC7072814 DOI: 10.3390/cells9020447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 01/02/2023] Open
Abstract
The peptide ERα17p, which corresponds to the 295-311 fragment of the hinge/AF2 domains of the human estrogen receptor α (ERα), exerts apoptosis in breast cancer cells through a mechanism involving the G protein-coupled estrogen-dependent receptor GPER. Besides this receptor-mediated mechanism, we have detected a direct interaction (Kd value in the micromolar range) of this peptide with lipid vesicles mimicking the plasma membrane of eukaryotes. The reversible and not reversible pools of interacting peptide may correspond to soluble and aggregated membrane-interacting peptide populations, respectively. By using circular dichroism (CD) spectroscopy, we have shown that the interaction of the peptide with this membrane model was associated with its folding into β sheet. A slight leakage of the 5(6)-fluorescein was also observed, indicating lipid bilayer permeability. When the peptide was incubated with living breast cancer cells at the active concentration of 10 μM, aggregates were detected at the plasma membrane under the form of spheres. This insoluble pool of peptide, which seems to result from a fibrillation process, is internalized in micrometric vacuoles under the form of fibrils, without evidence of cytotoxicity, at least at the microscopic level. This study provides new information on the interaction of ERα17p with breast cancer cell membranes as well as on its mechanism of action, with respect to direct membrane effects.
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Affiliation(s)
- Michaël Trichet
- Institut de Biologie Paris-Seine (IBPS), Service de Microscopie éLectronique (IBPS-SME), Sorbonne Université, CNRS, 75005 Paris, France;
| | - Rosamaria Lappano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy;
| | - Mathilde Belnou
- Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, Ecole Normale Supérieure, PSL University, 75005 Paris, France; (M.B.); (L.S.S.V.); (D.R.); (S.S.); (L.K.)
| | - Lilian Shadai Salazar Vazquez
- Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, Ecole Normale Supérieure, PSL University, 75005 Paris, France; (M.B.); (L.S.S.V.); (D.R.); (S.S.); (L.K.)
| | - Isabel Alves
- Institute of Chemistry & Biology of Membranes & Nanoobjects (CBMN), CNRS UMR 5248, Université de Bordeaux, Institut Polytechnique Bordeaux, 33600 Pessac, France;
| | - Delphine Ravault
- Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, Ecole Normale Supérieure, PSL University, 75005 Paris, France; (M.B.); (L.S.S.V.); (D.R.); (S.S.); (L.K.)
| | - Sandrine Sagan
- Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, Ecole Normale Supérieure, PSL University, 75005 Paris, France; (M.B.); (L.S.S.V.); (D.R.); (S.S.); (L.K.)
| | - Lucie Khemtemourian
- Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, Ecole Normale Supérieure, PSL University, 75005 Paris, France; (M.B.); (L.S.S.V.); (D.R.); (S.S.); (L.K.)
- Institute of Chemistry & Biology of Membranes & Nanoobjects (CBMN), CNRS UMR 5248, Université de Bordeaux, Institut Polytechnique Bordeaux, 33600 Pessac, France;
| | - Marcello Maggiolini
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy;
| | - Yves Jacquot
- Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, Ecole Normale Supérieure, PSL University, 75005 Paris, France; (M.B.); (L.S.S.V.); (D.R.); (S.S.); (L.K.)
- Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), CNRS UMR 8038, U1268 INSERM, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 75006 Paris, France
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15
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Hall F, Liceaga A. Effect of microwave-assisted enzymatic hydrolysis of cricket (Gryllodes sigillatus) protein on ACE and DPP-IV inhibition and tropomyosin-IgG binding. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103634] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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16
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Sethuraman S, Rajendran K. Is Gum Arabic a Good Emulsifier Due to CH...π Interactions? How Urea Effectively Destabilizes the Hydrophobic CH...π Interactions in the Proteins of Gum Arabic than Amides and GuHCl? ACS OMEGA 2019; 4:16418-16428. [PMID: 31616820 PMCID: PMC6787882 DOI: 10.1021/acsomega.9b01980] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 05/13/2023]
Abstract
The photophysical studies of gum arabic (GA) in the presence of urea, 1,3-dimethylurea (DMU), tetramethylurea (TMU), guanidine hydrochloride (GuHCl), formamide (FA), acetamide (AA), and dimethyl formamide (DMF) were carried out by monitoring the emission, three-dimensional emission contour, and time-correlated fluorescence lifetime techniques. On addition of only 1 × 10-3 M urea, 75.0% of the fluorescence of GA is quenched, while the same occurs in GuHCl at 3.0 M. FA quenched 50% of the fluorescence of GA at 5.0 M. However, DMU, TMU, AA, and DMF resulted in a fluorescence enhancement. The unusual fluorescence trends reveal the existence of CH...π interactions in the proteins of GA. The experimental results and the structural aspects of proteins in GA led us to propose that the aggregation of polyproline helices in GA, through several CH...π interactions, would have a major role to play in the emulsification mechanism of GA.
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Affiliation(s)
- Sowmiya Sethuraman
- Department of Chemistry, D.G. Vaishnav College, Autonomous (affiliated to the
University of Madras (Chennai)), 833, Periyar EVR Salai, Arumbakkam, Chennai 600 106, Tamil Nadu, India
| | - Kumaran Rajendran
- Department of Chemistry, D.G. Vaishnav College, Autonomous (affiliated to the
University of Madras (Chennai)), 833, Periyar EVR Salai, Arumbakkam, Chennai 600 106, Tamil Nadu, India
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17
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Batkhishig D, Bilguun K, Enkhbayar P, Miyashita H, Kretsinger RH, Matsushima N. Super Secondary Structure Consisting of a Polyproline II Helix and a β-Turn in Leucine Rich Repeats in Bacterial Type III Secretion System Effectors. Protein J 2019; 37:223-236. [PMID: 29651716 PMCID: PMC5976695 DOI: 10.1007/s10930-018-9767-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Leucine rich repeats (LRRs) are present in over 100,000 proteins from viruses to eukaryotes. The LRRs are 20–30 residues long and occur in tandem. LRRs form parallel stacks of short β-strands and then assume a super helical arrangement called a solenoid structure. Individual LRRs are separated into highly conserved segment (HCS) with the consensus of LxxLxLxxNxL and variable segment (VS). Eight classes have been recognized. Bacterial LRRs are short and characterized by two prolines in the VS; the consensus is xxLPxLPxx with Nine residues (N-subtype) and xxLPxxLPxx with Ten residues (T-subtype). Bacterial LRRs are contained in type III secretion system effectors such as YopM, IpaH3/9.8, SspH1/2, and SlrP from bacteria. Some LRRs in decorin, fribromodulin, TLR8/9, and FLRT2/3 from vertebrate also contain the motifs. In order to understand structural features of bacterial LRRs, we performed both secondary structures assignments using four programs—DSSP-PPII, PROSS, SEGNO, and XTLSSTR—and HELFIT analyses (calculating helix axis, pitch, radius, residues per turn, and handedness), based on the atomic coordinates of their crystal structures. The N-subtype VS adopts a left handed polyproline II helix (PPII) with four, five or six residues and a type I β-turn at the C-terminal side. Thus, the N-subtype is characterized by a super secondary structure consisting of a PPII and a β-turn. In contrast, the T-subtype VS prefers two separate PPIIs with two or three and two residues. The HELFIT analysis indicates that the type I β-turn is a right handed helix. The HELFIT analysis determines three unit vectors of the helix axes of PPII (P), β-turn (B), and LRR domain (A). Three structural parameters using these three helix axes are suggested to characterize the super secondary structure and the LRR domain.
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Affiliation(s)
- Dashdavaa Batkhishig
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia.,Department of Physics, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, 210648, Mongolia
| | - Khurelbaatar Bilguun
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia.,Institute of Physics and Technology, Mongolian Academy of Sciences, Enkhtaivan avenue 54B, Ulaanbaatar, 210651, Mongolia
| | - Purevjav Enkhbayar
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia.
| | - Hiroki Miyashita
- Hokubu Rinsho Co., Ltd, Sapporo, 060-0061, Japan.,Institute of Tandem Repeats, Sapporo, 004-0882, Japan
| | | | - Norio Matsushima
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia. .,Institute of Tandem Repeats, Sapporo, 004-0882, Japan. .,Sapporo Medical University, Sapporo, 060-8556, Japan.
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18
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Loney CN, Perez Bakovic SI, Xu C, Graybill A, Greenlee LF, Renner JN. Interactions of Polyproline II Helix Peptides with Iron(III) Oxide. ChemistrySelect 2019. [DOI: 10.1002/slct.201901817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Charles N. Loney
- Department of Chemical and Biomolecular EngineeringCase Western Reserve University 10900 Euclid Ave. Cleveland, OH 44106
| | - Sergio I. Perez Bakovic
- Ralph E. Martin Department of Chemical EngineeringUniversity of Arkansas 4183 Bell Engineering Center Fayetteville, AR 72701
| | - Cheyan Xu
- Department of Chemical and Biomolecular EngineeringCase Western Reserve University 10900 Euclid Ave. Cleveland, OH 44106
| | - Ashley Graybill
- Department of Chemical and Biomolecular EngineeringCase Western Reserve University 10900 Euclid Ave. Cleveland, OH 44106
| | - Lauren F. Greenlee
- Ralph E. Martin Department of Chemical EngineeringUniversity of Arkansas 4183 Bell Engineering Center Fayetteville, AR 72701
| | - Julie N. Renner
- Department of Chemical and Biomolecular EngineeringCase Western Reserve University 10900 Euclid Ave. Cleveland, OH 44106
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19
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Murthy AV, Sulu R, Koski MK, Tu H, Anantharajan J, Sah-Teli SK, Myllyharju J, Wierenga RK. Structural enzymology binding studies of the peptide-substrate-binding domain of human collagen prolyl 4-hydroxylase (type-II): High affinity peptides have a PxGP sequence motif. Protein Sci 2019; 27:1692-1703. [PMID: 30168208 DOI: 10.1002/pro.3450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 11/11/2022]
Abstract
The peptide-substrate-binding (PSB) domain of collagen prolyl 4-hydroxylase (C-P4H, an α2 β2 tetramer) binds proline-rich procollagen peptides. This helical domain (the middle domain of the α subunit) has an important role concerning the substrate binding properties of C-P4H, although it is not known how the PSB domain influences the hydroxylation properties of the catalytic domain (the C-terminal domain of the α subunit). The crystal structures of the PSB domain of the human C-P4H isoform II (PSB-II) complexed with and without various short proline-rich peptides are described. The comparison with the previously determined PSB-I peptide complex structures shows that the C-P4H-I substrate peptide (PPG)3 , has at most very weak affinity for PSB-II, although it binds with high affinity to PSB-I. The replacement of the middle PPG triplet of (PPG)3 to the nonhydroxylatable PAG, PRG, or PEG triplet, increases greatly the affinity of PSB-II for these peptides, leading to a deeper mode of binding, as compared to the previously determined PSB-I peptide complexes. In these PSB-II complexes, the two peptidyl prolines of its central P(A/R/E)GP region bind in the Pro5 and Pro8 binding pockets of the PSB peptide-binding groove, and direct hydrogen bonds are formed between the peptide and the side chains of the highly conserved residues Tyr158, Arg223, and Asn227, replacing water mediated interactions in the corresponding PSB-I complex. These results suggest that PxGP (where x is not a proline) is the common motif of proline-rich peptide sequences that bind with high affinity to PSB-II.
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Affiliation(s)
- Abhinandan V Murthy
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Ramita Sulu
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - M Kristian Koski
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Hongmin Tu
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Jothi Anantharajan
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Shiv K Sah-Teli
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Johanna Myllyharju
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Rik K Wierenga
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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20
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Michie KA, Bermeister A, Robertson NO, Goodchild SC, Curmi PMG. Two Sides of the Coin: Ezrin/Radixin/Moesin and Merlin Control Membrane Structure and Contact Inhibition. Int J Mol Sci 2019; 20:ijms20081996. [PMID: 31018575 PMCID: PMC6515277 DOI: 10.3390/ijms20081996] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 12/21/2022] Open
Abstract
The merlin-ERM (ezrin, radixin, moesin) family of proteins plays a central role in linking the cellular membranes to the cortical actin cytoskeleton. Merlin regulates contact inhibition and is an integral part of cell–cell junctions, while ERM proteins, ezrin, radixin and moesin, assist in the formation and maintenance of specialized plasma membrane structures and membrane vesicle structures. These two protein families share a common evolutionary history, having arisen and separated via gene duplication near the origin of metazoa. During approximately 0.5 billion years of evolution, the merlin and ERM family proteins have maintained both sequence and structural conservation to an extraordinary level. Comparing crystal structures of merlin-ERM proteins and their complexes, a picture emerges of the merlin-ERM proteins acting as switchable interaction hubs, assembling protein complexes on cellular membranes and linking them to the actin cytoskeleton. Given the high level of structural conservation between the merlin and ERM family proteins we speculate that they may function together.
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Affiliation(s)
- Katharine A Michie
- School of Physics, University of New South Wales, Sydney 2052, Australia.
| | - Adam Bermeister
- School of Physics, University of New South Wales, Sydney 2052, Australia.
| | - Neil O Robertson
- School of Physics, University of New South Wales, Sydney 2052, Australia.
| | - Sophia C Goodchild
- Department of Molecular Sciences, Macquarie University, Sydney 2109, Australia.
| | - Paul M G Curmi
- School of Physics, University of New South Wales, Sydney 2052, Australia.
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21
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Windsor IW, Gold B, Raines RT. An n→ π* Interaction in the Bound Substrate of Aspartic Proteases Replicates the Oxyanion Hole. ACS Catal 2019; 9:1464-1471. [PMID: 31093467 DOI: 10.1021/acscatal.8b04142] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aspartic proteases regulate many biological processes and are prominent targets for therapeutic intervention. Structural studies have captured intermediates along the reaction pathway, including the Michaelis complex and tetrahedral intermediate. Using a Ramachandran analysis of these structures, we discovered that residues occupying the P1 and P1' positions (which flank the scissile peptide bond) adopt the dihedral angle of an inverse γ-turn and polyproline type-II helix, respectively. Computational analyses reveal that the polyproline type-II helix engenders an n→π* interaction in which the oxygen of the scissile peptide bond is the donor. This interaction stabilizes the negative charge that develops in the tetrahedral intermediate, much like the oxyanion hole of serine proteases. The inverse γ-turn serves to twist the scissile peptide bond, vacating the carbonyl π* orbital and facilitating its hydration. These previously unappreciated interactions entail a form of substrate-assisted catalysis and offer opportunities for drug design.
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Affiliation(s)
- Ian W. Windsor
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Brian Gold
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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22
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Carver JA, Holt C. Functional and dysfunctional folding, association and aggregation of caseins. PROTEIN MISFOLDING 2019; 118:163-216. [DOI: 10.1016/bs.apcsb.2019.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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23
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Huang KY, Horng JC. Impacts of the Terminal Charged Residues on Polyproline Conformation. J Phys Chem B 2018; 123:138-147. [DOI: 10.1021/acs.jpcb.8b10864] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Abstract
The transcription factor NF-κB is a critical regulator of immune and inflammatory responses. In mammals, the NF-κB/Rel family comprises five members: p50, p52, p65 (Rel-A), c-Rel, and Rel-B proteins, which form homo- or heterodimers and remain as an inactive complex with the inhibitory molecules called IκB proteins in resting cells. Two distinct NF-κB signaling pathways have been described: 1) the canonical pathway primarily activated by pathogens and inflammatory mediators, and 2) the noncanonical pathway mostly activated by developmental cues. The most abundant form of NF-κB activated by pathologic stimuli via the canonical pathway is the p65:p50 heterodimer. Disproportionate increase in activated p65 and subsequent transactivation of effector molecules is integral to the pathogenesis of many chronic diseases such as the rheumatoid arthritis, inflammatory bowel disease, multiple sclerosis, and even neurodegenerative pathologies. Hence, the NF-κB p65 signaling pathway has been a pivotal point for intense drug discovery and development. This review begins with an overview of p65-mediated signaling followed by discussion of strategies that directly target NF-κB p65 in the context of chronic inflammation.
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Affiliation(s)
- Sivagami Giridharan
- Department of Oral Medicine, Madha Dental College, Kundrathur, Chennai, TN, India
| | - Mythily Srinivasan
- Department of Oral Pathology, Medicine and Radiology, Indiana University School of Dentistry, Indiana University Purdue University at Indianapolis, Indianapolis, IN, USA,
- Provaidya LLC, Indianapolis, IN, USA,
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25
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Srinivasan M, Lahiri N, Thyagarajan A, Witek E, Hickman D, Lahiri DK. Nuclear factor-kappa B: Glucocorticoid-induced leucine zipper interface analogs suppress pathology in an Alzheimer's disease model. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2018; 4:488-498. [PMID: 30338290 PMCID: PMC6186959 DOI: 10.1016/j.trci.2018.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Glucocorticoid-induced leucine zipper is a regulatory protein that sequesters activated nuclear factor-kappa B p65. Previously, we showed that rationally designed analogs of the p65-binding domain of glucocorticoid-induced leucine zipper, referred to as glucocorticoid-induced leucine zipper analogs (GAs), inhibited amyloid β-induced metabolic activity and inflammatory cytokines in mixed brain cell cultures. Here, we investigate the therapeutic efficacy of GA in an Alzheimer's disease model. METHODS GA and control peptides were synthesized covalently as peptide amides with the cell-penetrating agent. C57Bl/6J mice induced with lipopolysaccharide-mediated neuroinflammation (250 mg/kg i.p/day for six days) were treated on alternate days with GA-1, GA-2, or control peptides (25 mg/kg i.v). Brain tissues were assessed for gliosis, cytokines, and antiapoptotic factors. RESULTS The brain tissues of GA-1- and GA-2-treated mice exhibited significantly reduced gliosis, suppressed inflammatory cytokines, and elevated antiapoptotic factors. DISCUSSION The antineuroinflammatory effects of GA suggest potential therapeutic application for Alzheimer's disease.
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Affiliation(s)
- Mythily Srinivasan
- Department of Oral Pathology, Medicine and Radiology, Indiana University School of Dentistry, Indianapolis, IN, USA
| | - Niloy Lahiri
- Provaidya LLC, Indiana University School of Dentistry, Indianapolis, IN, USA
| | - Anish Thyagarajan
- Provaidya LLC, Indiana University School of Dentistry, Indianapolis, IN, USA
| | - Emily Witek
- Stark Neuroscience Research Institute, Department of Psychiatry, Institute of Psychiatry Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Debra Hickman
- Stark Neuroscience Research Institute, Department of Psychiatry, Institute of Psychiatry Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Debomoy K. Lahiri
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indiana University–Purdue University Indianapolis, Indianapolis, IN, USA
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Sabirzyanov FA, Sabirzyanova TA, Rekstina VV, Adzhubei AA, Kalebina TS. C-Terminal sequence is involved in the incorporation of Bgl2p glucanosyltransglycosylase in the cell wall of Saccharomyces cerevisiae. FEMS Yeast Res 2018; 18:4768138. [PMID: 29272386 DOI: 10.1093/femsyr/fox093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 12/18/2017] [Indexed: 01/01/2023] Open
Abstract
A cell wall (CW) provides a protective barrier for a yeast cell and is a firm structure that nevertheless dynamically changes during cell's growth. Bgl2p is a non-covalently anchored glucanosyltransglycosylase in the CW of the yeast Saccharomyces cerevisiae. The mode of its anchorage is poorly understood, while its association with CW components is tight and resistant to 1-h treatment with 1% SDS at 37°C. In order to demarcate the potential structural block responsible for incorporation of Bgl2p into the CW, bioinformatics analysis of its sequence was performed, and a conservative structural region was identified in the C-terminal region of Bgl2p, which was absent in its homologues in S. cerevisiae, the Scw4p and Scw10p. Deletion of this region disrupted the incorporation of Bgl2p into the CW and led to release of this protein through the CW into the culture medium. Two left-handed polyproline-II helices were identified in the C-terminal region of the structure model of a wild-type Bgl2p. These helices potentially formed binding sites, which were absent in the truncated protein. Using immune fluorescence microscopy, we demonstrated that C-truncated Bgl2p was exported into culture medium and lost its ability to form fibrils described earlier. It was also shown that the C-terminal truncation of Bgl2p led to a more severe decrease of cell survivability in extreme conditions than BGL2 deletion.
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Affiliation(s)
- F A Sabirzyanov
- Department of Molecular Biology, Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - T A Sabirzyanova
- Department of Molecular Biology, Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - V V Rekstina
- Department of Molecular Biology, Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - A A Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - T S Kalebina
- Department of Molecular Biology, Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
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Mortensen DN, Williams ER. Microsecond and nanosecond polyproline II helix formation in aqueous nanodrops measured by mass spectrometry. Chem Commun (Camb) 2018; 52:12218-12221. [PMID: 27711437 DOI: 10.1039/c6cc06423j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 1.5 μs and <400 ns time constants for the formation of polyproline II helix structures in 21 and 16 residue peptides, respectively, are measured using rapid mixing from theta-glass emitters coupled with mass spectrometry. Results from these studies should serve as useful benchmarks for comparison with computational simulation results.
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Affiliation(s)
- Daniel N Mortensen
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA.
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA.
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Yadav P, Shahane G, Gaikwad S. Amaranthus caudatus lectin with polyproline II fold: conformational and functional transitions and molecular dynamics. J Biomol Struct Dyn 2017; 36:2203-2215. [DOI: 10.1080/07391102.2017.1345328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Priya Yadav
- Academy of Scientific and Innovative Research (AcSIR) NCL campus, Biochemical Sciences Division, CSIR-NCL, Pune, India
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune 411008, India
| | - Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, UK
| | - Sushama Gaikwad
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune 411008, India
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Saravanan KM, Selvaraj S. Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins. J Biol Phys 2017; 43:265-278. [PMID: 28577238 PMCID: PMC5471173 DOI: 10.1007/s10867-017-9451-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 04/13/2017] [Indexed: 12/22/2022] Open
Abstract
In theory, a polypeptide chain can adopt a vast number of conformations, each corresponding to a set of backbone rotation angles. Many of these conformations are excluded due to steric overlaps. Ramachandran and coworkers were the first to look into this problem by plotting backbone dihedral angles in a two-dimensional plot. The conformational space in the Ramachandran map is further refined by considering the energetic contributions of various non-bonded interactions. Alternatively, the conformation adopted by a polypeptide chain may also be examined by investigating interactions between the residues. Since the Ramachandran map essentially focuses on local interactions (residues closer in sequence), out of interest, we have analyzed the dihedral angle preferences of residues that make non-local interactions (residues far away in sequence and closer in space) in the folded structures of proteins. The non-local interactions have been grouped into different types such as hydrogen bond, van der Waals interactions between hydrophobic groups, ion pairs (salt bridges), and ππ-stacking interactions. The results show the propensity of amino acid residues in proteins forming local and non-local interactions. Our results point to the vital role of different types of non-local interactions and their effect on dihedral angles in forming secondary and tertiary structural elements to adopt their native fold.
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Affiliation(s)
- Konda Mani Saravanan
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, 600 025, India
| | - Samuel Selvaraj
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, 600 025, India.
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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Lella M, Mahalakshmi R. Solvation driven conformational transitions in the second transmembrane domain of mycobacteriophage holin. Biopolymers 2017; 108. [DOI: 10.1002/bip.22894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/11/2016] [Accepted: 05/31/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Muralikrishna Lella
- Molecular Biophysics Laboratory, Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal 462023 India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal 462023 India
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Novel Nuclear Factor-KappaB Targeting Peptide Suppresses β-Amyloid Induced Inflammatory and Apoptotic Responses in Neuronal Cells. PLoS One 2016; 11:e0160314. [PMID: 27764084 PMCID: PMC5072831 DOI: 10.1371/journal.pone.0160314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 07/18/2016] [Indexed: 11/19/2022] Open
Abstract
In the central nervous system (CNS), activation of the transcription factor nuclear factor-kappa B (NF-κβ) is associated with both neuronal survival and increased vulnerability to apoptosis. The mechanisms underlying these dichotomous effects are attributed to the composition of NF-κΒ dimers. In Alzheimer’s disease (AD), β-amyloid (Aβ) and other aggregates upregulate activation of p65:p50 dimers in CNS cells and enhance transactivation of pathological mediators that cause neuroinflammation and neurodegeneration. Hence selective targeting of activated p65 is an attractive therapeutic strategy for AD. Here we report the design, structural and functional characterization of peptide analogs of a p65 interacting protein, the glucocorticoid induced leucine zipper (GILZ). By virtue of binding the transactivation domain of p65 exposed after release from the inhibitory IκΒ proteins in activated cells, the GILZ analogs can act as highly selective inhibitors of activated p65 with minimal potential for off-target effects.
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Adzhubei AA, Anashkina AA, Makarov AA. Left-handed polyproline-II helix revisited: proteins causing proteopathies. J Biomol Struct Dyn 2016; 35:2701-2713. [PMID: 27562438 DOI: 10.1080/07391102.2016.1229220] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Left-handed polyproline-II type helix is a regular conformation of polypeptide chain not only of fibrous, but also of folded and natively unfolded proteins and peptides. It is the only class of regular secondary structure substantially represented in non-fibrous proteins and peptides on a par with right-handed alpha-helix and beta-structure. In this study, we have shown that polyproline-II helix is abundant in several peptides and proteins involved in proteopathies, the amyloid-beta peptides, protein tau and prion protein. Polyproline-II helices form two interaction sites in the amyloid-beta peptides, which are pivotal for pathogenesis of Alzheimer's disease (AD). It also with high probability is the structure of the majority of tau phosphorylation sites, important for tau hyperphosphorylation and formation of neurofibrillary tangles, a hallmark of AD. Polyproline-II helices form large parts of the structure of the folded domain of prion protein. They can undergo conversion to beta-structure as a result of relatively small change of one torsional angle of polypeptide chain. We hypothesize that in prions and amyloids, in general polyproline-II helices can serve as structural elements of the normal structure as well as dormant nuclei of structure conversion, and thus play important role in structure changes leading to the formation of fibrils.
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Affiliation(s)
- Alexei A Adzhubei
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Vavilov St 32, Moscow 119991 , Russia
| | - Anastasia A Anashkina
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Vavilov St 32, Moscow 119991 , Russia
| | - Alexander A Makarov
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Vavilov St 32, Moscow 119991 , Russia
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Yazici H, O'Neill MB, Kacar T, Wilson BR, Oren EE, Sarikaya M, Tamerler C. Engineered Chimeric Peptides as Antimicrobial Surface Coating Agents toward Infection-Free Implants. ACS APPLIED MATERIALS & INTERFACES 2016; 8:5070-81. [PMID: 26795060 PMCID: PMC5310947 DOI: 10.1021/acsami.5b03697] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Prevention of bacterial colonization and consequent biofilm formation remains a major challenge in implantable medical devices. Implant-associated infections are not only a major cause of implant failures but also their conventional treatment with antibiotics brings further complications due to the escalation in multidrug resistance to a variety of bacterial species. Owing to their unique properties, antimicrobial peptides (AMPs) have gained significant attention as effective agents to combat colonization of microorganisms. These peptides have been shown to exhibit a wide spectrum of activities with specificity to a target cell while having a low tendency for developing bacterial resistance. Engineering biomaterial surfaces that feature AMP properties, therefore, offer a promising approach to prevent implant infections. Here, we engineered a chimeric peptide with bifunctionality that both forms a robust solid-surface coating while presenting antimicrobial property. The individual domains of the chimeric peptides were evaluated for their solid-binding kinetics to titanium substrate as well as for their antimicrobial properties in solution. The antimicrobial efficacy of the chimeric peptide on the implant material was evaluated in vitro against infection by a variety of bacteria, including Streptococcus mutans, Staphylococcus. epidermidis, and Escherichia coli, which are commonly found in oral and orthopedic implant related surgeries. Our results demonstrate significant improvement in reducing bacterial colonization onto titanium surfaces below the detectable limit. Engineered chimeric peptides with freely displayed antimicrobial domains could be a potential solution for developing infection-free surfaces by engineering implant interfaces with highly reduced bacterial colonization property.
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Affiliation(s)
- Hilal Yazici
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Department of Molecular Biology and Genetics, Molecular Biology, Biotechnology and Genetic Center, Istanbul Technical University, Istanbul 34469, Turkey
| | - Mary B. O'Neill
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Turgay Kacar
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Department of Molecular Biology and Genetics, Molecular Biology, Biotechnology and Genetic Center, Istanbul Technical University, Istanbul 34469, Turkey
| | - Brandon R. Wilson
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - E. Emre Oren
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Mehmet Sarikaya
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Candan Tamerler
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Department of Mechanical Engineering, Bioengineering Research Center, University of Kansas, Lawrence, Kansas 66045, United States
- Corresponding Author Phone: 785-864-2984. . Corresponding author address: Bioengineering Research Center, Department of Mechanical Engineering, 1530 W, 15th St, Learned Hall, Lawrence, KS 66047
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Erdogan H, Babur E, Yilmaz M, Candas E, Gordesel M, Dede Y, Oren EE, Demirel GB, Ozturk MK, Yavuz MS, Demirel G. Morphological Versatility in the Self-Assembly of Val-Ala and Ala-Val Dipeptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:7337-7345. [PMID: 26086903 DOI: 10.1021/acs.langmuir.5b01406] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Since the discovery of dipeptide self-assembly, diphenylalanine (Phe-Phe)-based dipeptides have been widely investigated in a variety of fields. Although various supramolecular Phe-Phe-based structures including tubes, vesicles, fibrils, sheets, necklaces, flakes, ribbons, and wires have been demonstrated by manipulating the external physical or chemical conditions applied, studies of the morphological diversity of dipeptides other than Phe-Phe are still required to understand both how these small molecules respond to external conditions such as the type of solvent and how the peptide sequence affects self-assembly and the corresponding molecular structures. In this work, we investigated the self-assembly of valine-alanine (Val-Ala) and alanine-valine (Ala-Val) dipeptides by varying the solvent medium. It was observed that Val-Ala dipeptide molecules may generate unique self-assembly-based morphologies in response to the solvent medium used. Interestingly, when Ala-Val dipeptides were utilized as a peptide source instead of Val-Ala, we observed distinct differences in the final dipeptide structures. We believe that such manipulation may not only provide us with a better understanding of the fundamentals of the dipeptide self-assembly process but also may enable us to generate novel peptide-based materials for various applications.
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Affiliation(s)
- Hakan Erdogan
- †Bio-inspired Materials Research Laboratory (BIMREL), Department of Chemistry, Gazi University, 06500 Ankara, Turkey
| | - Esra Babur
- †Bio-inspired Materials Research Laboratory (BIMREL), Department of Chemistry, Gazi University, 06500 Ankara, Turkey
| | - Mehmet Yilmaz
- †Bio-inspired Materials Research Laboratory (BIMREL), Department of Chemistry, Gazi University, 06500 Ankara, Turkey
| | - Elif Candas
- ‡Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, 06560 Ankara, Turkey
| | - Merve Gordesel
- §Theoretical/Computational Chemistry Research Laboratory, Department of Chemistry, Gazi University, 06900 Ankara, Turkey
| | - Yavuz Dede
- §Theoretical/Computational Chemistry Research Laboratory, Department of Chemistry, Gazi University, 06900 Ankara, Turkey
| | - Ersin Emre Oren
- ‡Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, 06560 Ankara, Turkey
| | | | | | - Mustafa Selman Yavuz
- #Department of Metallurgy and Materials Engineering, Selcuk University, 42075 Konya, Turkey
| | - Gokhan Demirel
- †Bio-inspired Materials Research Laboratory (BIMREL), Department of Chemistry, Gazi University, 06500 Ankara, Turkey
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Integrating solid-state NMR and computational modeling to investigate the structure and dynamics of membrane-associated ghrelin. PLoS One 2015; 10:e0122444. [PMID: 25803439 PMCID: PMC4372444 DOI: 10.1371/journal.pone.0122444] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 02/11/2015] [Indexed: 12/18/2022] Open
Abstract
The peptide hormone ghrelin activates the growth hormone secretagogue receptor 1a, also known as the ghrelin receptor. This 28-residue peptide is acylated at Ser3 and is the only peptide hormone in the human body that is lipid-modified by an octanoyl group. Little is known about the structure and dynamics of membrane-associated ghrelin. We carried out solid-state NMR studies of ghrelin in lipid vesicles, followed by computational modeling of the peptide using Rosetta. Isotropic chemical shift data of isotopically labeled ghrelin provide information about the peptide’s secondary structure. Spin diffusion experiments indicate that ghrelin binds to membranes via its lipidated Ser3. Further, Phe4, as well as electrostatics involving the peptide’s positively charged residues and lipid polar headgroups, contribute to the binding energy. Other than the lipid anchor, ghrelin is highly flexible and mobile at the membrane surface. This observation is supported by our predicted model ensemble, which is in good agreement with experimentally determined chemical shifts. In the final ensemble of models, residues 8–17 form an α-helix, while residues 21–23 and 26–27 often adopt a polyproline II helical conformation. These helices appear to assist the peptide in forming an amphipathic conformation so that it can bind to the membrane.
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Srinivasan M, Blackburn C, Lahiri DK. Functional characterization of a competitive peptide antagonist of p65 in human macrophage-like cells suggests therapeutic potential for chronic inflammation. Drug Des Devel Ther 2014; 8:2409-21. [PMID: 25584020 PMCID: PMC4262379 DOI: 10.2147/dddt.s59722] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Glucocorticoid-induced leucine zipper (GILZ) is a glucocorticoid responsive protein that links the nuclear factor-kappa B (NFκB) and the glucocorticoid signaling pathways. Functional and binding studies suggest that the proline-rich region at the carboxy terminus of GILZ binds the p65 subunit of NFκB and suppresses the immunoinflammatory response. A widely-used strategy in the discovery of peptide drugs involves exploitation of the complementary surfaces of naturally occurring binding partners. Previously, we observed that a synthetic peptide (GILZ-P) derived from the proline-rich region of GILZ bound activated p65 and ameliorated experimental encephalomyelitis. Here we characterize the secondary structure of GILZ-P by circular dichroic analysis. GILZ-P adopts an extended polyproline type II helical conformation consistent with the structural conformation commonly observed in interfaces of transient intermolecular interactions. To determine the potential application of GILZ-P in humans, we evaluated the toxicity and efficacy of the peptide drug in mature human macrophage-like THP-1 cells. Treatment with GILZ-P at a wide range of concentrations commonly used for peptide drugs was nontoxic as determined by cell viability and apoptosis assays. Functionally, GILZ-P suppressed proliferation and glutamate secretion by activated macrophages by inhibiting nuclear translocation of p65. Collectively, our data suggest that the GILZ-P has therapeutic potential in chronic CNS diseases where persistent inflammation leads to neurodegeneration such as multiple sclerosis and Alzheimer's disease.
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Affiliation(s)
- Mythily Srinivasan
- Department of Oral Pathology, Medicine and Radiology, Indiana University School of Dentistry, Indianapolis, IN, USA
| | - Corinne Blackburn
- Department of Oral Pathology, Medicine and Radiology, Indiana University School of Dentistry, Indianapolis, IN, USA
| | - Debomoy K Lahiri
- Institute of Psychiatry Research, Department of Psychiatry, Indiana University-Purdue University, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University-Purdue University, Indianapolis, IN, USA
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Bijl E, van Valenberg H, Sikkes S, Jumelet S, Sala G, Olieman K, van Hooijdonk T, Huppertz T. Chymosin-induced hydrolysis of caseins: Influence of degree of phosphorylation of alpha-s1-casein and genetic variants of beta-casein. Int Dairy J 2014. [DOI: 10.1016/j.idairyj.2014.07.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Andreotti G, Cabeza de Vaca I, Poziello A, Monti MC, Guallar V, Cubellis MV. Conformational response to ligand binding in phosphomannomutase2: insights into inborn glycosylation disorder. J Biol Chem 2014; 289:34900-10. [PMID: 25324542 PMCID: PMC4263888 DOI: 10.1074/jbc.m114.586362] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The most common glycosylation disorder is caused by mutations in the gene encoding phosphomannomutase2, producing a disease still without a cure. Phosphomannomutase2, a homodimer in which each chain is composed of two domains, requires a bisphosphate sugar (either mannose or glucose) as activator, opening a possible drug design path for therapeutic purposes. The crystal structure of human phosphomannomutase2, however, lacks bound substrate and a key active site loop. To speed up drug discovery, we present here the first structural model of a bisphosphate substrate bound to human phosphomannomutase2. Taking advantage of recent developments in all-atom simulation techniques in combination with limited and site-directed proteolysis, we demonstrated that α-glucose 1,6-bisphosphate can adopt two low energy orientations as required for catalysis. Upon ligand binding, the two domains come close, making the protein more compact, in analogy to the enzyme in the crystals from Leishmania mexicana. Moreover, proteolysis was also carried out on two common mutants, R141H and F119L. It was an unexpected finding that the mutant most frequently found in patients, R141H, although inactive, does bind α-glucose 1,6-bisphosphate and changes conformation.
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Affiliation(s)
- Giuseppina Andreotti
- From the Istituto di Chimica Biomolecolare-Consiglio Nazionale Delle Ricerche, 80078 Pozzuoli, Italy
| | - Israel Cabeza de Vaca
- Joint Barcelona Supercomputing Center-Center for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Angelita Poziello
- From the Istituto di Chimica Biomolecolare-Consiglio Nazionale Delle Ricerche, 80078 Pozzuoli, Italy, Dipartimento di Biologia, Università Federico II, 80126 Naples, Italy
| | - Maria Chiara Monti
- Dipartimento di Farmacia, Università degli Studi di Salerno, 84084 Fisciano, Italy
| | - Victor Guallar
- Joint Barcelona Supercomputing Center-Center for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010 Barcelona, Spain, and
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Sun X, Greenwood DR, Templeton MD, Libich DS, McGhie TK, Xue B, Yoon M, Cui W, Kirk CA, Jones WT, Uversky VN, Rikkerink EHA. The intrinsically disordered structural platform of the plant defence hub protein RPM1-interacting protein 4 provides insights into its mode of action in the host-pathogen interface and evolution of the nitrate-induced domain protein family. FEBS J 2014; 281:3955-79. [DOI: 10.1111/febs.12937] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 07/01/2014] [Accepted: 07/15/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaolin Sun
- The New Zealand Institute of Plant & Food Research (PFR); Palmerston North New Zealand
| | - David R. Greenwood
- PFR; Auckland New Zealand
- School of Biological Sciences; University of Auckland; New Zealand
| | - Matthew D. Templeton
- PFR; Auckland New Zealand
- School of Biological Sciences; University of Auckland; New Zealand
| | - David S. Libich
- Centre for Structural Biology; Institute of Fundamental Sciences; Massey University; Palmerston North New Zealand
| | - Tony K. McGhie
- The New Zealand Institute of Plant & Food Research (PFR); Palmerston North New Zealand
| | - Bin Xue
- Department of Cell Biology; Microbiology and Molecular Biology; College of Fine Arts and Sciences; University of South Florida; Tampa FL USA
| | | | | | - Christopher A. Kirk
- The New Zealand Institute of Plant & Food Research (PFR); Palmerston North New Zealand
| | - William T. Jones
- The New Zealand Institute of Plant & Food Research (PFR); Palmerston North New Zealand
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa FL USA
- Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino Moscow Region Russia
- Biology Department; Faculty of Science; King Abdulaziz University; Jeddah Kingdom of Saudi Arabia
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42
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Lin YJ, Horng JC. Impacts of terminal (4R)-fluoroproline and (4S)-fluoroproline residues on polyproline conformation. Amino Acids 2014; 46:2317-24. [DOI: 10.1007/s00726-014-1783-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 06/07/2014] [Indexed: 10/25/2022]
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Liu C, Tai L, Zhang W, Wei G, Pan W, Lu W. Penetratin, a potentially powerful absorption enhancer for noninvasive intraocular drug delivery. Mol Pharm 2014; 11:1218-27. [PMID: 24521351 DOI: 10.1021/mp400681n] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Intraocular drug delivery is extraordinarily hampered by the impermeability of defensive barriers of the eye. In this study, the ocular permeability of fluorophore-labeled cell-penetrating peptides (CPPs), including penetratin, TAT, low molecular weight protamine, and poly(arginine)8, was investigated based on multilevel evaluations. The human conjunctival epithelial cell (NHC) was exposed to various CPPs to determine the cytotoxicity and cellular uptake. Ex vivo studies with rabbit cornea were performed using side-by-side diffusion chambers to evaluate the apparent permeability coefficients and acute tissue tolerance of the CPP candidates. Among all examined CPPs, penetratin shows an outstanding cellular uptake, by increasing more than 16 and 25 times at low and high concentrations, compared to the control peptide poly(serine)8 respectively. Additionally, the permeability of penetratin across excised cornea is 87.5 times higher in comparison with poly(serine)8. More importantly, after instilled in the conjunctival sac of rat eyes, fluorophore-labeled penetratin displayed a rapid and wide distribution in both anterior and posterior segment of the eye, and could be observed in the corneal epithelium and retina lasting for at least 6 h. Interestingly, penetratin showed the lowest ocular cell and tissue toxicities among all examined CPPs. The high ocular permeability of penetratin could be attributed to its amphipathicity and spatial conformation determined by circular dichroism. Taken together, these data demonstrate that penetratin is potentially useful as an absorption enhancer for intraocular drug delivery.
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Affiliation(s)
- Chang Liu
- Key Laboratory of Smart Drug Delivery, Ministry of Education; Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, China
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Berisio R, Vitagliano L. Polyproline and triple helix motifs in host-pathogen recognition. Curr Protein Pept Sci 2013; 13:855-65. [PMID: 23305370 PMCID: PMC3707005 DOI: 10.2174/138920312804871157] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/10/2012] [Accepted: 08/30/2012] [Indexed: 01/18/2023]
Abstract
Secondary structure elements often mediate protein-protein interactions. Despite their low abundance in folded proteins, polyproline II (PPII) and its variant, the triple helix, are frequently involved in protein-protein interactions, likely due to their peculiar propensity to be solvent-exposed. We here review the role of PPII and triple helix in mediating host-pathogen interactions, with a particular emphasis to the structural aspects of these processes. After a brief description of the basic structural features of these elements, examples of host-pathogen interactions involving these motifs are illustrated. Literature data suggest that the role played by PPII motif in these processes is twofold. Indeed, PPII regions may directly mediate interactions between proteins of the host and the pathogen. Alternatively, PPII may act as structural spacers needed for the correct positioning of the elements needed for adhesion and infectivity. Recent investigations have highlighted that collagen triple helix is also a common target for bacterial adhesins. Although structural data on complexes between adhesins and collagen models are rather limited, experimental and theoretical studies have unveiled some interesting clues of the recognition process. Interestingly, very recent data show that not only is the triple helix used by pathogens as a target in the host-pathogen interaction but it may also act as a bait in these processes since bacterial proteins containing triple helix regions have been shown to interact with host proteins. As both PPII and triple helix expose several main chain non-satisfied hydrogen bond acceptors and donors, both elements are highly solvated. The preservation of the solvation state of both PPII and triple helix upon protein-protein interaction is an emerging aspect that will be here thoroughly discussed.
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Affiliation(s)
- Rita Berisio
- Istituto di Biostrutture e Bioimmagini, CNR via Mezzocannone 16, I-80134 Napoli, Italy
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Holt C, Carver JA, Ecroyd H, Thorn DC. Invited review: Caseins and the casein micelle: their biological functions, structures, and behavior in foods. J Dairy Sci 2013; 96:6127-46. [PMID: 23958008 DOI: 10.3168/jds.2013-6831] [Citation(s) in RCA: 286] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/09/2013] [Indexed: 12/27/2022]
Abstract
A typical casein micelle contains thousands of casein molecules, most of which form thermodynamically stable complexes with nanoclusters of amorphous calcium phosphate. Like many other unfolded proteins, caseins have an actual or potential tendency to assemble into toxic amyloid fibrils, particularly at the high concentrations found in milk. Fibrils do not form in milk because an alternative aggregation pathway is followed that results in formation of the casein micelle. As a result of forming micelles, nutritious milk can be secreted and stored without causing either pathological calcification or amyloidosis of the mother's mammary tissue. The ability to sequester nanoclusters of amorphous calcium phosphate in a stable complex is not unique to caseins. It has been demonstrated using a number of noncasein secreted phosphoproteins and may be of general physiological importance in preventing calcification of other biofluids and soft tissues. Thus, competent noncasein phosphoproteins have similar patterns of phosphorylation and the same type of flexible, unfolded conformation as caseins. The ability to suppress amyloid fibril formation by forming an alternative amorphous aggregate is also not unique to caseins and underlies the action of molecular chaperones such as the small heat-shock proteins. The open structure of the protein matrix of casein micelles is fragile and easily perturbed by changes in its environment. Perturbations can cause the polypeptide chains to segregate into regions of greater and lesser density. As a result, the reliable determination of the native structure of casein micelles continues to be extremely challenging. The biological functions of caseins, such as their chaperone activity, are determined by their composition and flexible conformation and by how the casein polypeptide chains interact with each other. These same properties determine how caseins behave in the manufacture of many dairy products and how they can be used as functional ingredients in other foods.
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Affiliation(s)
- C Holt
- Institute of Molecular, Cell and Systems Biology, School of Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
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Byrne C, Miclet E, Broutin I, Gallo D, Pelekanou V, Kampa M, Castanas E, Leclercq G, Jacquot Y. Identification of polyproline II regions derived from the proline-rich nuclear receptor coactivators PNRC and PNRC2: new insights for ERα coactivator interactions. Chirality 2013; 25:628-42. [PMID: 23925889 DOI: 10.1002/chir.22188] [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] [Received: 07/02/2012] [Accepted: 04/12/2013] [Indexed: 11/07/2022]
Abstract
Protein-protein interactions are crucial for signal transductions required for cell differentiation and proliferation. Their modulation is therefore key to the development of therapeutic alternatives, particularly in the context of cancer. According to literature data, the polyproline-rich nuclear receptor coactivators PNRC and PNRC2 interact with estrogen receptor (ERα) through their PxxP SH3-binding motifs. In a search to identify the molecular features governing this interaction, we explored using electronic circular dichroism (ECD) spectroscopy and molecular dynamics (MD) calculations, the capacity of a range of putative biologically active peptides derived from these proteins and containing this PxxP motif(s) to form polyproline II (PPII) domains. An additional more exhaustive structural study on a lead PPII peptide was also performed using 2D nuclear magnetic resonance (NMR) spectroscopy. With the exception of one of all the investigated peptides (PNRC-D), binding assays failed to detect any affinity for Grb2 SH3 domains, suggesting that PPII motifs issued from Grb2 antagonists have a binding mode distinct from those derived from Grb2 agonists. Instead, the peptides revealed a competitive binding ability against a synthetic peptide (ERα17p) with a putative PPII-cognate domain located within a coregulator recruitment region of ERα (AF-2 site). Our work, which constitutes the first structure-related interaction study concerning PNRC and PNRC2, supports not only the existence of PxxP-induced PPII sequences in these coregulators, but also confirms the presence of a PPII recognition site in the AF-2 of the steroid receptor ERα, a region important for transcription regulation.
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Affiliation(s)
- C Byrne
- Laboratoire des BioMolécules (LBM), CNRS - UMR 7203, Ecole Normale Supérieure / Université Pierre et Marie Curie 24, rue Lhomond, 75231, Paris Cedex 05, France; Fondation Pierre-Gilles de Gennes pour la Recherche, 29, rue d'Ulm, 75005, Paris, France
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Polyproline-II Helix in Proteins: Structure and Function. J Mol Biol 2013; 425:2100-32. [DOI: 10.1016/j.jmb.2013.03.018] [Citation(s) in RCA: 363] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/28/2013] [Accepted: 03/11/2013] [Indexed: 12/31/2022]
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Theillet FX, Kalmar L, Tompa P, Han KH, Selenko P, Dunker AK, Daughdrill GW, Uversky VN. The alphabet of intrinsic disorder: I. Act like a Pro: On the abundance and roles of proline residues in intrinsically disordered proteins. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e24360. [PMID: 28516008 PMCID: PMC5424786 DOI: 10.4161/idp.24360] [Citation(s) in RCA: 186] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 03/17/2013] [Indexed: 11/19/2022]
Abstract
A significant fraction of every proteome is occupied by biologically active proteins that do not form unique three-dimensional structures. These intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) have essential biological functions and are characterized by extensive structural plasticity. Such structural and functional behavior is encoded in the amino acid sequences of IDPs/IDPRs, which are enriched in disorder-promoting residues and depleted in order-promoting residues. In fact, amino acid residues can be arranged according to their disorder-promoting tendency to form an alphabet of intrinsic disorder that defines the structural complexity and diversity of IDPs/IDPRs. This review is the first in a series of publications dedicated to the roles that different amino acid residues play in defining the phenomenon of protein intrinsic disorder. We start with proline because data suggests that of the 20 common amino acid residues, this one is the most disorder-promoting.
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Affiliation(s)
- Francois-Xavier Theillet
- In-cell NMR Spectroscopy; Leibniz Institute of Molecular Pharmacology (FMP Berlin); Berlin, Germany
| | - Lajos Kalmar
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium
| | - Peter Tompa
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium.,Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest, Hungary
| | - Kyou-Hoon Han
- Department of Bioinformatics; University of Science and Technology; Daejeon, Yuseong-gu, Korea.,Biomedical Translational Research Center; Division of Convergent Biomedical Research; Korea Research Institute of Bioscience and Biotechnology; Daejeon, Yuseong-gu, Korea
| | - Philipp Selenko
- In-cell NMR Spectroscopy; Leibniz Institute of Molecular Pharmacology (FMP Berlin); Berlin, Germany
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics; Department of Biochemistry and Molecular Biology; Indiana University School of Medicine; Indianapolis, IN USA
| | - Gary W Daughdrill
- Center for Drug Discovery and Innovation; Department of Cell Biology, Microbiology and Molecular Biology; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
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Yazici H, Fong H, Wilson B, Oren E, Amos F, Zhang H, Evans J, Snead M, Sarikaya M, Tamerler C. Biological response on a titanium implant-grade surface functionalized with modular peptides. Acta Biomater 2013; 9:5341-52. [PMID: 23159566 DOI: 10.1016/j.actbio.2012.11.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 10/18/2012] [Accepted: 11/02/2012] [Indexed: 12/21/2022]
Abstract
Titanium (Ti) and its alloys are among the most successful implantable materials for dental and orthopedic applications. The combination of excellent mechanical and corrosion resistance properties makes them highly desirable as endosseous implants that can withstand a demanding biomechanical environment. Yet, the success of the implant depends on its osteointegration, which is modulated by the biological reactions occurring at the interface of the implant. A recent development for improving biological responses on the Ti-implant surface has been the realization that bifunctional peptides can impart material binding specificity not only because of their molecular recognition of the inorganic material surface, but also through their self-assembly and ease of biological conjugation properties. To assess peptide-based functionalization on bioactivity, the present authors generated a set of peptides for implant-grade Ti, using cell surface display methods. Out of 60 unique peptides selected by this method, two of the strongest titanium binding peptides, TiBP1 and TiBP2, were further characterized for molecular structure and adsorption properties. These two peptides demonstrated unique, but similar molecular conformations different from that of a weak binder peptide, TiBP60. Adsorption measurements on a Ti surface revealed that their disassociation constants were 15-fold less than TiBP60. Their flexible and modular use in biological surface functionalization were demonstrated by conjugating them with an integrin recognizing peptide motif, RGDS. The functionalization of the Ti surface by the selected peptides significantly enhanced the bioactivity of osteoblast and fibroblast cells on implant-grade materials.
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Korneta I, Bujnicki JM. Intrinsic disorder in the human spliceosomal proteome. PLoS Comput Biol 2012; 8:e1002641. [PMID: 22912569 PMCID: PMC3415423 DOI: 10.1371/journal.pcbi.1002641] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 06/16/2012] [Indexed: 12/11/2022] Open
Abstract
The spliceosome is a molecular machine that performs the excision of introns from eukaryotic pre-mRNAs. This macromolecular complex comprises in human cells five RNAs and over one hundred proteins. In recent years, many spliceosomal proteins have been found to exhibit intrinsic disorder, that is to lack stable native three-dimensional structure in solution. Building on the previous body of proteomic, structural and functional data, we have carried out a systematic bioinformatics analysis of intrinsic disorder in the proteome of the human spliceosome. We discovered that almost a half of the combined sequence of proteins abundant in the spliceosome is predicted to be intrinsically disordered, at least when the individual proteins are considered in isolation. The distribution of intrinsic order and disorder throughout the spliceosome is uneven, and is related to the various functions performed by the intrinsic disorder of the spliceosomal proteins in the complex. In particular, proteins involved in the secondary functions of the spliceosome, such as mRNA recognition, intron/exon definition and spliceosomal assembly and dynamics, are more disordered than proteins directly involved in assisting splicing catalysis. Conserved disordered regions in spliceosomal proteins are evolutionarily younger and less widespread than ordered domains of essential spliceosomal proteins at the core of the spliceosome, suggesting that disordered regions were added to a preexistent ordered functional core. Finally, the spliceosomal proteome contains a much higher amount of intrinsic disorder predicted to lack secondary structure than the proteome of the ribosome, another large RNP machine. This result agrees with the currently recognized different functions of proteins in these two complexes.
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Affiliation(s)
- Iga Korneta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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