1
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Shaw WJ, Tarasevich BJ, Buchko GW, Arachchige RMJ, Burton SD. Controls of nature: Secondary, tertiary, and quaternary structure of the enamel protein amelogenin in solution and on hydroxyapatite. J Struct Biol 2020; 212:107630. [PMID: 32979496 PMCID: PMC7744360 DOI: 10.1016/j.jsb.2020.107630] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/12/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
Abstract
Amelogenin, a protein critical to enamel formation, is presented as a model for understanding how the structure of biomineralization proteins orchestrate biomineral formation. Amelogenin is the predominant biomineralization protein in the early stages of enamel formation and contributes to the controlled formation of hydroxyapatite (HAP) enamel crystals. The resulting enamel mineral is one of the hardest tissues in the human body and one of the hardest biominerals in nature. Structural studies have been hindered by the lack of techniques to evaluate surface adsorbed proteins and by amelogenin's disposition to self-assemble. Recent advancements in solution and solid state nuclear magnetic resonance (NMR) spectroscopy, atomic force microscopy (AFM), and recombinant isotope labeling strategies are now enabling detailed structural studies. These recent studies, coupled with insights from techniques such as CD and IR spectroscopy and computational methodologies, are contributing to important advancements in our structural understanding of amelogenesis. In this review we focus on recent advances in solution and solid state NMR spectroscopy and in situ AFM that reveal new insights into the secondary, tertiary, and quaternary structure of amelogenin by itself and in contact with HAP. These studies have increased our understanding of the interface between amelogenin and HAP and how amelogenin controls enamel formation.
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Affiliation(s)
- Wendy J Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Barbara J Tarasevich
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Garry W Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA; School of Molecular Bioscience, Washington State University, Pullman, WA 99164, USA
| | - Rajith M J Arachchige
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sarah D Burton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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2
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Iqbal M, Karim A, Ali S, Bilal H, Rehman AU. Synthesis, Characterization, Structural Description, Micellization Behavior, DNA Binding Study and Antioxidant Activity of 4, 5 and 6‐Coordinated Copper(II) and Zinc(II) Complexes. Z Anorg Allg Chem 2020. [DOI: 10.1002/zaac.202000139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Muhammad Iqbal
- Department of Chemistry Bacha Khan University 24420 Charsadda KPK Pakistan
| | - Amir Karim
- Department of Chemistry Bacha Khan University 24420 Charsadda KPK Pakistan
| | - Saqib Ali
- Department of Chemistry Quaid‐i‐Azam University 45320 Islamabad Pakistan
| | - Hazrat Bilal
- Department of Chemistry Bacha Khan University 24420 Charsadda KPK Pakistan
| | - Ata Ur Rehman
- Department of Chemistry Bacha Khan University 24420 Charsadda KPK Pakistan
- School of Chemical Engineering Northwest University Xi'an Shaanxi P. R. China
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3
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Zhong H, Xie Z, Zhang S, Wei H, Song Y, Zhang Y, Wang M. Brevinin-GR23 from frog Hylarana guentheri with antimicrobial and antibiofilm activities against Staphylococcus aureus. Biosci Biotechnol Biochem 2019; 84:143-153. [PMID: 31549575 DOI: 10.1080/09168451.2019.1670045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Brevinin-GR23 (B-GR23) was a brevinin-2 like antimicrobial peptide, which had antimicrobial activity against Staphylococcus aureus with minimum inhibitory concentration (MIC) of 16 μM. B-GR23 increased the bacterial membrane permeation, leading to the damage of membrane integrity and the leakage of genomic DNA, then causing the cell death. The peptide nearly inhibited all plantonic bacteria to start the initial attachment of biofilm at the concentration of 1 × MIC. Whereas the disruption rates on immature and mature biofilm decreased from 60% to 20%. B-GR23 reduced the production of extracellular polysaccharides (EPS) in the planktonic growth of S. aureus, which is a crucial structure of biofilm formation. B-GR23 with the concentration of ½ × MIC inhibited 50% water-soluble EPS, and 48% water-insoluble EPS, which contributed to the antibiofilm activity. B-GR23 had no significant toxicity to human blood cells under-tested concentration (200 μM), making it a potential template for designing antimicrobial peptides.
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Affiliation(s)
- Hengren Zhong
- Key Laboratory of Tropical Biological Resources of Ministry of Education; School of Life and Pharmaceutical Sciences, Hainan University, Haikou, Hainan, P. R. China
| | - Zhipeng Xie
- Key Laboratory of Tropical Biological Resources of Ministry of Education; School of Life and Pharmaceutical Sciences, Hainan University, Haikou, Hainan, P. R. China
| | - Shuxia Zhang
- Key Laboratory of Tropical Biological Resources of Ministry of Education; School of Life and Pharmaceutical Sciences, Hainan University, Haikou, Hainan, P. R. China
| | - Hanqi Wei
- Key Laboratory of Tropical Biological Resources of Ministry of Education; School of Life and Pharmaceutical Sciences, Hainan University, Haikou, Hainan, P. R. China
| | - Yanting Song
- Key Laboratory of Tropical Biological Resources of Ministry of Education; School of Life and Pharmaceutical Sciences, Hainan University, Haikou, Hainan, P. R. China
| | - Yingxia Zhang
- Key Laboratory of Tropical Biological Resources of Ministry of Education; School of Life and Pharmaceutical Sciences, Hainan University, Haikou, Hainan, P. R. China
| | - Manchuriga Wang
- College of Animal Science, Hainan University, Haikou, Hainan, P. R. China
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4
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Zerfaß C, Buchko GW, Shaw WJ, Hobe S, Paulsen H. Secondary structure and dynamics study of the intrinsically disordered silica-mineralizing peptide P 5 S 3 during silicic acid condensation and silica decondensation. Proteins 2017; 85:2111-2126. [PMID: 28799215 PMCID: PMC5760248 DOI: 10.1002/prot.25366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 11/08/2022]
Abstract
The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5 S3 , a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains 5 protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated orthosilicic acid P5 S3 enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2 ) at globally undersaturated concentrations. The secondary structure of P5 S3 during these 2 processes was studied by circular dichroism (CD) spectroscopy, complemented by nuclear magnetic resonance (NMR) spectroscopy of the peptide in the absence of silicate. The NMR studies of dual-labeled (13 C, 15 N) P5 S3 revealed a disordered structure at pH 2.8 and 4.5. Within the pH range of 4.5-9.5 in the absence of silicic acid, the CD data showed a disordered structure with the suggestion of some polyproline II character. Upon silicic acid polymerization and during dissolution of preformed silica, the CD spectrum of P5 S3 indicated partial transition into an α-helical conformation which was transient during silica-dissolution. The secondary structural changes observed for P5 S3 correlate with the presence of oligomeric/polymeric silicic acid, presumably due to P5 S3 -silica interactions. These P5 S3 -silica interactions appear, at least in part, ionic in nature since negatively charged dodecylsulfate caused similar perturbations to the P5 S3 CD spectrum as observed with silica, while uncharged ß-d-dodecyl maltoside did not affect the CD spectrum of P5 S3 . Thus, with an associated increase in α-helical character, P5 S3 influences both the condensation of silicic acid into silica and its decondensation back to silicic acid.
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Affiliation(s)
- Christian Zerfaß
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
- Graduate School Materials Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Garry W. Buchko
- Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Wendy J. Shaw
- Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Stephan Hobe
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Harald Paulsen
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
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5
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Atkinson J, Clarke MW, Warnica JM, Boddington KF, Graether SP. Structure of an Intrinsically Disordered Stress Protein Alone and Bound to a Membrane Surface. Biophys J 2017; 111:480-491. [PMID: 27508433 DOI: 10.1016/j.bpj.2016.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 06/25/2016] [Accepted: 07/01/2016] [Indexed: 12/19/2022] Open
Abstract
Dehydrins are a group of intrinsically disordered proteins that protect plants from damage caused by drought, cold, and high salinity. Like other intrinsically disordered proteins, dehydrins can gain structure when bound to a ligand. Previous studies have shown that dehydrins are able to protect liposomes from cold damage, but the interactions that drive membrane binding and the detailed structure of the bound and unbound forms are not known. We use an ensemble-structure approach to generate models of a dehydrin known as K2 in the presence and absence of sodium dodecyl sulfate micelles, and we docked the bound structure to the micelle. The collection of residual dipolar coupling data, amide protection factors, and paramagnetic relaxation enhancement distances, in combination with chemical shifts and relaxation measurements, allows for determining plausible structures that are not otherwise visible in time-averaged structural data. The results show that in the bound structure, the conserved lysines are important for membrane binding, whereas the flanking hydrophobic residues play a lesser role. The unbound structure shows a high level of disorder and an extended structure. We propose that the structural differences between bound and unbound forms allow dehydrins to act as molecular shields in their unbound state and as membrane protectants in their bound state. Unlike α-synuclein, the significant gain of α-helicity in K2 at low concentrations of sodium dodecyl sulfate is not due to a decrease in the critical micelle concentration. The study provides structural insight into how a disordered protein can interact with a membrane surface.
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Affiliation(s)
- John Atkinson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Matthew W Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Josephine M Warnica
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Kelly F Boddington
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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6
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DeForte S, Uversky VN. Quarterly intrinsic disorder digest (April-May-June, 2014). INTRINSICALLY DISORDERED PROTEINS 2017; 5:e1287505. [PMID: 28321370 DOI: 10.1080/21690707.2017.1287505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This is the 6th issue of the Digested Disorder series that continues to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the second quarter of 2014; i.e., during the period of April, May, and June of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Département De Biochimie and Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, Succursale Centre-Ville, Montreal, Quebec, Canada
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Laboratory of New Methods in Biology, Institute of Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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Abstract
Interactions between enamel matrix proteins are important
for enamel biomineralization. In recent in situ studies, we
showed that the N-terminal proteolytic product of ameloblastin co-localized with
amelogenin around the prism boundaries. However, the molecular mechanisms of such
interactions are still unclear. Here, in order to determine the interacting domains
between amelogenin and ameloblastin, we designed four ameloblastin peptides derived
from different regions of the full-length protein (AB1, AB2 and AB3 at N-terminus,
and AB6 at C-terminus) and studied their interactions with recombinant amelogenin
(rP172), and the tyrosine-rich amelogenin polypeptide (TRAP). A series of amelogenin
Trp variants (rP172(W25), rP172(W45) and rP172(W161)) were also used for intrinsic
fluorescence spectroscopy. Fluorescence spectra of rP172 titrated with AB3, a peptide
encoded by exon 5 of ameloblastin, showed a shift in λmax in a
dose-dependent manner, indicating molecular interactions in the region encoded by
exon 5 of ameloblastin. Circular dichroism (CD) spectra of amelogenin titrated with
AB3 showed that amelogenin was responsible for forming α-helix in the presence of
ameloblastin. Fluorescence spectra of amelogenin Trp variants as well as the spectra
of TRAP titrated with AB3 showed that the N-terminus of amelogenin is involved in the
interaction between ameloblastin and amelogenin. We suggest that macromolecular
co-assembly between amelogenin and ameloblastin may play important roles in enamel
biomineralization. An in vitro approach to study
ameloblastin-amelogenin interactions is presented. Intrinsic fluorescence of tryptophan and Circular Dichroism
were utilized. We report that amelogenin has ameloblastin-binding ability
via its N-terminal close to Trp 25. We report that ameloblastin has amelogenin-binding ability
via a peptide encoded by exon 5. Macromolecular co-assembly between amelogenin and
ameloblastin may play important roles in enamel biomineralization.
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Lokappa SB, Chandrababu KB, Moradian-Oldak J. Tooth enamel protein amelogenin binds to ameloblast cell membrane-mimicking vesicles via its N-terminus. Biochem Biophys Res Commun 2015; 464:956-61. [PMID: 26188506 PMCID: PMC4532586 DOI: 10.1016/j.bbrc.2015.07.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/16/2015] [Indexed: 11/18/2022]
Abstract
We have recently reported that the extracellular enamel protein amelogenin has affinity to interact with phospholipids and proposed that such interactions may play key roles in enamel biomineralization as well as reported amelogenin signaling activities. Here, in order to identify the liposome-interacting domains of amelogenin we designed four different amelogenin mutants containing only a single tryptophan at positions 25, 45, 112 and 161. Circular dichroism studies of the mutants confirmed that they are structurally similar to the wild-type amelogenin. Utilizing the intrinsic fluorescence of single tryptophan residue and fluorescence resonance energy transfer [FRET], we analyzed the accessibility and strength of their binding with an ameloblast cell membrane-mimicking model membrane (ACML) and a negatively charged liposome used as a membrane model. We found that amelogenin has membrane-binding ability mainly via its N-terminal, close to residues W25 and W45. Significant blue shift was also observed in the fluorescence of a N-terminal peptide following addition of liposomes. We suggest that, among other mechanisms, enamel malformation in cases of Amelogenesis Imperfecta (AI) with mutations at the N-terminal may be the result of defective amelogenin-cell interactions.
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Affiliation(s)
- Sowmya Bekshe Lokappa
- Center for Craniofacial Molecular Biology, Division of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, 2250 Alcazar Street, Los Angeles, CA 90033, USA
| | - Karthik Balakrishna Chandrababu
- Center for Craniofacial Molecular Biology, Division of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, 2250 Alcazar Street, Los Angeles, CA 90033, USA
| | - Janet Moradian-Oldak
- Center for Craniofacial Molecular Biology, Division of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, 2250 Alcazar Street, Los Angeles, CA 90033, USA.
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9
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Abstract
Mature tooth enamel is acellular and does not regenerate itself. Developing technologies that rebuild tooth enamel and preserve tooth structure is therefore of great interest. Considering the importance of amelogenin protein in dental enamel formation, its ability to control apatite mineralization in vitro, and its potential to be applied in fabrication of future bio-inspired dental material this review focuses on two major subjects: amelogenin and enamel biomimetics. We review the most recent findings on amelogenin secondary and tertiary structural properties with a focus on its interactions with different targets including other enamel proteins, apatite mineral, and phospholipids. Following a brief overview of enamel hierarchical structure and its mechanical properties we will present the state-of-the-art strategies in the biomimetic reconstruction of human enamel.
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Affiliation(s)
- Qichao Ruan
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Janet Moradian-Oldak
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
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10
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Lokappa SB, Chandrababu KB, Dutta K, Perovic I, Evans JS, Moradian-Oldak J. Interactions of amelogenin with phospholipids. Biopolymers 2015; 103:96-108. [PMID: 25298002 PMCID: PMC4415992 DOI: 10.1002/bip.22573] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/29/2014] [Accepted: 10/02/2014] [Indexed: 11/08/2022]
Abstract
Amelogenin protein has the potential to interact with other enamel matrix proteins, mineral, and cell surfaces. We investigated the interactions of recombinant amelogenin rP172 with small unilamellar vesicles as model membranes, toward the goal of understanding the mechanisms of amelogenin-cell interactions during amelogenesis. Dynamic light scattering (DLS), fluorescence spectroscopy, circular dichroism (CD), and nuclear magnetic resonance (NMR) were used. In the presence of phospholipid vesicles, a blue shift in the Trp fluorescence emission maxima of rP172 was observed (∼334 nm) and the Trp residues of rP172 were inaccessible to the aqueous quencher acrylamide. DLS studies indicated complexation of rP172 and phospholipids, although the possibility of fusion of phospholipids following amelogenin addition cannot be ruled out. NMR and CD studies revealed a disorder-order transition of rP172 in a model membrane environment. Strong fluorescence resonance energy transfer from Trp in rP172 to DNS-bound-phospholipid was observed, and fluorescence polarization studies indicated that rP172 interacted with the hydrophobic core region of model membranes. Our data suggest that amelogenin has ability to interact with phospholipids and that such interactions may play key roles in enamel biomineralization as well as reported amelogenin signaling activities.
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Affiliation(s)
- Sowmya Bekshe Lokappa
- Center for Craniofacial Molecular Biology, University of Southern California, School of Dentistry, Los Angeles, California 90033
| | - Karthik Balakrishna Chandrababu
- Center for Craniofacial Molecular Biology, University of Southern California, School of Dentistry, Los Angeles, California 90033
| | - Kaushik Dutta
- Laboratory for Chemical Physics, Division of Basic Sciences and Craniofacial Biology, New York University, New York, New York 10010
| | - Iva Perovic
- Laboratory for Chemical Physics, Division of Basic Sciences and Craniofacial Biology, New York University, New York, New York 10010
| | - John Spencer Evans
- Laboratory for Chemical Physics, Division of Basic Sciences and Craniofacial Biology, New York University, New York, New York 10010
| | - Janet Moradian-Oldak
- Center for Craniofacial Molecular Biology, University of Southern California, School of Dentistry, Los Angeles, California 90033
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11
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Ruan Q, Moradian-Oldak J. Amelogenin and enamel biomimetics. J Mater Chem B 2015. [DOI: 10.1039/c5tb00163c and 21=21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mature tooth enamel is acellular and does not regenerate itself.
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Affiliation(s)
- Qichao Ruan
- Center for Craniofacial Molecular Biology
- Herman Ostrow School of Dentistry
- University of Southern California
- Los Angeles
- USA
| | - Janet Moradian-Oldak
- Center for Craniofacial Molecular Biology
- Herman Ostrow School of Dentistry
- University of Southern California
- Los Angeles
- USA
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12
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Perovic I, Chang EP, Lui M, Rao A, Cölfen H, Evans JS. A Nacre Protein, n16.3, Self-Assembles To Form Protein Oligomers That Dimensionally Limit and Organize Mineral Deposits. Biochemistry 2014; 53:2739-48. [DOI: 10.1021/bi401721z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Iva Perovic
- Laboratory
for Chemical Physics, Division of Basic Sciences and Craniofacial
Biology, New York University, 345 East 24th Street, New York, New York 10010, United States
| | - Eric P. Chang
- Laboratory
for Chemical Physics, Division of Basic Sciences and Craniofacial
Biology, New York University, 345 East 24th Street, New York, New York 10010, United States
| | - Michael Lui
- Laboratory
for Chemical Physics, Division of Basic Sciences and Craniofacial
Biology, New York University, 345 East 24th Street, New York, New York 10010, United States
| | - Ashit Rao
- Department
of Chemistry, Physical Chemistry, Universität Konstanz, Universitätstrasse
10, Konstanz D-78457, Germany
| | - Helmut Cölfen
- Department
of Chemistry, Physical Chemistry, Universität Konstanz, Universitätstrasse
10, Konstanz D-78457, Germany
| | - John Spencer Evans
- Laboratory
for Chemical Physics, Division of Basic Sciences and Craniofacial
Biology, New York University, 345 East 24th Street, New York, New York 10010, United States
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