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Arad E, Levi T, Yosefi G, Kass I, Cohen-Erez I, Azoulay Z, Bitton R, Jelinek R, Rapaport H. A Matter of Charge: Electrostatically Tuned Coassembly of Amphiphilic Peptides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404324. [PMID: 39155426 DOI: 10.1002/smll.202404324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/04/2024] [Indexed: 08/20/2024]
Abstract
Coassembly of peptide biomaterials offers a compelling avenue to broaden the spectrum of hierarchically ordered supramolecular nanoscale structures that may be relevant for biomedical and biotechnological applications. In this work coassemblies of amphiphilic and oppositely charged, anionic and cationic, β-sheet peptides are studied, which may give rise to a diverse range of coassembled forms. Mixtures of the peptides show significantly lower critical coassembly concentration (CCC) values compared to those of the individual pure peptides. Intriguingly, the highest formation of coassembled fibrils is found to require excess of the cationic peptide whereas equimolar mixtures of the peptides exhibited the maximum folding into β-sheet structures. Mixtures of the peptides coassembled sequentially from solutions at concentrations surpassing each peptide's intrinsic critical assembly concentration (CAC), are also found to require a higher portion of the cationic peptide to stabilize hydrogels. This study illuminates a systematic investigation of oppositely charged β-sheet peptides over a range of concentrations, in solutions and in hydrogels. The results may be relevant to the fundamental understanding of such intricate charge-driven assembly systems and to the formulation of peptide-based nanostructures with diverse functionalities.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Department of Chemical Engineering, Columbia University in the City of New York, New York, NY, 10027, USA
| | - Topaz Levi
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Gal Yosefi
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Itamar Kass
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Ifat Cohen-Erez
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Ziv Azoulay
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Ronit Bitton
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Raz Jelinek
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Hanna Rapaport
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
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2
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Denesyuk AI, Denessiouk K, Johnson MS, Uversky VN. Structural Catalytic Core of the Members of the Superfamily of Acid Proteases. Molecules 2024; 29:3451. [PMID: 39124857 PMCID: PMC11313796 DOI: 10.3390/molecules29153451] [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: 06/21/2024] [Revised: 07/13/2024] [Accepted: 07/20/2024] [Indexed: 08/12/2024] Open
Abstract
The superfamily of acid proteases has two catalytic aspartates for proteolysis of their peptide substrates. Here, we show a minimal structural scaffold, the structural catalytic core (SCC), which is conserved within each family of acid proteases, but varies between families, and thus can serve as a structural marker of four individual protease families. The SCC is a dimer of several structural blocks, such as the DD-link, D-loop, and G-loop, around two catalytic aspartates in each protease subunit or an individual chain. A dimer made of two (D-loop + DD-link) structural elements makes a DD-zone, and the D-loop + G-loop combination makes a psi-loop. These structural markers are useful for protein comparison, structure identification, protein family separation, and protein engineering.
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Affiliation(s)
- Alexander I. Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland; (K.D.); (M.S.J.)
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland; (K.D.); (M.S.J.)
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland; (K.D.); (M.S.J.)
| | - 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 33612, USA
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3
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Wlodawer A, Dauter Z, Lubkowski J, Loch JI, Brzezinski D, Gilski M, Jaskolski M. Towards a dependable data set of structures for L-asparaginase research. Acta Crystallogr D Struct Biol 2024; 80:506-527. [PMID: 38935343 PMCID: PMC11220836 DOI: 10.1107/s2059798324005461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
The Protein Data Bank (PDB) includes a carefully curated treasury of experimentally derived structural data on biological macromolecules and their various complexes. Such information is fundamental for a multitude of projects that involve large-scale data mining and/or detailed evaluation of individual structures of importance to chemistry, biology and, most of all, to medicine, where it provides the foundation for structure-based drug discovery. However, despite extensive validation mechanisms, it is almost inevitable that among the ∼215 000 entries there will occasionally be suboptimal or incorrect structure models. It is thus vital to apply careful verification procedures to those segments of the PDB that are of direct medicinal interest. Here, such an analysis was carried out for crystallographic models of L-asparaginases, enzymes that include approved drugs for the treatment of certain types of leukemia. The focus was on the adherence of the atomic coordinates to the rules of stereochemistry and their agreement with the experimental electron-density maps. Whereas the current clinical application of L-asparaginases is limited to two bacterial proteins and their chemical modifications, the field of investigations of such enzymes has expanded tremendously in recent years with the discovery of three entirely different structural classes and with numerous reports, not always quite reliable, of the anticancer properties of L-asparaginases of different origins.
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Affiliation(s)
- Alexander Wlodawer
- Center for Structural Biology, Center for Cancer ResearchNational Cancer InstituteMarylandUSA
| | - Zbigniew Dauter
- Center for Structural Biology, Center for Cancer ResearchNational Cancer InstituteMarylandUSA
| | - Jacek Lubkowski
- Center for Structural Biology, Center for Cancer ResearchNational Cancer InstituteMarylandUSA
| | - Joanna I. Loch
- Department of Crystal Chemistry and Crystal Physics, Faculty of ChemistryJagiellonian UniversityCracowPoland
| | - Dariusz Brzezinski
- Institute of Computing SciencePoznan University of TechnologyPoznanPoland
| | - Miroslaw Gilski
- Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
- Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
| | - Mariusz Jaskolski
- Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
- Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
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4
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Galindo C, Livshits L, Tarabeih L, Barshtein G, Einav S, Feldman Y. The effect of ionic redistributions on the microwave dielectric response of cytosol water upon glucose uptake. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024:10.1007/s00249-024-01708-w. [PMID: 38647542 DOI: 10.1007/s00249-024-01708-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/27/2024] [Accepted: 04/07/2024] [Indexed: 04/25/2024]
Abstract
The sensitivity of cytosol water's microwave dielectric (MD) response to D-glucose uptake in Red Blood Cells (RBCs) allows the detailed study of cellular mechanisms as a function of controlled exposures to glucose and other related analytes like electrolytes. However, the underlying mechanism behind the sensitivity to glucose exposure remains a topic of debate. In this research, we utilize MDS within the frequency range of 0.5-40 GHz to explore how ionic redistributions within the cell impact the microwave dielectric characteristics associated with D-glucose uptake in RBC suspensions. Specifically, we compare glucose uptake in RBCs exposed to the physiological concentration of Ca2+ vs. Ca-free conditions. We also investigate the potential involvement of Na+/K+ redistribution in glucose-mediated dielectric response by studying RBCs treated with a specific Na+/K+ pump inhibitor, ouabain. We present some insights into the MD response of cytosol water when exposed to Ca2+ in the absence of D-glucose. The findings from this study confirm that ion-induced alterations in bound/bulk water balance do not affect the MD response of cytosol water during glucose uptake.
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Affiliation(s)
- Cindy Galindo
- Institute of Applied Physics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Leonid Livshits
- Institute of Veterinary Physiology, University of Zurich, Zurich, Switzerland
| | - Lama Tarabeih
- Institute of Applied Physics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gregory Barshtein
- Biochemistry Department, The Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sharon Einav
- The Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuri Feldman
- Institute of Applied Physics, The Hebrew University of Jerusalem, Jerusalem, Israel.
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5
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Sulatsky MI, Stepanenko OV, Stepanenko OV, Kuznetsova IM, Turoverov KK, Sulatskaya AI. Prediction of the Feasibility of Using the ≪Gold Standard≫ Thioflavin T to Detect Amyloid Fibril in Acidic Media. Anal Chem 2024; 96:2158-2164. [PMID: 38269442 DOI: 10.1021/acs.analchem.3c05118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Ordered protein aggregates, amyloid fibrils, form toxic plaques in the human body in amyloidosis and neurodegenerative diseases and provide adaptive benefits to pathogens and to reduce the nutritional value of legumes. To identify the amyloidogenic properties of proteins and study the processes of amyloid fibril formation and degradation, the cationic dye thioflavin T (ThT) is the most commonly used. However, its use in acidic environments that induce amyloid formation in vitro can sometimes lead to misinterpretation of experimental results due to electrostatic repulsion. In this work, we show that calculating the net charge per residue of amyloidogenic proteins or peptides is a simple and effective approach for predicting whether their fibrils will interact with ThT at acidic pH. In particular, it was shown that at pH 2, proteins and peptides with a net charge per residue > +0.18 are virtually unstained by this fluorescent probe. The applicability of the proposed approach was demonstrated by predicting and experimentally confirming the absence of ThT interaction with amyloids formed from green fluorescent (sfGFP) and odorant-binding (bOBP) proteins, whose fibrillogenesis was first carried out in an acidic environment. Correct experimental evidence that the inability to detect these fibrils under acidic conditions is precisely because of the lack of dye binding to amyloids (and not their specific structure or the low fluorescence quantum yield of the bound dye) and that the number of ThT molecules associated with fibrils increases with decreasing acidity of the medium was obtained by using the equilibrium microdialysis approach.
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Affiliation(s)
- Maksim I Sulatsky
- Laboratory of cell morphology, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Olesya V Stepanenko
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Olga V Stepanenko
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Irina M Kuznetsova
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Konstantin K Turoverov
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Anna I Sulatskaya
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
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6
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Krishna de Guzman M, Stanic-Vucinic D, Gligorijevic N, Wimmer L, Gasparyan M, Lujic T, Vasovic T, Dailey LA, Van Haute S, Cirkovic Velickovic T. Small polystyrene microplastics interfere with the breakdown of milk proteins during static in vitro simulated human gastric digestion. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 335:122282. [PMID: 37516294 DOI: 10.1016/j.envpol.2023.122282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 07/31/2023]
Abstract
Human ingestion of microplastics (MPs) is common and inevitable due to the widespread contamination of food items, but implications on the gastric digestion of food proteins are still unknown. In this study, the interactions between pepsin and polystyrene (PS) MPs were evaluated by investigating enzyme activity and conformation in a simulated human gastric environment in the presence or absence of PS MPs. The impact on food digestion was also assessed by monitoring the kinetics of protein hydrolysis through static in vitro gastric digestion of cow's milk contaminated with PS. The binding of pepsin to PS showed that the surface chemistry of MPs dictates binding affinity. The key contributor to pepsin adsorption seems to be π-π interactions between the aromatic residues and the PS phenyl rings. During quick exposure (10 min) of pepsin to increasing concentrations (222, 2219, 22188 particles/mL) of 10 μm PS (PS10) and 100 μm PS (PS100), total enzymatic activities were not affected remarkably. However, upon prolonged exposure at 1 and 2 h, preferential binding of pepsin to the small, low zeta-potential PS caused structural changes in the protein which led to a significant reduction of its activity. Digestion of cow's milk mixed with PS10 resulted in transient accumulation of larger peptides (10-35 kDa) and reduced bioavailability of short peptides (2-9 kDa) in the gastric phase. This, however, was only observed at extremely high PS10 concentration (0.3 mg/mL or 5.46E+05 particles/mL). The digestion of milk peptides, bound preferentially over pepsin within the hard corona on the PS10 surface, was delayed up to 15 min in comparison to bulk protein digestion. Intact caseins, otherwise rapidly digested, remained bound to PS10 in the hard corona for up to 15 min. This work presents valuable insights regarding the interaction of MPs, food proteins, and pepsin, and their dynamics during gastric digestion.
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Affiliation(s)
- Maria Krishna de Guzman
- Department of Food Technology, Safety, and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Center for Food Chemistry and Technology, Ghent University Global Campus, Incheon, Republic of Korea
| | - Dragana Stanic-Vucinic
- Center of Excellence for Molecular Food Sciences, Department of Biochemistry, University of Belgrade - Faculty of Chemistry, Belgrade, Serbia
| | - Nikola Gligorijevic
- Department of Chemistry, University of Belgrade - Institute of Chemistry, Technology and Metallurgy, National Institute of Republic of Serbia, Belgrade, Serbia
| | - Lukas Wimmer
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Manvel Gasparyan
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Republic of Korea; School of Environmental Engineering, University of Seoul, Seoul, Republic of Korea
| | - Tamara Lujic
- Center of Excellence for Molecular Food Sciences, Department of Biochemistry, University of Belgrade - Faculty of Chemistry, Belgrade, Serbia
| | - Tamara Vasovic
- Center of Excellence for Molecular Food Sciences, Department of Biochemistry, University of Belgrade - Faculty of Chemistry, Belgrade, Serbia
| | - Lea Ann Dailey
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Sam Van Haute
- Department of Food Technology, Safety, and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Center for Food Chemistry and Technology, Ghent University Global Campus, Incheon, Republic of Korea
| | - Tanja Cirkovic Velickovic
- Department of Food Technology, Safety, and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Center for Food Chemistry and Technology, Ghent University Global Campus, Incheon, Republic of Korea; Center of Excellence for Molecular Food Sciences, Department of Biochemistry, University of Belgrade - Faculty of Chemistry, Belgrade, Serbia; Serbian Academy of Sciences and Arts, Belgrade, Serbia.
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7
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Dutta S, Jiang J, Ghosh S, Patel S, Bhikadiya C, Lowe R, Voigt M, Goodsell D, Zardecki C, Burley SK. An idea to explore: How an interdisciplinary undergraduate course exploring a global health challenge in molecular detail enabled science communication and collaboration in diverse audiences. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:137-145. [PMID: 36495283 PMCID: PMC10050141 DOI: 10.1002/bmb.21699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 11/15/2022] [Indexed: 06/17/2023]
Abstract
Communication and collaboration are key science competencies that support sharing of scientific knowledge with experts and non-experts alike. On the one hand, they facilitate interdisciplinary conversations between students, educators, and researchers, while on the other they improve public awareness, enable informed choices, and impact policy decisions. Herein, we describe an interdisciplinary undergraduate course focused on using data from various bioinformatics data resources to explore the molecular underpinnings of diabetes mellitus (Types 1 and 2) and introducing students to science communication. Building on course materials and original student-generated artifacts, a series of collaborative activities engaged students, educators, researchers, healthcare professionals and community members in exploring, learning about, and discussing the molecular bases of diabetes. These collaborations generated novel educational materials and approaches to learning and presenting complex ideas about major global health challenges in formats accessible to diverse audiences.
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Affiliation(s)
- Shuchismita Dutta
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey, USA
- Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Jennifer Jiang
- Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey, USA
| | - Sutapa Ghosh
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Shriya Patel
- Rowan University School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Charmi Bhikadiya
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Robert Lowe
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - David Goodsell
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey, USA
- Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, San Diego, California, USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey, USA
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey, USA
- Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, San Diego, California, USA
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8
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Chernysheva MG, Shnitko AV, Skrabkova HS, Badun GA. Peculiarities of alkylamidopropyldimethylbenzylammonium (Miramistin) in the relationship to lysozyme in comparison with quaternary ammonium surfactants: Coadsorption at the interfaces, enzymatic activity and molecular docking. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.127503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Parhi S, Pal S, Das SK, Ghosh P. Strategies toward development of antimicrobial biomaterials for dental healthcare applications. Biotechnol Bioeng 2021; 118:4590-4622. [PMID: 34599764 DOI: 10.1002/bit.27948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/19/2021] [Accepted: 09/26/2021] [Indexed: 12/25/2022]
Abstract
Several approaches for elimination of oral pathogens are being explored at the present time since oral diseases remain prevalent affecting approximately 3.5 billion people worldwide. Need for antimicrobial biomaterials in dental healthcare include but is not restricted to designing resin composites and adhesives for prevention of dental caries. Constant efforts are also being made to develop antimicrobial strategies for clearance of endodontic space prior root canal treatment and for treatment of periimplantitis and periodontitis. This article discusses various conventional and nanotechnology-based strategies to achieve antimicrobial efficacy in dental biomaterials. Recent developments in the design and synthesis of antimicrobial peptides and antifouling zwitterionic polymers to effectively lessen the risks of antimicrobial drug resistance are also outlined in this review. Further, the role of contemporary strategies such as use of smart biomaterials, ionic solvent-based biomaterials and quorum quenchers incorporated biomaterials in the elimination of dental pathogens are described in detail. Lastly, we mentioned the approach of using polymers to print custom-made three-dimensional antibacterial dental products via additive manufacturing technologies. This review provides a critical perspective on the chemical, biomimetic, and engineering strategies intended for developing antimicrobial biomaterials that have the potential to substantially improve the dental health.
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Affiliation(s)
- Shivangi Parhi
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), AcSIR Headquarters CSIR-HRDC Campus, Ghaziabad, India
| | - Sreyasi Pal
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sujoy K Das
- Academy of Scientific and Innovative Research (AcSIR), AcSIR Headquarters CSIR-HRDC Campus, Ghaziabad, India.,Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Paulomi Ghosh
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), AcSIR Headquarters CSIR-HRDC Campus, Ghaziabad, India
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10
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Castro C, Johnson RJ, Kieffer B, Means JA, Taylor A, Telford J, Thompson LK, Sussman JL, Prilusky J, Theis K. A practical guide to teaching with Proteopedia. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:707-719. [PMID: 34080750 DOI: 10.1002/bmb.21548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 04/19/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
Proteopedia (proteopedia.org) is an open resource to explore the structure-function relationship of proteins and other biomolecules. This guide provides practical advice on how to incorporate Proteopedia into teaching the structure and function of proteins and other biomolecules. For 11 activities, we discuss desired outcomes, setting expectations, preparing students for the tasks, using resources within Proteopedia, and evaluating student work. We point out features of Proteopedia that make it especially suitable for teaching and give examples of how to avoid common pitfalls.
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Affiliation(s)
- Claudia Castro
- National University of Cuyo, School of Medical Science, Biochemical and Biotechnology Institute, Mendoza, Argentina
| | - R Jeremy Johnson
- Department of Chemistry, Butler University, Indianapoli, Indiana, USA
| | | | - John A Means
- School of Natural & Social Sciences, University of Rio Grande, Rio Grande, Ohio, USA
| | - Ann Taylor
- Department of Chemistry, Wabash College, Crawfordsville, Indiana, USA
| | - Jason Telford
- College of Arts and Sciences, Maryville University of Saint Louis, St. Louis, Missouri, USA
| | - Lynmarie K Thompson
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Joel L Sussman
- The Weizmann Institute of Science, Department of Chemical and Structural Biology, Rehovot, Israel
| | - Jaime Prilusky
- The Weizmann Institute of Science, Life Sciences Core Facilities, Rehovot, Israel
| | - Karsten Theis
- Department of Chemical and Physical Sciences, Westfield State University, Westfield, Massachusetts, USA
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11
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Deaconescu AM. Mfd - at the crossroads of bacterial DNA repair, transcriptional regulation and molecular evolvability. Transcription 2021; 12:156-170. [PMID: 34674614 PMCID: PMC8632110 DOI: 10.1080/21541264.2021.1982628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/06/2021] [Accepted: 09/14/2021] [Indexed: 12/21/2022] Open
Abstract
For survival, bacteria need to continuously evolve and adapt to complex environments, including those that may impact the integrity of the DNA, the repository of genetic information to be passed on to future generations. The multiple factors of DNA repair share the substrate on which they operate with other key cellular machineries, principally those of replication and transcription, implying a high degree of coordination of DNA-based activities. In this review, I focus on progress made in the understanding of the protein factors operating at the crossroads of these three fundamental processes, with emphasis on the mutation frequency decline protein (Mfd, aka TRCF). Although Mfd research has a rich history that goes back in time for more than half a century, recent reports hint that much remains to be uncovered. I argue that besides being a transcription-repair coupling factor (TRCF), Mfd is also a global regulator of transcription and a pro-mutagenic factor, and that the way it interfaces with transcription, replication and nucleotide excision repair makes it an attractive candidate for the development of strategies to curb molecular evolution, hence, antibiotic resistance.
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Affiliation(s)
- Alexandra M. Deaconescu
- CONTACT Alexandra M. Deaconescu Molecular Biology, Cell Biology and Biochemistry, Laboratories of Molecular Medicine, Brown University, 70 Ship St. G-E4, Providence, RI02903, USA
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12
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Croll TI, Diederichs K, Fischer F, Fyfe CD, Gao Y, Horrell S, Joseph AP, Kandler L, Kippes O, Kirsten F, Müller K, Nolte K, Payne AM, Reeves M, Richardson JS, Santoni G, Stäb S, Tronrud DE, von Soosten LC, Williams CJ, Thorn A. Making the invisible enemy visible. Nat Struct Mol Biol 2021; 28:404-408. [PMID: 33972785 DOI: 10.1038/s41594-021-00593-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | - Florens Fischer
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, Hamburg, Germany.,Rudolf-Virchow-Zentrum, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | - Yunyun Gao
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, Hamburg, Germany.,Rudolf-Virchow-Zentrum, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | | | - Luise Kandler
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, Hamburg, Germany.,Rudolf-Virchow-Zentrum, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Oliver Kippes
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, Hamburg, Germany.,Rudolf-Virchow-Zentrum, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Ferdinand Kirsten
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, Hamburg, Germany.,Rudolf-Virchow-Zentrum, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Konstantin Müller
- Rudolf-Virchow-Zentrum, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Kristopher Nolte
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, Hamburg, Germany.,Rudolf-Virchow-Zentrum, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | - Matthew Reeves
- Rudolf-Virchow-Zentrum, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | | | - Sabrina Stäb
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, Hamburg, Germany.,Rudolf-Virchow-Zentrum, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | - Lea C von Soosten
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, Hamburg, Germany.,Rudolf-Virchow-Zentrum, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | - Andrea Thorn
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, Hamburg, Germany. .,Rudolf-Virchow-Zentrum, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
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Filatova LY, Balabushevich NG, Klyachko NL. A physicochemical, structural, microbiological and kinetic study of hen egg white lysozyme in complexes with alginate and chitosan. BIOCATAL BIOTRANSFOR 2021. [DOI: 10.1080/10242422.2021.1909001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Lyubov Y. Filatova
- Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Nadezhda G. Balabushevich
- Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Natalia L. Klyachko
- Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
- Division of Molecular Pharmaceutics, Center for Nanotechnology in Drug Delivery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Croll T, Diederichs K, Fischer F, Fyfe C, Gao Y, Horrell S, Joseph AP, Kandler L, Kippes O, Kirsten F, Müller K, Nolte K, Payne A, Reeves MG, Richardson J, Santoni G, Stäb S, Tronrud D, von Soosten L, Williams C, Thorn A. Making the invisible enemy visible. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.10.07.307546. [PMID: 33052340 PMCID: PMC7553165 DOI: 10.1101/2020.10.07.307546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
During the COVID-19 pandemic, structural biologists rushed to solve the structures of the 28 proteins encoded by the SARS-CoV-2 genome in order to understand the viral life cycle and enable structure-based drug design. In addition to the 204 previously solved structures from SARS-CoV-1, 548 structures covering 16 of the SARS-CoV-2 viral proteins have been released in a span of only 6 months. These structural models serve as the basis for research to understand how the virus hijacks human cells, for structure-based drug design, and to aid in the development of vaccines. However, errors often occur in even the most careful structure determination - and may be even more common among these structures, which were solved quickly and under immense pressure. The Coronavirus Structural Task Force has responded to this challenge by rapidly categorizing, evaluating and reviewing all of these experimental protein structures in order to help downstream users and original authors. In addition, the Task Force provided improved models for key structures online, which have been used by Folding@Home, OpenPandemics, the EU JEDI COVID-19 challenge and others.
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15
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Arad E, Green H, Jelinek R, Rapaport H. Revisiting thioflavin T (ThT) fluorescence as a marker of protein fibrillation - The prominent role of electrostatic interactions. J Colloid Interface Sci 2020; 573:87-95. [PMID: 32272300 DOI: 10.1016/j.jcis.2020.03.075] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/07/2020] [Accepted: 03/21/2020] [Indexed: 12/25/2022]
Abstract
Thioflavin T (ThT), a benzothiazole-based fluorophore, is a prominent dye widely employed for monitoring amyloid fibril assembly. Despite the near-universal presumption that ThT binds to β-sheet domains upon fibrillar surface via hydrophobic forces, the contribution of the positive charge of ThT to fibril binding and concomitant fluorescence enhancement have not been thoroughly assessed. Here we demonstrate a considerable interdependence between ThT fluorescence and electrostatic charges of peptide fibrils. Specifically, by analyzing both fibril-forming synthetic peptides and prominent natural fibrillar peptides, we demonstrate pronounced modulations of ThT fluorescence signal that were solely dependent upon electrostatic interactions between ThT and peptide surface. The results further attest to the fact that fibril ζ-potential rather than pH-dependent assembly of the fibrils constitute the primary factor affecting ThT binding and fluorescence. This study provides the first quantitative assessment of electrostatically driven ThT fluorescence upon adsorption to amyloid fibrils.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel; Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Hodaya Green
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Raz Jelinek
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel; Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel.
| | - Hanna Rapaport
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel; Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel.
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16
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Angles R, Arenas-Salinas M, García R, Reyes-Suarez JA, Pohl E. GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns. BMC Bioinformatics 2020; 21:85. [PMID: 32164553 PMCID: PMC7068854 DOI: 10.1186/s12859-020-3352-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND In the field of protein engineering and biotechnology, the discovery and characterization of structural patterns is highly relevant as these patterns can give fundamental insights into protein-ligand interaction and protein function. This paper presents GSP4PDB, a bioinformatics web tool that enables the user to visualize, search and explore protein-ligand structural patterns within the entire Protein Data Bank. RESULTS We introduce the notion of graph-based structural pattern (GSP) as an abstract model for representing protein-ligand interactions. A GSP is a graph where the nodes represent entities of the protein-ligand complex (amino acids and ligands) and the edges represent structural relationships (e.g. distances ligand - amino acid). The novel feature of GSP4PDB is a simple and intuitive graphical interface where the user can "draw" a GSP and execute its search in a relational database containing the structural data of each PDB entry. The results of the search are displayed using the same graph-based representation of the pattern. The user can further explore and analyse the results using a wide range of filters, or download their related information for external post-processing and analysis. CONCLUSIONS GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction.
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Affiliation(s)
- Renzo Angles
- Department of Computer Science, Universidad de Talca, Camino Los Niches Km 1, Curicó, Chile
- Millennium Institute for Foundational Research on Data, Santiago, Chile
| | - Mauricio Arenas-Salinas
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile
- Faculty of Engineering, Universidad de Talca, Camino Los Niches Km 1, Curicó, Chile
| | - Roberto García
- Millennium Institute for Foundational Research on Data, Santiago, Chile
- Faculty of Engineering, Universidad de Talca, Camino Los Niches Km 1, Curicó, Chile
| | - Jose Antonio Reyes-Suarez
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile
- Faculty of Engineering, Universidad de Talca, Camino Los Niches Km 1, Curicó, Chile
| | - Ehmke Pohl
- Department of Chemistry, Durham University, Durham, DH1 3LE United Kingdom
- Department of Biosciences, Durham University, Durham, DH1 3LE United Kingdom
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17
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Communicating 3D data-interactive 3D PDF documents for expert reports and scientific publications in the field of forensic medicine. Int J Legal Med 2019; 134:1175-1183. [PMID: 31602494 DOI: 10.1007/s00414-019-02156-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/05/2019] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Modern forensic investigations increasingly revert to 3D imaging techniques, such as computed tomography, magnetic resonance imaging, and 3D surface imaging. Findings are therefore often based on 3D data sets; however, this information is commonly reported and communicated within 2D imagery. The use of interactive 3D PDFs is already established in the scientific community but has yet to be implemented in the field of forensic medicine. METHODS AND MATERIALS Three example cases were chosen to serve as exemplary data for the most commonly applied imaging techniques in postmortem imaging. 3D surface models were created from postmortem magnetic resonance imaging (PMMR), postmortem computed tomography (PMCT), and 3D surface imaging data sets. RESULTS PMMR revealed a space-occupying subdural hemorrhage that led to ipsilateral compression of the brain tissue of the right hemisphere. PMCT displayed a defect in the skull on the left side of the temporal bone. 3D surface imaging data displayed a patterned discoloration on the inside of the left forearm. DISCUSSION Interactive 3D PDFs offer the possibility to communicate 3D information to the reader while maintaining all the benefits of a regular 2D PDF. With Adobe Acrobat, the reader can interactively navigate through 3D data sets and create sufficient depth cues to generate a realistic 3D perception of the data. CONCLUSION The interactive 3D PDF is a useful extension of standard 2D PDFs and has the potential to communicate 3D data to the reader in a more complete, more comprehensible, and less subjective manner than 2D PDFs.
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Moldenhauer D, Fuenzalida Werner JP, Strassert CA, Gröhn F. Light-Responsive Size of Self-Assembled Spiropyran-Lysozyme Nanoparticles with Enzymatic Function. Biomacromolecules 2019; 20:979-991. [PMID: 30570257 DOI: 10.1021/acs.biomac.8b01605] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Novel light-responsive nanoassemblies with switchable size and enzymatic activity are built from a protein and a water-soluble spiropyran. Assemblies are created by electrostatic self-assembly in aqueous solution such that the photochromic property of the spiropyran enables light responsiveness. Upon visible light exposure, the aggregate size increases from 200 to 400 nm. The enzyme retains its activity upon aggregation into the assembly, while it decreases through visible light irradiation. Fundamentally, we show how the two different spiropyran isomers, the open-ring merocyanine form and the closed-ring spiropyran form, bind differently to the protein, which triggers the assembly size and use of thermodynamic data to understand the binding process and the size response. Thus, as a proof of concept, a self-assembly driven light-tunable enzyme activity in conjunction with a triggerable assembly size is demonstrated for a model system. The concept bears future potential for various possible biological applications ranging from genetic control over vaccine applications to the detection of certain proteins.
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Affiliation(s)
- Daniel Moldenhauer
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM) , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 3 , D-91058 Erlangen , Germany
| | - Juan Pablo Fuenzalida Werner
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM) , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 3 , D-91058 Erlangen , Germany
| | - Cristian A Strassert
- Institute of Physics and Center for Nanotechnology , Westfälische Wilhelms-Universität Münster , Heisenbergstraße 11 , D-48149 Münster , Germany
| | - Franziska Gröhn
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM) , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 3 , D-91058 Erlangen , Germany
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19
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Chechetkin VR, Lobzin VV. Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences. J Biomol Struct Dyn 2018; 37:2322-2338. [PMID: 30044190 DOI: 10.1080/07391102.2018.1479660] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The assembly and maturation of viruses with icosahedral capsids must be coordinated with icosahedral symmetry. The icosahedral symmetry imposes also the restrictions on the cooperative specific interactions between genomic RNA/DNA and coat proteins that should be reflected in quasi-regular segmentation of viral genomic sequences. Combining discrete direct and double Fourier transforms, we studied the quasi-regular large-scale segmentation in genomic sequences of different ssRNA, ssDNA, and dsDNA viruses. The particular representatives included satellite tobacco mosaic virus (STMV) and the strains of satellite tobacco necrosis virus (STNV), STNV-C, STNV-1, STNV-2, Escherichia phages MS2, ϕX174, α3, and HK97, and Simian virus 40. In all their genomes, we found the significant quasi-regular segmentation of genomic sequences related to the virion assembly and the genome packaging within icosahedral capsid. We also found good correspondence between our results and available cryo-electron microscopy data on capsid structures and genome packaging in these viruses. Fourier analysis of genomic sequences provides the additional insight into mechanisms of hierarchical genome packaging and may be used for verification of the concepts of 3-fold or 5-fold intermediates in virion assembly. The results of sequence analysis should be taken into account at the choice of models and data interpretation. They also may be helpful for the development of antiviral drugs.
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Affiliation(s)
- V R Chechetkin
- a Engelhardt Institute of Molecular Biology of Russian Academy of Sciences , Moscow , Russia.,b Theoretical Department of Division for Perspective Investigations , Troitsk Institute of Innovation and Thermonuclear Investigations (TRINITI) , Moscow , Troitsk District , Russia
| | - V V Lobzin
- c School of Physics , University of Sydney , Sydney , NSW , Australia
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20
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Newe A, Becker L. Three-Dimensional Portable Document Format (3D PDF) in Clinical Communication and Biomedical Sciences: Systematic Review of Applications, Tools, and Protocols. JMIR Med Inform 2018; 6:e10295. [PMID: 30087092 PMCID: PMC6103636 DOI: 10.2196/10295] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 05/07/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
Background The Portable Document Format (PDF) is the standard file format for the communication of biomedical information via the internet and for electronic scholarly publishing. Although PDF allows for the embedding of three-dimensional (3D) objects and although this technology has great potential for the communication of such data, it is not broadly used by the scientific community or by clinicians. Objective The objective of this review was to provide an overview of existing publications that apply 3D PDF technology and the protocols and tools for the creation of model files and 3D PDFs for scholarly purposes to demonstrate the possibilities and the ways to use this technology. Methods A systematic literature review was performed using PubMed and Google Scholar. Articles searched for were in English, peer-reviewed with biomedical reference, published since 2005 in a journal or presented at a conference or scientific meeting. Ineligible articles were removed after screening. The found literature was categorized into articles that (1) applied 3D PDF for visualization, (2) showed ways to use 3D PDF, and (3) provided tools or protocols for the creation of 3D PDFs or necessary models. Finally, the latter category was analyzed in detail to provide an overview of the state of the art. Results The search retrieved a total of 902 items. Screening identified 200 in-scope publications, 13 covering the use of 3D PDF for medical purposes. Only one article described a clinical routine use case; all others were pure research articles. The disciplines that were covered beside medicine were many. In most cases, either animal or human anatomies were visualized. A method, protocol, software, library, or other tool for the creation of 3D PDFs or model files was described in 19 articles. Most of these tools required advanced programming skills and/or the installation of further software packages. Only one software application presented an all-in-one solution with a graphical user interface. Conclusions The use of 3D PDF for visualization purposes in clinical communication and in biomedical publications is still not in common use, although both the necessary technique and suitable tools are available, and there are many arguments in favor of this technique. The potential of 3D PDF usage should be disseminated in the clinical and biomedical community. Furthermore, easy-to-use, standalone, and free-of-charge software tools for the creation of 3D PDFs should be developed.
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Affiliation(s)
- Axel Newe
- Chair of Medical Informatics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.,NewTec GmbH, Pfaffenhofen an der Roth, Germany
| | - Linda Becker
- Chair of Health Psychology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
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21
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Wlodawer A. Online tools for enhancing presentation, understanding, and retention of 3D structural data. FEBS J 2017; 284:3974-3976. [DOI: 10.1111/febs.14316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander Wlodawer
- Macromolecular Crystallography Laboratory; National Cancer Institute; Frederick MD USA
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22
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Sheng L, Su P, Han K, Chen J, Cao A, Zhang Z, Jin Y, Ma M. Synthesis and structural characterization of lysozyme–pullulan conjugates obtained by the Maillard reaction. Food Hydrocoll 2017. [DOI: 10.1016/j.foodhyd.2017.04.026] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Chatonnet A, Lenfant N, Marchot P, Selkirk ME. Natural genomic amplification of cholinesterase genes in animals. J Neurochem 2017; 142 Suppl 2:73-81. [PMID: 28382676 DOI: 10.1111/jnc.13990] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/07/2017] [Accepted: 02/09/2017] [Indexed: 12/31/2022]
Abstract
Tight control of the concentration of acetylcholine at cholinergic synapses requires precise regulation of the number and state of the acetylcholine receptors, and of the synthesis and degradation of the neurotransmitter. In particular, the cholinesterase activity has to be controlled exquisitely. In the genome of the first experimental models used (man, mouse, zebrafish and drosophila), there are only one or two genes coding for cholinesterases, whereas there are more genes for their closest relatives the carboxylesterases. Natural amplification of cholinesterase genes was first found to occur in some cancer cells and in insect species subjected to evolutionary pressure by insecticides. Analysis of the complete genome sequences of numerous representatives of the various metazoan phyla show that moderate amplification of cholinesterase genes is not uncommon in molluscs, echinoderms, hemichordates, prochordates or lepidosauria. Amplification of acetylcholinesterase genes is also a feature of parasitic nematodes or ticks. In these parasites, over-production of cholinesterase-like proteins in secreted products and the saliva are presumed to have effector roles related to host infection. These amplification events raise questions about the role of the amplified gene products, and the adaptation processes necessary to preserve efficient cholinergic transmission. This is an article for the special issue XVth International Symposium on Cholinergic Mechanisms.
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Affiliation(s)
- Arnaud Chatonnet
- Dynamique Musculaire et Métabolisme, INRA, Université Montpellier, Place Viala, Montpellier France
| | - Nicolas Lenfant
- Dynamique Musculaire et Métabolisme, INRA, Université Montpellier, Place Viala, Montpellier France.,Aix-Marseille Université / Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques laboratory, Marseille, France
| | - Pascale Marchot
- Aix-Marseille Université / Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques laboratory, Marseille, France
| | - Murray E Selkirk
- Department of Life Sciences, Imperial College London, London, UK
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Sheng L, Wang J, Huang M, Xu Q, Ma M. The changes of secondary structures and properties of lysozyme along with the egg storage. Int J Biol Macromol 2016; 92:600-606. [DOI: 10.1016/j.ijbiomac.2016.07.068] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/18/2016] [Accepted: 07/21/2016] [Indexed: 10/21/2022]
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25
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Valdepérez D, del Pino P, Sánchez L, Parak WJ, Pelaz B. Highly active antibody-modified magnetic polyelectrolyte capsules. J Colloid Interface Sci 2016; 474:1-8. [DOI: 10.1016/j.jcis.2016.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 01/27/2023]
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
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Relationships of human α/β hydrolase fold proteins and other organophosphate-interacting proteins. Chem Biol Interact 2016; 259:343-351. [PMID: 27109753 DOI: 10.1016/j.cbi.2016.04.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/29/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022]
Abstract
Organophosphates (OPs) are either found in nature or synthetized for use as pesticides, flame retardants, neurotoxic warfare agents or drugs (cholinergic enhancers in Alzheimer's disease and myasthenia gravis, or inhibitors of lipases in metabolic diseases). Because of the central role of acetylcholinesterase cholinergic neurotransmission in humans, one of the main purposes for using OPs is inactivation of the enzyme by phosphorylation of the nucleophilic serine residue in the active center. However, hundreds of serine hydrolases are expressed in the human proteome, and many of them are potential targets for OP adduction. In this review, we first situate the α/β hydrolase fold proteins among the distinctively folded proteins known to interact with OPs, in particular the different lipases, peptidases, and enzymes hydrolyzing OPs. Second, we compile the human α/β hydrolases and review those that have been experimentally shown to interact with OPs. Among the 120 human α/β hydrolase fold proteins, 102 have a serine in the consensus GXSXG pentapeptide compatible with an active site, 6 have an aspartate or a cysteine as the active site nucleophile residue, and 12 evidently lack an active site. 76 of the 120 have been experimentally shown to bind an OP.
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The impact of structural genomics: the first quindecennial. ACTA ACUST UNITED AC 2016; 17:1-16. [PMID: 26935210 DOI: 10.1007/s10969-016-9201-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 02/17/2016] [Indexed: 12/21/2022]
Abstract
The period 2000-2015 brought the advent of high-throughput approaches to protein structure determination. With the overall funding on the order of $2 billion (in 2010 dollars), the structural genomics (SG) consortia established worldwide have developed pipelines for target selection, protein production, sample preparation, crystallization, and structure determination by X-ray crystallography and NMR. These efforts resulted in the determination of over 13,500 protein structures, mostly from unique protein families, and increased the structural coverage of the expanding protein universe. SG programs contributed over 4400 publications to the scientific literature. The NIH-funded Protein Structure Initiatives alone have produced over 2000 scientific publications, which to date have attracted more than 93,000 citations. Software and database developments that were necessary to handle high-throughput structure determination workflows have led to structures of better quality and improved integrity of the associated data. Organized and accessible data have a positive impact on the reproducibility of scientific experiments. Most of the experimental data generated by the SG centers are freely available to the community and has been utilized by scientists in various fields of research. SG projects have created, improved, streamlined, and validated many protocols for protein production and crystallization, data collection, and functional analysis, significantly benefiting biological and biomedical research.
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Fuenzalida JP, Nareddy PK, Moreno-Villoslada I, Moerschbacher BM, Swamy MJ, Pan S, Ostermeier M, Goycoolea FM. On the role of alginate structure in complexing with lysozyme and application for enzyme delivery. Food Hydrocoll 2016. [DOI: 10.1016/j.foodhyd.2015.04.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Safdari R, Shahmoradi L, Hosseini-Beheshti MS, Nejad AF, Hosseiniravandi M. Quantitative and Qualitative Evaluation of The Structural Designing of Medical Informatics Dynamic Encyclopedia. Acta Inform Med 2015; 23:306-10. [PMID: 26635440 PMCID: PMC4639356 DOI: 10.5455/aim.2015.23.306-310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/05/2015] [Indexed: 11/03/2022] Open
Abstract
Introduction: Encyclopedias and their compilation have become so prevalent as a valid cultural medium in the world. The daily development of computer industry and the expansion of various sciences have made indispensable the compilation of electronic, specialized encyclopedias, especially the web-based ones. Materials and Methods: This is an applied-developmental study conducted in 2014. First, the main terms in the field of medical informatics were gathered using MeSH Online 2014 and the supplementary terms of each were determined, and then the tree diagram of the terms was drawn based on their relationship in MeSH. Based on the studies done by the researchers, the tree diagram of the encyclopedia was drawn with respect to the existing areas in this field, and the terms gathered were put in related domains. Findings: In MeSH, 75 preferred terms together with 249 supplementary ones were indexed. One of the informatics’ sub-branches is biomedical informatics and health which itself consists of three sub-divisions of bioinformatics, clinical informatics, and health informatics. Medical informatics which is a subdivision of clinical informatics has developed from the three fields of medical sciences, management and social sciences, and computational sciences and mathematics. Results and Discussion: Medical Informatics is created of confluence and fusion and applications of the three major scientific branches include health and biological sciences, social sciences and management sciences, computing and mathematical sciences, and according to that the structure of MeSH is weak for future development of Encyclopedia of Medical Informatics.
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Affiliation(s)
- Reza Safdari
- Health Information Management Department, Tehran University of Medical Sciences, Tehran, Iran
| | - Leila Shahmoradi
- Health Information Management Department, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | - Mohammad Hosseiniravandi
- School of Allied Medical Sciences, Health Information Management Department, Tehran University of Medical Sciences, Tehran, Iran
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Johnson DK, Karanicolas J. Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations. PLoS Comput Biol 2015; 11:e1004081. [PMID: 25706586 PMCID: PMC4338137 DOI: 10.1371/journal.pcbi.1004081] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/10/2014] [Indexed: 12/13/2022] Open
Abstract
Small-molecules that inhibit interactions between specific pairs of proteins have long represented a promising avenue for therapeutic intervention in a variety of settings. Structural studies have shown that in many cases, the inhibitor-bound protein adopts a conformation that is distinct from its unbound and its protein-bound conformations. This plasticity of the protein surface presents a major challenge in predicting which members of a protein family will be inhibited by a given ligand. Here, we use biased simulations of Bcl-2-family proteins to generate ensembles of low-energy conformations that contain surface pockets suitable for small molecule binding. We find that the resulting conformational ensembles include surface pockets that mimic those observed in inhibitor-bound crystal structures. Next, we find that the ensembles generated using different members of this protein family are overlapping but distinct, and that the activity of a given compound against a particular family member (ligand selectivity) can be predicted from whether the corresponding ensemble samples a complementary surface pocket. Finally, we find that each ensemble includes certain surface pockets that are not shared by any other family member: while no inhibitors have yet been identified to take advantage of these pockets, we expect that chemical scaffolds complementing these “distinct” pockets will prove highly selective for their targets. The opportunity to achieve target selectivity within a protein family by exploiting differences in surface fluctuations represents a new paradigm that may facilitate design of family-selective small-molecule inhibitors of protein-protein interactions. Despite intense interest and considerable effort, there are few examples of small molecules that directly inhibit protein-protein interactions. Crystal structures of early successes have highlighted the plasticity of the protein surface, as some inhibitor-bound proteins are captured in conformations that are distinct from both their unbound and their protein-bound conformations. The lack of a single well-defined structure presents a challenge for predicting the members of a protein family to which a given compound will show activity (ligand selectivity). Here we generate ensembles of conformations from simulation, and show that we can predict ligand selectivity based on which family members sample conformations complementary to the ligand. This approach may present a new avenue for designing highly-selective inhibitors of protein-protein interactions.
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Affiliation(s)
- David K. Johnson
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - John Karanicolas
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- * E-mail:
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32
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Abstract
A key reason three-dimensional (3-D) protein structures are annotated with supporting or derived information is to understand the molecular basis of protein function. To this end, protein structure annotation databases curate key facts and observations, based on community-accepted standards, about the ~100,000 3-D experimental protein structures to date. This review will introduce the primary structure repositories, databases, and value-added structural annotation databases, as well as the range of information they provide. The different levels of annotation data (primary vs. derived vs. inferred) and how they should all be considered accordingly will also be described.
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Affiliation(s)
- Margaret J. Gabanyi
- Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Helen M. Berman
- Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
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33
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Johnson RJ. Teaching foundational topics and scientific skills in biochemistry within the conceptual framework of HIV protease. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 42:299-304. [PMID: 24652697 DOI: 10.1002/bmb.20793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/03/2014] [Indexed: 06/03/2023]
Abstract
HIV protease has served as a model protein for understanding protein structure, enzyme kinetics, structure-based drug design, and protein evolution. Inhibitors of HIV protease are also an essential part of effective HIV/AIDS treatment and have provided great societal benefits. The broad applications for HIV protease and its inhibitors make it a perfect framework for integrating foundational topics in biochemistry around a big picture scientific and societal issue. Herein, I describe a series of classroom exercises that integrate foundational topics in biochemistry around the structure, biology, and therapeutic inhibition of HIV protease. These exercises center on foundational topics in biochemistry including thermodynamics, acid/base properties, protein structure, ligand binding, and enzymatic catalysis. The exercises also incorporate regular student practice of scientific skills including analysis of primary literature, evaluation of scientific data, and presentation of technical scientific arguments. Through the exercises, students also gain experience accessing computational biochemical resources such as the protein data bank, Proteopedia, and protein visualization software. As these HIV centered exercises cover foundational topics common to all first semester biochemistry courses, these exercises should appeal to a broad audience of undergraduate students and should be readily integrated into a variety of teaching styles and classroom sizes.
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Affiliation(s)
- R Jeremy Johnson
- Department of Chemistry, Butler University, Indianapolis, Indiana, 46208
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34
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Jaswal SS, O'Hara PB, Williamson PL, Springer AL. Teaching structure: student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 41:351-359. [PMID: 24019219 DOI: 10.1002/bmb.20718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 06/11/2013] [Indexed: 06/02/2023]
Abstract
Because understanding the structure of biological macromolecules is critical to understanding their function, students of biochemistry should become familiar not only with viewing, but also with generating and manipulating structural representations. We report a strategy from a one-semester undergraduate biochemistry course to integrate use of structural representation tools into both laboratory and homework activities. First, early in the course we introduce the use of readily available open-source software for visualizing protein structure, coincident with modules on amino acid and peptide bond properties. Second, we use these same software tools in lectures and incorporate images and other structure representations in homework tasks. Third, we require a capstone project in which teams of students examine a protein-nucleic acid complex and then use the software tools to illustrate for their classmates the salient features of the structure, relating how the structure helps explain biological function. To ensure engagement with a range of software and database features, we generated a detailed template file that can be used to explore any structure, and that guides students through specific applications of many of the software tools. In presentations, students demonstrate that they are successfully interpreting structural information, and using representations to illustrate particular points relevant to function. Thus, over the semester students integrate information about structural features of biological macromolecules into the larger discussion of the chemical basis of function. Together these assignments provide an accessible introduction to structural representation tools, allowing students to add these methods to their biochemical toolboxes early in their scientific development.
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Affiliation(s)
- Sheila S Jaswal
- Department of Chemistry, Amherst College, Amherst, Massachusetts
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35
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Craig PA, Michel LV, Bateman RC. A survey of educational uses of molecular visualization freeware. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 41:193-205. [PMID: 23649886 PMCID: PMC4098825 DOI: 10.1002/bmb.20693] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 02/07/2013] [Indexed: 05/11/2023]
Abstract
As biochemists, one of our most captivating teaching tools is the use of molecular visualization. It is a compelling medium that can be used to communicate structural information much more effectively with interactive animations than with static figures. We have conducted a survey to begin a systematic evaluation of the current classroom usage of molecular visualization. Participants (n = 116) were asked to complete 11 multiple choice and 3 open ended questions. To provide more depth to these results, interviews were conducted with 12 of the participants. Many common themes arose in the survey and the interviews: a shared passion for the use of molecular visualization in teaching, broad diversity in software preference, the lack of uniform standards for assessment, a desire for more quality resources, and the challenge of enabling students to incorporate visualization in their learning. The majority of respondents had used molecular visualization for more than 5 years and mentioned 32 different visualization tools used, with Jmol and PyMOL clearly standing out as the most frequently used programs at the present time. The most common uses of molecular visualization in teaching were lecture and lab illustrations, followed by exam questions, in-class or in-laboratory exercises, and student projects, which frequently included presentations. While a minority of instructors used a grading rubric/scoring matrix for assessment of student learning with molecular visualization, many expressed a desire for common use assessment tools.
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Affiliation(s)
- Paul A Craig
- Rochester Institute of Technology, School of Chemistry and Materials Science, Rochester, NY 14623, USA.
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36
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Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL. JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied toProteopedia. Isr J Chem 2013. [DOI: 10.1002/ijch.201300024] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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Proteins with an alpha/beta hydrolase fold: Relationships between subfamilies in an ever-growing superfamily. Chem Biol Interact 2013; 203:266-8. [DOI: 10.1016/j.cbi.2012.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/07/2012] [Accepted: 09/10/2012] [Indexed: 12/19/2022]
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38
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Lenfant N, Hotelier T, Velluet E, Bourne Y, Marchot P, Chatonnet A. ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions. Nucleic Acids Res 2012. [PMID: 23193256 PMCID: PMC3531081 DOI: 10.1093/nar/gks1154] [Citation(s) in RCA: 198] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The ESTHER database, which is freely available via a web server (http://bioweb.ensam.inra.fr/esther) and is widely used, is dedicated to proteins with an α/β-hydrolase fold, and it currently contains >30 000 manually curated proteins. Herein, we report those substantial changes towards improvement that we have made to improve ESTHER during the past 8 years since our 2004 update. In particular, we generated 87 new families and increased the coverage of the UniProt Knowledgebase (UniProtKB). We also renewed the ESTHER website and added new visualization tools, such as the Overall Table and the Family Tree. We also address two topics of particular interest to the ESTHER users. First, we explain how the different enzyme classifications (bacterial lipases, peptidases, carboxylesterases) used by different communities of users are combined in ESTHER. Second, we discuss how variations of core architecture or in predicted active site residues result in a more precise clustering of families, and whether this strategy provides trustable hints to identify enzyme-like proteins with no catalytic activity.
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Affiliation(s)
- Nicolas Lenfant
- Dynamique Musculaire et Métabolisme, INRA-UM1, Place Viala, 34060 Montpellier, France
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39
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Machado ACD, Saleebyan SB, Holmes BT, Karelina M, Tam J, Kim SY, Kim KH, Dror I, Hodis E, Martz E, Compeau PA, Rohs R. Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 40:400-401. [PMID: 23166030 DOI: 10.1002/bmb.20650] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/14/2012] [Indexed: 06/01/2023]
Abstract
3D visualization assists in identifying diverse mechanisms of protein-DNA recognition that can be observed for transcription factors and other DNA binding proteins. We used Proteopedia to illustrate transcription factor-DNA readout modes with a focus on DNA shape, which can be a function of either nucleotide sequence (Hox proteins) or base pairing geometry (p53). © 2012 by The International Union of Biochemistry and Molecular Biology.
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Affiliation(s)
- Ana Carolina Dantas Machado
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, and Physics and Astronomy, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA
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40
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Abstract
Aminoacyl-tRNAsynthetases (aaRSs) are modular enzymesglobally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation.Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g.,in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show hugestructural plasticity related to function andlimited idiosyncrasies that are kingdom or even speciesspecific (e.g.,the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS).Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably betweendistant groups such as Gram-positive and Gram-negative Bacteria.Thereview focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation,and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulatedin last two decades is reviewed,showing how thefield moved from essentially reductionist biologytowards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRSparalogs (e.g., during cellwall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointedthroughout the reviewand distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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41
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Xu D. Protein databases on the internet. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2012; Chapter 2:2.6.1-2.6.17. [PMID: 23151744 DOI: 10.1002/0471140864.ps0206s70] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein databases have become a crucial part of modern biology. Huge amounts of data for protein structures, functions, and particularly sequences are being generated. Searching databases is often the first step in the study of a new protein. Comparison between proteins or between protein families provides information about the relationship between proteins within a genome or across different species, and hence offers much more information than can be obtained by studying only an isolated protein. In addition, secondary databases derived from experimental databases are also widely available. These databases reorganize and annotate the data or provide predictions. The use of multiple databases often helps researchers understand the structure and function of a protein. Although some protein databases are widely known, they are far from being fully utilized in the protein science community. This unit provides a starting point for readers to explore the potential of protein databases on the Internet.
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Affiliation(s)
- Dong Xu
- Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri
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42
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Joosten RP, Joosten K, Murshudov GN, Perrakis A. PDB_REDO: constructive validation, more than just looking for errors. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:484-96. [PMID: 22505269 PMCID: PMC3322608 DOI: 10.1107/s0907444911054515] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 12/18/2011] [Indexed: 11/17/2022]
Abstract
Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R(free) and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise `static' structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets.
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Affiliation(s)
- Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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43
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Affiliation(s)
- Dong Xu
- Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri Columbia Missouri
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44
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45
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Abstract
Protein databases have become a crucial part of modern biology. Huge amounts of data for protein structures, functions, and particularly sequences are being generated. Searching databases is often the first step in the study of a new protein. Comparison between proteins and between protein families in databases provides information about the relationship between proteins within a genome or across different species, and hence offers much more information than can be obtained by studying only an isolated protein. In addition, secondary databases derived from experimental databases are also widely available. These databases reorganize and annotate the data or provide predictions. The use of multiple databases often helps researchers understand the structure and function of proteins. Although some protein databases are widely known, they are far from being fully utilized in the protein science community. This unit provides a starting point for readers to explore the potential of protein databases on the Internet.
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Affiliation(s)
- Dong Xu
- Digital Biology Laboratory, University of Missouri-Columbia, Columbia, Missouri, USA
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