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Campos MN, Giraldo EL, Del Rio Portilla F, Fernández-Velasco DA, Arzate H, Romo-Arévalo E. Solution NMR structure of cementum protein 1 derived peptide (CEMP1-p1) and its role in the mineralization process. J Pept Sci 2023; 29:e3494. [PMID: 37051739 DOI: 10.1002/psc.3494] [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: 01/26/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/14/2023]
Abstract
We report the characterization of the three-dimensional structure of the CEMP1-p1 peptide [MGTSSTDSQQAQHRRCSTSN: corresponding to residues 1-20 of the N-terminus of cementum protein 1 (CEMP1)]. This peptide imitates the capacity of CEMP1 to stimulate hydroxyapatite (HA) crystal nucleation and growth, and promotes the differentiation of periodontal ligament cells into a cementoblastic phenotype. Additionally, in experimental models of critical-sized calvarial defects in Wistar rats, CEMP1-p1 has shown osteogenic properties that enhanced the physiological deposition and maturation of newly formed bone. In this work, studies of CEMP1-p1 by circular dichroism (CD) and nuclear magnetic resonance (NMR) were performed in trifluoroethanol D2 (TFED2) and aqueous solution to determine the 3D structure of the peptide. Using the 3D model, experimental data from HA crystals formation and calcium fluorescence emission, we explain the biological mechanisms involved in CEMP1-p1 activity to promote calcium recruitment and its affinity to HA crystals. This information is valuable because it proposes, for the first time, a plausible molecular mechanism during the mineralization process, from a specific cementum protein-derived peptide.
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Affiliation(s)
- Mikado Nidome Campos
- Laboratorio de Biología Periodontal, Facultad de Odontología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | | | - Higinio Arzate
- Laboratorio de Biología Periodontal, Facultad de Odontología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Enrique Romo-Arévalo
- Laboratorio de Biología Periodontal, Facultad de Odontología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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2
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Lawanprasert A, Sloand JN, Vargas MG, Singh H, Eldor T, Miller MA, Pimcharoen S, Wang J, Leighow SM, Pritchard JR, Dokholyan NV, Medina SH. Deciphering the Mechanistic Basis for Perfluoroalkyl-Protein Interactions. Chembiochem 2023; 24:e202300159. [PMID: 36943393 PMCID: PMC10364144 DOI: 10.1002/cbic.202300159] [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: 02/27/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/23/2023]
Abstract
Although rarely used in nature, fluorine has emerged as an important elemental ingredient in the design of proteins with altered folding, stability, oligomerization propensities, and bioactivity. Adding to the molecular modification toolbox, here we report the ability of privileged perfluorinated amphiphiles to noncovalently decorate proteins to alter their conformational plasticity and potentiate their dispersion into fluorous phases. Employing a complementary suite of biophysical, in-silico and in-vitro approaches, we establish structure-activity relationships defining these phenomena and investigate their impact on protein structural dynamics and intracellular trafficking. Notably, we show that the lead compound, perfluorononanoic acid, is 106 times more potent in inducing non-native protein secondary structure in select proteins than is the well-known helix inducer trifluoroethanol, and also significantly enhances the cellular uptake of complexed proteins. These findings could advance the rational design of fluorinated proteins, inform on potential modes of toxicity for perfluoroalkyl substances, and guide the development of fluorine-modified biologics with desirable functional properties for drug discovery and delivery applications.
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Affiliation(s)
- Atip Lawanprasert
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Janna N. Sloand
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Mariangely González Vargas
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
- Department of Industrial Engineering, University of Puerto Rico, Mayagüez, Puerto Rico 00682
| | - Harminder Singh
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Tomer Eldor
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Michael A. Miller
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Sopida Pimcharoen
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Jian Wang
- Department of Pharmacology, Penn State College of Medicine, Pennsylvania State University, Hershey, PA, USA, 17033
| | - Scott M. Leighow
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Justin R. Pritchard
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA, 16802
| | - Nikolay V. Dokholyan
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
- Department of Pharmacology, Penn State College of Medicine, Pennsylvania State University, Hershey, PA, USA, 17033
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, PA, USA, 17033
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA, 16802
| | - Scott H. Medina
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA, 16802
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3
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Medina L, Guzmán F, Álvarez C, Delgado JP, Carbonell-M B. Ramosin: The First Antibacterial Peptide Identified on Bolitoglossa ramosi Colombian Salamander. Pharmaceutics 2022; 14:pharmaceutics14122579. [PMID: 36559073 PMCID: PMC9782819 DOI: 10.3390/pharmaceutics14122579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022] Open
Abstract
The discovery and improvements of antimicrobial peptides (AMPs) have become an alternative to conventional antibiotics. They are usually small and heat-stable peptides, exhibiting inhibitory activity against Gram-negative and Gram-positive bacteria. In this way, studies on broad-spectrum AMPs found in amphibians with the remarkable capability to regenerate a wide array of tissues are of particular interest in the search for new strategies to treat multidrug-resistant bacterial strains. In this work, the use of bioinformatic approaches such as sequence alignment with Fasta36 and prediction of antimicrobial activity allowed the identification of the Ramosin peptide from the de novo assembled transcriptome of the plethodontid salamander Bolitoglossa ramosi obtained from post-amputation of the upper limb tissue, heart, and intestine samples. BLAST analysis revealed that the Ramosin peptide sequence is unique in Bolitoglossa ramosi. The peptide was chemically synthesized, and physicochemical properties were characterized. Furthermore, the in vitro antimicrobial activity against relevant Gram-positive and Gram-negative human pathogenic bacteria was demonstrated. Finally, no effect against eukaryotic cells or human red blood cells was evidenced. This is the first antibacterial peptide identified from a Colombian endemic salamander with interesting antimicrobial properties and no hemolytic activity.
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Affiliation(s)
- Laura Medina
- Grupo Genética, Regeneración y Cáncer, Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín 050010, Colombia
- Correspondence:
| | - Fanny Guzmán
- Núcleo de Biotecnología Curauma (NBC), Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Claudio Álvarez
- Laboratorio de Fisiología y Genética Marina (FIGEMA), Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo 1781421, Chile
- Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo 1781421, Chile
| | - Jean Paul Delgado
- Grupo Genética, Regeneración y Cáncer, Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín 050010, Colombia
| | - Belfran Carbonell-M
- Grupo Genética, Regeneración y Cáncer, Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín 050010, Colombia
- Departamento de Estudios Básicos Integrados, Facultad de Odontología, Universidad de Antioquia, Medellín 050010, Colombia
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4
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Stable Dried Catalase Particles Prepared by Electrospraying. NANOMATERIALS 2022; 12:nano12142484. [PMID: 35889708 PMCID: PMC9322511 DOI: 10.3390/nano12142484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/07/2022] [Accepted: 07/14/2022] [Indexed: 11/17/2022]
Abstract
Therapeutic proteins and peptides are clinically important, offering potency while reducing the potential for off-target effects. Research interest in developing therapeutic polypeptides has grown significantly during the last four decades. However, despite the growing research effort, maintaining the stability of polypeptides throughout their life cycle remains a challenge. Electrohydrodynamic (EHD) techniques have been widely explored for encapsulation and delivery of many biopharmaceuticals. In this work, we explored monoaxial electrospraying for encapsulation of bovine liver catalase, investigating the effects of the different components of the electrospraying solution on the integrity and bioactivity of the enzyme. The catalase was successfully encapsulated within polymeric particles made of polyvinylpyrrolidone (PVP), dextran, and polysucrose. The polysorbate 20 content within the electrospraying solution (50 mM citrate buffer, pH 5.4) affected the catalase loading—increasing the polysorbate 20 concentration to 500 μg/mL resulted in full protein encapsulation but did not prevent loss in activity. The addition of ethanol (20% v/v) to a fully aqueous solution improves the electrospraying process by reducing surface tension, without loss of catalase activity. The polymer type was shown to have the greatest impact on preserving catalase activity within the electrosprayed particles. When PVP was the carrier there was no loss in activity compared with fresh aqueous solutions of catalase. The optimum particles were obtained from a 20% w/v PVP or 30% w/v PVP-trehalose (1:1 w/w) solution. The addition of trehalose confers stability advantages to the catalase particles. When trehalose-PVP particles were stored at 5 °C, enzymatic activity was maintained over 3 months, whereas for the PVP-only analogue a 50% reduction in activity was seen. This demonstrates that processing catalase by monoaxial electrospraying can, under optimised conditions, result in stable polymeric particles with no loss of activity.
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5
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Ayotte Y, Woo S, LaPlante SR. Practical Considerations and Guidelines for Spectral Referencing for Fluorine NMR Ligand Screening. ACS OMEGA 2022; 7:13155-13163. [PMID: 35474811 PMCID: PMC9026065 DOI: 10.1021/acsomega.2c00613] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Fluorine (19F) NMR strategies are increasingly being employed for evaluating ligand binding to macromolecules, among many other uses. 19F NMR offers many advantages as a result of its sensitive spin 1/2 nucleus, 100% natural abundance, and wide chemical shift range. Moreover, because of its absence from biological samples, one can directly monitor ligand binding without background interference from the macromolecule. Therefore, all these aforementioned features make it an attractive approach for screening compounds. However, the detection of ligand binding, especially those with weak affinities, can require interpretations of minor changes in chemical shifts. Thus, chemical shift referencing is critical for accurate measurements and interpretations. Unfortunately, one cannot rely on spectrometer indirect referencing alone, and internal chemical references have sample-dependent issues. Here, we evaluated 10 potential candidate compounds that could serve as 19F NMR chemical references. Multiple factors were systematically evaluated for each candidate to monitor the suitability for 19F NMR screening purposes. These factors include aqueous solubility, buffer compatibility, salt compatibility, aqueous stability, tolerability to pH changes, temperature changes, and compound pooling. It was concluded that there was no ideal candidate, but five compounds had properties that met the screening requirements.
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Affiliation(s)
- Yann Ayotte
- Centre
Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
- NMX
Research and Solutions Inc., 500 boulevard Cartier Ouest, Suite 6000, Laval, Québec H7V 5B7, Canada
| | - Simon Woo
- Centre
Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
- NMX
Research and Solutions Inc., 500 boulevard Cartier Ouest, Suite 6000, Laval, Québec H7V 5B7, Canada
| | - Steven R. LaPlante
- Centre
Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
- NMX
Research and Solutions Inc., 500 boulevard Cartier Ouest, Suite 6000, Laval, Québec H7V 5B7, Canada
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6
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Le HH, Cinaroglu SS, Manalo EC, Ors A, Gomes MM, Duan Sahbaz B, Bonic K, Origel Marmolejo CA, Quentel A, Plaut JS, Kawashima TE, Ozdemir ES, Malhotra SV, Ahiska Y, Sezerman U, Bayram Akcapinar G, Saldivar JC, Timucin E, Fischer JM. Molecular modelling of the FOXO4-TP53 interaction to design senolytic peptides for the elimination of senescent cancer cells. EBioMedicine 2021; 73:103646. [PMID: 34689087 PMCID: PMC8546421 DOI: 10.1016/j.ebiom.2021.103646] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Senescent cells accumulate in tissues over time as part of the natural ageing process and the removal of senescent cells has shown promise for alleviating many different age-related diseases in mice. Cancer is an age-associated disease and there are numerous mechanisms driving cellular senescence in cancer that can be detrimental to recovery. Thus, it would be beneficial to develop a senolytic that acts not only on ageing cells but also senescent cancer cells to prevent cancer recurrence or progression. METHODS We used molecular modelling to develop a series of rationally designed peptides to mimic and target FOXO4 disrupting the FOXO4-TP53 interaction and releasing TP53 to induce apoptosis. We then tested these peptides as senolytic agents for the elimination of senescent cells both in cell culture and in vivo. FINDINGS Here we show that these peptides can act as senolytics for eliminating senescent human cancer cells both in cell culture and in orthotopic mouse models. We then further characterized one peptide, ES2, showing that it disrupts FOXO4-TP53 foci, activates TP53 mediated apoptosis and preferentially binds FOXO4 compared to TP53. Next, we show that intratumoural delivery of ES2 plus a BRAF inhibitor results in a significant increase in apoptosis and a survival advantage in mouse models of melanoma. Finally, we show that repeated systemic delivery of ES2 to older mice results in reduced senescent cell numbers in the liver with minimal toxicity. INTERPRETATION Taken together, our results reveal that peptides can be generated to specifically target and eliminate FOXO4+ senescent cancer cells, which has implications for eradicating residual disease and as a combination therapy for frontline treatment of cancer. FUNDING This work was supported by the Cancer Early Detection Advanced Research Center at Oregon Health & Science University.
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Affiliation(s)
- Hillary H Le
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Suleyman S Cinaroglu
- Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Atasehir Istanbul 34752, Turkey; Eternans Ltd., UK
| | - Elise C Manalo
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Aysegul Ors
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Michelle M Gomes
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | | | - Karla Bonic
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Carlos A Origel Marmolejo
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Arnaud Quentel
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Justin S Plaut
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA; Dept of Bioengineering, University of California San Diego, USA
| | - Taryn E Kawashima
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - E Sila Ozdemir
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Sanjay V Malhotra
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA; Dept of Cell, Developmental and Cancer Biology, Oregon Health & Science University, USA
| | | | - Ugur Sezerman
- Eternans Ltd., UK; School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir Istanbul 34752, Turkey
| | - Gunseli Bayram Akcapinar
- Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Atasehir Istanbul 34752, Turkey; Eternans Ltd., UK
| | - Joshua C Saldivar
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA; Division of Oncological Sciences, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Emel Timucin
- Eternans Ltd., UK; School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir Istanbul 34752, Turkey
| | - Jared M Fischer
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA; Dept of Molecular and Medical Genetics, Oregon Health & Science University, USA.
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7
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Haraguchi K, Kimura Y. New Aqueous Solutions with Lower Viscosities than Water. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kazutoshi Haraguchi
- Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, 1-2-1 Izumi-cho, Narashino, Chiba 275-8575, Japan
| | - Yuji Kimura
- Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, 1-2-1 Izumi-cho, Narashino, Chiba 275-8575, Japan
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8
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Khatoon H, Abdulmalek E. Novel Synthetic Routes to Prepare Biologically Active Quinoxalines and Their Derivatives: A Synthetic Review for the Last Two Decades. Molecules 2021; 26:molecules26041055. [PMID: 33670436 PMCID: PMC7923122 DOI: 10.3390/molecules26041055] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/31/2022] Open
Abstract
Quinoxalines, a class of N-heterocyclic compounds, are important biological agents, and a significant amount of research activity has been directed towards this class. They have several prominent pharmacological effects like antifungal, antibacterial, antiviral, and antimicrobial. Quinoxaline derivatives have diverse therapeutic uses and have become the crucial component in drugs used to treat cancerous cells, AIDS, plant viruses, schizophrenia, certifying them a great future in medicinal chemistry. Due to the current pandemic situation caused by SARS-COVID 19, it has become essential to synthesize drugs to combat deadly pathogens (bacteria, fungi, viruses) for now and near future. Since quinoxalines is an essential moiety to treat infectious diseases, numerous synthetic routes have been developed by researchers, with a prime focus on green chemistry and cost-effective methods. This review paper highlights the various synthetic routes to prepare quinoxaline and its derivatives, covering the literature for the last two decades. A total of 31 schemes have been explained using the green chemistry approach, cost-effective methods, and quinoxaline derivatives' therapeutic uses.
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Affiliation(s)
- Hena Khatoon
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
- Correspondence: (H.K.); (E.A.)
| | - Emilia Abdulmalek
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
- Integrated Chemical BioPhysics Research, Faculty of Science, University Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
- Correspondence: (H.K.); (E.A.)
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9
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Notti A, Pisagatti I, Nastasi F, Patanè S, Parisi MF, Gattuso G. Stimuli-Responsive Internally Ion-Paired Supramolecular Polymer Based on a Bis-pillar[5]arene Dicarboxylic Acid Monomer. J Org Chem 2020; 86:1676-1684. [PMID: 33369427 PMCID: PMC7871325 DOI: 10.1021/acs.joc.0c02501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
A novel
bis-pillar[5]arene dicarboxylic acid self-assembles in
the presence of 1,12-diaminododecane to yield overall neutral, internally
ion-paired supramolecular polymers. Their aggregation, binding mode,
and morphology can be tuned by external stimuli such as solvent polarity,
concentration, and base treatment.
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Affiliation(s)
- Anna Notti
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Ilenia Pisagatti
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Francesco Nastasi
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Salvatore Patanè
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Melchiorre F Parisi
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Giuseppe Gattuso
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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10
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Naidu KT, Rao DK, Prabhu NP. Cryo vs Thermo: Duality of Ethylene Glycol on the Stability of Proteins. J Phys Chem B 2020; 124:10077-10088. [PMID: 33143422 DOI: 10.1021/acs.jpcb.0c06247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Osmolytes are known to stabilize proteins under stress conditions. Thermal denaturation studies on globular proteins (β-lactoglobulin, cytochrome c, myoglobin, α-chymotrypsin) in the presence of ethylene glycol (EG), a polyol class of osmolyte, demonstrate a unique property of EG. EG stabilizes proteins against cold denaturation and destabilizes them during heat-induced denaturation. Further, chemical denaturation experiments performed at room temperature and at a sub-zero temperature (-10 °C) show that EG stabilizes the proteins at subzero temperature but destabilizes them at room temperature. The experiments carried out in the presence of glycerol, however, showed that glycerol stabilizes proteins against all of the denaturing conditions. This differential effect has not been reported for any other polyol class of osmolyte and might be specific to EG. Moreover, molecular dynamics simulations of all of the four proteins were carried out at three different temperatures, 240, 300, and 340 K, in the absence and presence of EG (20 and 40%). The results suggest that EG preferably accumulates around the hydrophobic residues and reduces the hydrophobic hydration of the proteins at a low temperature leading to stabilization of the proteins. At 340 K, the preferential hydration of the proteins is significantly reduced and the preferential binding of EG destabilizes the proteins like common denaturants.
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Affiliation(s)
- K Tejaswi Naidu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - D Krishna Rao
- Tata Institute of Fundamental Research (TIFR) Centre for Interdisciplinary Sciences, Hyderabad 500107, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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11
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Quevedo DF, Habibi N, Gregory JV, Hernandez Y, Brown TD, Miki R, Plummer BN, Rahmani S, Raymond JE, Mitragotri S, Lahann J. Multifunctional Synthetic Protein Nanoparticles via Reactive Electrojetting. Macromol Rapid Commun 2020; 41:e2000425. [PMID: 32974989 DOI: 10.1002/marc.202000425] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/31/2020] [Indexed: 12/20/2022]
Abstract
Protein nanoparticles are a promising approach for nanotherapeutics, as proteins combine versatile chemical and biological function with controlled biodegradability. In this work, the development of an adaptable synthesis method is presented for synthetic protein nanoparticles (SPNPs) based on reactive electrojetting. In contrast to past work with electrohydrodynamic cojetting using inert polymers, the jetting solutions are comprised of proteins and chemically activated macromers, designed to react with each other during the processing step, to form insoluble nanogel particles. SPNPs made from a variety of different proteins, such as transferrin, insulin, or hemoglobin, are stable and uniform under physiological conditions and maintain monodisperse sizes of around 200 nm. SPNPs comprised of transferrin and a disulfide containing macromer are stimuli-responsive, and serve as markers of oxidative stress within HeLa cells. Beyond isotropic SPNPs, bicompartmental nanoparticles containing human serum albumin and transferrin in two distinct hemispheres are prepared via reactive electrojetting. This novel platform provides access to a novel class of versatile protein particles with nanoscale architectures that i) can be made from a variety of proteins and macromers, ii) have tunable biological responses, and iii) can be multicompartmental, a prerequisite for controlled release of multiple drugs.
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Affiliation(s)
- Daniel F Quevedo
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nahal Habibi
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jason V Gregory
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yazmin Hernandez
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Tyler D Brown
- Wyss Institute of Biologically Inspired Engineering and John A Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Rikako Miki
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bradley N Plummer
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sahar Rahmani
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeffery E Raymond
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Samir Mitragotri
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.,Wyss Institute of Biologically Inspired Engineering and John A Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Joerg Lahann
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
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12
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Kakinoki S, Kitamura M, Noguchi Y, Arichi Y. Effect of residue insertion on the stability of polyproline‐I and II structures: Circular dichroism spectroscopic analyses of block‐type oligo‐prolines
(Pro)
m
‐Gly/Ala‐(Pro)
n
. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sachiro Kakinoki
- Faculty of Chemistry, Materials and Bioengineering Kansai University Osaka Japan
- Organization for Research and Development of Innovative Science and Technology Kansai University Osaka Japan
| | - Makoto Kitamura
- Department of Liberal Studies Nara National College of Technology Nara Japan
| | - Yuri Noguchi
- Graduate School of Science and Engineering Kansai University Osaka Japan
| | - Yuki Arichi
- Graduate School of Science and Engineering Kansai University Osaka Japan
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13
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Fluorine induced conformational switching and modulation in photophysical properties of 7-fluorotryptophan: Spectroscopic, quantum chemical calculation and molecular dynamics simulation studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2020. [DOI: 10.1016/j.jpap.2020.100011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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14
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Vincenzi M, Mercurio FA, Leone M. About TFE: Old and New Findings. Curr Protein Pept Sci 2019; 20:425-451. [PMID: 30767740 DOI: 10.2174/1389203720666190214152439] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 01/28/2023]
Abstract
The fluorinated alcohol 2,2,2-Trifluoroethanol (TFE) has been implemented for many decades now in conformational studies of proteins and peptides. In peptides, which are often disordered in aqueous solutions, TFE acts as secondary structure stabilizer and primarily induces an α -helical conformation. The exact mechanism through which TFE plays its stabilizing roles is still debated and direct and indirect routes, relying either on straight interaction between TFE and molecules or indirect pathways based on perturbation of solvation sphere, have been proposed. Another still unanswered question is the capacity of TFE to favor in peptides a bioactive or a native-like conformation rather than simply stimulate the raise of secondary structure elements that reflect only the inherent propensity of a specific amino-acid sequence. In protein studies, TFE destroys unique protein tertiary structure and often leads to the formation of non-native secondary structure elements, but, interestingly, gives some hints about early folding intermediates. In this review, we will summarize proposed mechanisms of TFE actions. We will also describe several examples, in which TFE has been successfully used to reveal structural properties of different molecular systems, including antimicrobial and aggregation-prone peptides, as well as globular folded and intrinsically disordered proteins.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia A Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
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15
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Visentin C, Navarro S, Grasso G, Regonesi ME, Deriu MA, Tortora P, Ventura S. Protein Environment: A Crucial Triggering Factor in Josephin Domain Aggregation: The Role of 2,2,2-Trifluoroethanol. Int J Mol Sci 2018; 19:ijms19082151. [PMID: 30042316 PMCID: PMC6121581 DOI: 10.3390/ijms19082151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 11/28/2022] Open
Abstract
The protein ataxin-3 contains a polyglutamine stretch that triggers amyloid aggregation when it is expanded beyond a critical threshold. This results in the onset of the spinocerebellar ataxia type 3. The protein consists of the globular N-terminal Josephin domain and a disordered C-terminal tail where the polyglutamine stretch is located. Expanded ataxin-3 aggregates via a two-stage mechanism: first, Josephin domain self-association, then polyQ fibrillation. This highlights the intrinsic amyloidogenic potential of Josephin domain. Therefore, much effort has been put into investigating its aggregation mechanism(s). A key issue regards the conformational requirements for triggering amyloid aggregation, as it is believed that, generally, misfolding should precede aggregation. Here, we have assayed the effect of 2,2,2-trifluoroethanol, a co-solvent capable of stabilizing secondary structures, especially α-helices. By combining biophysical methods and molecular dynamics, we demonstrated that both secondary and tertiary JD structures are virtually unchanged in the presence of up to 5% 2,2,2-trifluoroethanol. Despite the preservation of JD structure, 1% of 2,2,2-trifluoroethanol suffices to exacerbate the intrinsic aggregation propensity of this domain, by slightly decreasing its conformational stability. These results indicate that in the case of JD, conformational fluctuations might suffice to promote a transition towards an aggregated state without the need for extensive unfolding, and highlights the important role played by the environment on the aggregation of this globular domain.
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Affiliation(s)
- Cristina Visentin
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
| | - Gianvito Grasso
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), CH-6928 Manno, Switzerland.
| | - Maria Elena Regonesi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy.
- Centro di Neuroscienze di Milano (Neuro-MI), 20126 Milano, Italy.
| | - Marco Agostino Deriu
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), CH-6928 Manno, Switzerland.
| | - Paolo Tortora
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy.
- Centro di Neuroscienze di Milano (Neuro-MI), 20126 Milano, Italy.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
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16
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Casanova-Morales N, Alavi Z, Wilson CAM, Zocchi G. Identifying Chaotropic and Kosmotropic Agents by Nanorheology. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.7b12782] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nathalie Casanova-Morales
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380494, Chile
| | - Zahra Alavi
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380494, Chile
- Department of Physics, Loyola Marymount University, Los Angeles 90045, United States
| | - Christian A. M. Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380494, Chile
| | - Giovanni Zocchi
- Department of Physics and Astronomy, University of California—Los Angeles, Los Angeles, California 90095, United States
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17
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McWhinnie FS, Sepp K, Wilson C, Kunath T, Hupp TR, Baker TS, Houston DR, Hulme AN. Mono-Substituted Hydrocarbon Diastereomer Combinations Reveal Stapled Peptides with High Structural Fidelity. Chemistry 2018; 24:2094-2097. [DOI: 10.1002/chem.201705983] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Fergus S. McWhinnie
- EaStChem School of Chemistry; University of Edinburgh; David Brewster Road Edinburgh EH9 3FJ UK
- MRC Centre for Regenerative Medicine, ISCR; University of Edinburgh; Edinburgh EH16 4UU UK
| | - Kristel Sepp
- EaStChem School of Chemistry; University of Edinburgh; David Brewster Road Edinburgh EH9 3FJ UK
| | - Charlotte Wilson
- EaStChem School of Chemistry; University of Edinburgh; David Brewster Road Edinburgh EH9 3FJ UK
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine, ISCR; University of Edinburgh; Edinburgh EH16 4UU UK
| | - Ted R. Hupp
- Institute of Genetics and Molecular Medicine; University of Edinburgh; Edinburgh EH4 2XR UK
| | | | - Douglas R. Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology; University of Edinburgh; Edinburgh EH9 3BF UK
| | - Alison N. Hulme
- EaStChem School of Chemistry; University of Edinburgh; David Brewster Road Edinburgh EH9 3FJ UK
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18
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Salehi Marzijarani N, Yousefi R, Jaganathan A, Ashtekar KD, Jackson JE, Borhan B. Absolute and relative facial selectivities in organocatalytic asymmetric chlorocyclization reactions. Chem Sci 2018; 9:2898-2908. [PMID: 29719676 PMCID: PMC5896375 DOI: 10.1039/c7sc04430e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/24/2017] [Indexed: 12/16/2022] Open
Abstract
For four related 1,1-disubstituted olefins, (DHQD)2PHAL-catalyzed asymmetric chlorocyclization delivers Cl+ uniformly to one π face, but cyclizes with strong but differing net syn vs. anti addition.
Though (DHQD)2PHAL-catalyzed chlorocyclizations of 1,1-disubstituted olefins show useful (and in some cases, reversible) asymmetric induction, stereochemically complete descriptions of these alkene additions have remained largely unknown. Herein, based on a combination of NMR, derivative, isotope labeling, and computational studies, we present detailed stereochemical analyses of chlorocyclizations of nucleophile-tethered 1,1-disubstituted styryl systems. The selectivities of the two asymmetric bond-forming processes, namely electrophilic chlorine attack and nucleophilic ring closure, are thus mapped out independently. Under the established optimal conditions, four related chlorocyclizations were subjected to this analysis. All showed a strong preference for Cl+ delivery from the same face of the alkene. However, depending on reaction conditions and substrate identity (carboxylic acid, amide or carbamate), the internal nucleophiles may close with a strong net preference for either syn or anti addition relative to the Cl atom. Studies of both uncatalyzed and (DHQD)2PHAL-catalyzed processes place new boundary conditions on the role of the catalyst in these reactions.
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Affiliation(s)
| | - Roozbeh Yousefi
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , USA . ;
| | - Arvind Jaganathan
- Dow AgroSciences LLC , 9330 Zionsville Road , Indianapolis , IN 46268 , USA
| | - Kumar Dilip Ashtekar
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , USA . ;
| | - James E Jackson
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , USA . ;
| | - Babak Borhan
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , USA . ;
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19
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Lun CM, Bishop BM, Smith LC. Multitasking Immune Sp185/333 Protein, rSpTransformer-E1, and Its Recombinant Fragments Undergo Secondary Structural Transformation upon Binding Targets. THE JOURNAL OF IMMUNOLOGY 2017; 198:2957-2966. [PMID: 28242650 DOI: 10.4049/jimmunol.1601795] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/26/2017] [Indexed: 12/31/2022]
Abstract
The purple sea urchin, Strongylocentrotus purpuratus, expresses a diverse immune response protein family called Sp185/333. A recombinant Sp185/333 protein, previously called rSp0032, shows multitasking antipathogen binding ability, suggesting that the protein family mediates a flexible and effective immune response to multiple foreign cells. Bioinformatic analysis predicts that rSp0032 is intrinsically disordered, and its multiple binding characteristic suggests structural flexibility to adopt different conformations depending on the characteristics of the target. To address the flexibility and structural shifting hypothesis, circular dichroism analysis of rSp0032 suggests that it transforms from disordered (random coil) to α helical structure. This structural transformation may be the basis for the strong affinity between rSp0032 and several pathogen-associated molecular patterns. The N-terminal Gly-rich fragment of rSp0032 and the C-terminal His-rich fragment show unique transformations by either intensifying the α helical structure or changing from α helical to β strand depending on the solvents and molecules added to the buffer. Based on these results, we propose a name change from rSp0032 to rSpTransformer-E1 to represent its flexible structural conformations and its E1 element pattern. Given that rSpTransformer-E1 shifts its conformation in the presence of solvents and binding targets and that all Sp185/333 proteins are predicted to be disordered, many or all of these proteins may undergo structural transformation to enable multitasking binding activity toward a wide range of targets. Consequently, we also propose an overarching name change for the entire family from Sp185/333 proteins to SpTransformer proteins.
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Affiliation(s)
- Cheng Man Lun
- Department of Biological Sciences, George Washington University, Washington, DC 20052; and
| | - Barney M Bishop
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110
| | - L Courtney Smith
- Department of Biological Sciences, George Washington University, Washington, DC 20052; and
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20
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Thomas J, Seifert NA, Jäger W, Xu Y. A Direct Link from the Gas to the Condensed Phase: A Rotational Spectroscopic Study of 2,2,2-Trifluoroethanol Trimers. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612161] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Javix Thomas
- Department of Chemistry; University of Alberta; Edmonton Alberta T6G 2G2 Canada
| | - Nathan A. Seifert
- Department of Chemistry; University of Alberta; Edmonton Alberta T6G 2G2 Canada
| | - Wolfgang Jäger
- Department of Chemistry; University of Alberta; Edmonton Alberta T6G 2G2 Canada
| | - Yunjie Xu
- Department of Chemistry; University of Alberta; Edmonton Alberta T6G 2G2 Canada
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21
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Thomas J, Seifert NA, Jäger W, Xu Y. A Direct Link from the Gas to the Condensed Phase: A Rotational Spectroscopic Study of 2,2,2-Trifluoroethanol Trimers. Angew Chem Int Ed Engl 2017; 56:6289-6293. [PMID: 28229516 DOI: 10.1002/anie.201612161] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Indexed: 11/07/2022]
Abstract
Rotational spectra of the three most stable conformers (I, II, III) of the ternary 2,2,2-trifluoroethanol (TFE) cluster were measured using Fourier transform microwave spectrometers, and unambiguously assigned with the aid of ab initio calculations. The most stable conformer, I, contains one trans-TFE subunit which is unstable in its isolated gas phase form. The study offers new insights into how the trans conformation is stabilized in TFE clusters of increasing size, and eventually becomes a dominant conformation in the liquid phase. A detailed analysis shows that while O-H⋅⋅⋅O-H and O-H⋅⋅⋅F-C hydrogen bonds are the most significant attractive interactions which stabilize all three conformers, the main driving force for the stability of I over III, which has all gauche-TFE subunits, is the attractive interaction of C-F⋅⋅⋅F-C contact pairs. A new type of three-point F⋅⋅⋅F⋅⋅⋅F attractive contact interaction is also identified.
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Affiliation(s)
- Javix Thomas
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Nathan A Seifert
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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22
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Structural coalescence underlies the aggregation propensity of a β-barrel protein motif. PLoS One 2017; 12:e0170607. [PMID: 28187186 PMCID: PMC5302452 DOI: 10.1371/journal.pone.0170607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/07/2017] [Indexed: 02/07/2023] Open
Abstract
A clear understanding of the structural foundations underlying protein aggregation is an elusive goal of central biomedical importance. A step toward this aim is exemplified by the β-barrel motif represented by the intestinal fatty acid binding protein (IFABP) and two abridged all-β sheet forms (Δ98Δ and Δ78Δ). At odds with the established notion that a perturbation of the native fold should necessarily favor a buildup of intermediate forms with an enhanced tendency to aggregate, the intrinsic stability (ΔG°H2O) of these proteins does not bear a straightforward correlation with their trifluoroethanol (TFE)-induced aggregation propensity. In view of this fact, we found it more insightful to delve into the connection between structure and stability under sub-aggregating conditions (10% TFE). In the absence of the co-solvent, the abridged variants display a common native-like region decorated with a disordered C-terminal stretch. Upon TFE addition, an increase in secondary structure content is observed, assimilating them to the parent protein. In this sense, TFE perturbs a common native like region while exerting a global compaction effect. Importantly, in all cases, fatty acid binding function is preserved. Interestingly, energetic as well as structural diversity in aqueous solution evolves into a common conformational ensemble more akin in stability. These facts reconcile apparent paradoxical findings related to stability and rates of aggregation. This scenario likely mimics the accrual of aggregation-prone species in the population, an early critical event for the development of fibrillation.
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23
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Barreto-Santamaría A, Curtidor H, Arévalo-Pinzón G, Herrera C, Suárez D, Pérez WH, Patarroyo ME. A New Synthetic Peptide Having Two Target of Antibacterial Action in E. coli ML35. Front Microbiol 2016; 7:2006. [PMID: 28066341 PMCID: PMC5167725 DOI: 10.3389/fmicb.2016.02006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/30/2016] [Indexed: 11/13/2022] Open
Abstract
The increased resistance of microorganisms to the different antimicrobials available to today has highlighted the need to find new therapeutic agents, including natural and/or synthetic antimicrobial peptides (AMPs). This study has evaluated the antimicrobial activity of synthetic peptide 35409 (RYRRKKKMKKALQYIKLLKE) against Staphylococcus aureus ATCC 29213, Pseudomonas aeruginosa ATCC 15442 and Escherichia coli ML 35 (ATCC 43827). The results have shown that peptide 35409 inhibited the growth of these three bacterial strains, having 16-fold greater activity against E. coli and P. aeruginosa, but requiring less concentration regarding E. coli (22 μM). When analyzing this activity against E. coli compared to time taken, it was found that this peptide inhibited bacterial growth during the first 60 min and reduced CFU/mL 1 log after 120 min had elapsed. This AMP permeabilized the E. coli membrane by interaction with membrane phospholipids, mainly phosphatidylethanolamine, inhibited cell division and induced filamentation, suggesting two different targets of action within a bacterial cell. Cytotoxicity studies revealed that peptide 35409 had low hemolytic activity and was not cytotoxic for two human cell lines. We would thus propose, in the light of these findings, that the peptide 35409 sequence should provide a promising template for designing broad-spectrum AMPs.
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Affiliation(s)
- Adriana Barreto-Santamaría
- Receptor-Ligand Department, Fundación Instituto de Inmunología de ColombiaBogotá, Colombia; Faculty of Sciences and Education, Universidad Distrital Francisco José de CaldasBogotá, Colombia; School of Medicine and Health sciences, Universidad del RosarioBogotá, Colombia
| | - Hernando Curtidor
- Receptor-Ligand Department, Fundación Instituto de Inmunología de ColombiaBogotá, Colombia; School of Medicine and Health sciences, Universidad del RosarioBogotá, Colombia
| | - Gabriela Arévalo-Pinzón
- Receptor-Ligand Department, Fundación Instituto de Inmunología de ColombiaBogotá, Colombia; School of Medicine and Health sciences, Universidad del RosarioBogotá, Colombia
| | - Chonny Herrera
- Receptor-Ligand Department, Fundación Instituto de Inmunología de ColombiaBogotá, Colombia; School of Medicine and Health sciences, Universidad del RosarioBogotá, Colombia
| | - Diana Suárez
- Receptor-Ligand Department, Fundación Instituto de Inmunología de ColombiaBogotá, Colombia; School of Medicine and Health sciences, Universidad del RosarioBogotá, Colombia
| | - Walter H Pérez
- Escuela Colombiana de Carreras Industriales Bogotá, Colombia
| | - Manuel E Patarroyo
- Receptor-Ligand Department, Fundación Instituto de Inmunología de ColombiaBogotá, Colombia; Faculty of Medicine, Universidad Nacional de ColombiaBogotá, Colombia
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24
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Naeem A, Bhat SA, Iram A, Khan RH. Aggregation of intrinsically disordered fibrinogen as the influence of backbone conformation. Arch Biochem Biophys 2016; 603:38-47. [DOI: 10.1016/j.abb.2016.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 04/13/2016] [Accepted: 04/30/2016] [Indexed: 10/21/2022]
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25
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Sanfelice D, Temussi PA. Cold denaturation as a tool to measure protein stability. Biophys Chem 2016; 208:4-8. [PMID: 26026885 PMCID: PMC4671483 DOI: 10.1016/j.bpc.2015.05.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/18/2015] [Accepted: 05/18/2015] [Indexed: 11/30/2022]
Abstract
Protein stability is an important issue for the interpretation of a wide variety of biological problems but its assessment is at times difficult. The most common parameter employed to describe protein stability is the temperature of melting, at which the populations of folded and unfolded species are identical. This parameter may yield ambiguous results. It would always be preferable to measure the whole stability curve. The calculation of this curve is greatly facilitated whenever it is possible to observe cold denaturation. Using Yfh1, one of the few proteins whose cold denaturation occurs at neutral pH and low ionic strength, we could measure the variation of its full stability curve under several environmental conditions. Here we show the advantages of gauging stability as a function of external variables using stability curves.
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Affiliation(s)
| | - Piero Andrea Temussi
- MRC National Institute for Medical Research, The Ridgeway, London, UK; Dipartimento di Chimica, Universita' di Napoli Federico II, Napoli, Italy.
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26
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Gourbatsi E, Povey J, Uddin S, Smales CM. Biotherapeutic protein formulation variables influence protein integrity and can promote post-translational modifications as shown using chicken egg white lysozyme as a model system. Biotechnol Lett 2015; 38:589-96. [PMID: 26699895 PMCID: PMC4796366 DOI: 10.1007/s10529-015-2014-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/02/2015] [Indexed: 11/28/2022]
Abstract
Objectives The effect of different formulations variables on protein integrity were investigated using lysozyme as a model protein for the development of biotherapeutic protein formulations for use in the clinic. Results Buffer composition/concentration was the key variable of formulation reagents investigated in determining lysozyme stability and authenticity independent of protein concentration whilst the storage temperature and time, not surprisingly, were also key variables. Tryptic peptide mapping of the protein showed that the modifications occurred when formulated under specific conditions but not others. A model peptide system was developed that reflected the same behavior under formulation conditions as intact lysozyme. Conclusions Peptide models may mirror the stability of proteins, or regions of proteins, in the same formulations and be used to help develop a rapid screen of formulations for stabilisation of biotherapeutic proteins. Electronic supplementary material The online version of this article (doi:10.1007/s10529-015-2014-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evdoxia Gourbatsi
- School of Biosciences and Centre for Molecular Processing, University of Kent, Canterbury, CT2 7NJ, UK
| | - Jane Povey
- School of Biosciences and Centre for Molecular Processing, University of Kent, Canterbury, CT2 7NJ, UK
| | - Shahid Uddin
- Formulation Sciences, AKB Building, MedImmune, Granta Park, Cambridge, CB21 6GH, UK
| | - C Mark Smales
- School of Biosciences and Centre for Molecular Processing, University of Kent, Canterbury, CT2 7NJ, UK.
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27
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Barman A, Smitherman C, Souffrant M, Gadda G, Hamelberg D. Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. J Chem Inf Model 2015; 56:139-47. [DOI: 10.1021/acs.jcim.5b00560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Arghya Barman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Crystal Smitherman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Michael Souffrant
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Giovanni Gadda
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
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28
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MyelStones: the executive roles of myelin basic protein in myelin assembly and destabilization in multiple sclerosis. Biochem J 2015; 472:17-32. [DOI: 10.1042/bj20150710] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The classic isoforms of myelin basic protein (MBP, 14–21.5 kDa) are essential to formation of the multilamellar myelin sheath of the mammalian central nervous system (CNS). The predominant 18.5-kDa isoform links together the cytosolic surfaces of oligodendrocytes, but additionally participates in cytoskeletal turnover and membrane extension, Fyn-mediated signalling pathways, sequestration of phosphoinositides and maintenance of calcium homoeostasis. All MBP isoforms are intrinsically disordered proteins (IDPs) that interact via molecular recognition fragments (MoRFs), which thereby undergo local disorder-to-order transitions. Their conformations and associations are modulated by environment and by a dynamic barcode of post-translational modifications, particularly phosphorylation by mitogen-activated and other protein kinases and deimination [a hallmark of demyelination in multiple sclerosis (MS)]. The MBPs are thus to myelin what basic histones are to chromatin. Originally thought to be merely structural proteins forming an inert spool, histones are now known to be dynamic entities involved in epigenetic regulation and diseases such as cancer. Analogously, the MBPs are not mere adhesives of compact myelin, but active participants in oligodendrocyte proliferation and in membrane process extension and stabilization during myelinogenesis. A central segment of these proteins is pivotal in membrane-anchoring and SH3 domain (Src homology 3) interaction. We discuss in the present review advances in our understanding of conformational conversions of this classic basic protein upon membrane association, including new thermodynamic analyses of transitions into different structural ensembles and how a shift in the pattern of its post-translational modifications is associated with the pathogenesis and potentially onset of demyelination in MS.
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29
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Szabados H, Uray K, Majer Z, Silló P, Kárpáti S, Hudecz F, Bősze S. Characterization of desmoglein-3 epitope region peptides as synthetic antigens: analysis of their in vitro T cell stimulating efficacy, cytotoxicity, stability, and their conformational features. J Pept Sci 2015; 21:731-42. [PMID: 26250896 DOI: 10.1002/psc.2800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/05/2015] [Accepted: 06/13/2015] [Indexed: 11/09/2022]
Abstract
Desmoglein-3 (Dsg3) adhesion protein is the main target of autoantibodies and autoreactive T cells in Pemphigus vulgaris (PV) autoimmune skin disorder. Several mapping studies of Dsg3 T cell epitope regions were performed, and based on those data, we designed and synthesized four peptide series corresponding to Dsg3 T cell epitope regions. Each peptide series consists of a 17mer full-length peptide (Dsg3/189-205, Dsg3/206-222, Dsg3/342-358, and Dsg3/761-777) and its N-terminally truncated derivatives, resulting in 15 peptides altogether. The peptides were prepared on solid phase and were chemically characterized. In order to establish a structure-activity relationship, the solution conformation of the synthetic peptides has been investigated using electronic circular dichroism spectroscopy. The in vitro T cell stimulating efficacy of the peptides has been determined on peripheral blood mononuclear cells isolated from whole blood of PV patients and also from healthy donors. After 20 h of stimulation, the interferon (IFN)-γ content of the supernatants was measured by enzyme-linked immunosorbent assay. In the in vitro conditions, peptides were stable and non-cytotoxic. The in vitro IFN-γ production profile of healthy donors and PV patients, induced by peptides as synthetic antigens, was markedly different. The most unambiguous differences were observed after stimulation with 17mer peptide Dsg3/342-358, and three truncated derivatives from two other peptide series, namely, peptides Dsg3/192-205, Dsg3/763-777, and Dsg3/764-777. Comparative analysis of in vitro activity and the capability of oligopeptides to form ordered or unordered secondary structure showed that peptides bearing high solvent sensibility and backbone flexibility were the most capable to distinguish between healthy and PV donors.
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Affiliation(s)
- Hajnalka Szabados
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, PO Box 32 H-1518, Budapest, 112, Hungary
| | - Katalin Uray
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, PO Box 32 H-1518, Budapest, 112, Hungary
| | - Zsuzsa Majer
- Laboratory for Chiroptical Structure Analysis, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Pálma Silló
- Department of Dermatology, Venereology and Dermato-Oncology, Semmelweis University, Budapest, Hungary
| | - Sarolta Kárpáti
- Department of Dermatology, Venereology and Dermato-Oncology, Semmelweis University, Budapest, Hungary
| | - Ferenc Hudecz
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, PO Box 32 H-1518, Budapest, 112, Hungary.,Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Szilvia Bősze
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, PO Box 32 H-1518, Budapest, 112, Hungary
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30
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Chong Y, Kleinhammes A, Tang P, Xu Y, Wu Y. Dominant Alcohol-Protein Interaction via Hydration-Enabled Enthalpy-Driven Binding Mechanism. J Phys Chem B 2015; 119:5367-75. [PMID: 25856773 DOI: 10.1021/acs.jpcb.5b00378] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water plays an important role in weak associations of small drug molecules with proteins. Intense focus has been on binding-induced structural changes in the water network surrounding protein binding sites, especially their contributions to binding thermodynamics. However, water is also tightly coupled to protein conformations and dynamics, and so far little is known about the influence of water-protein interactions on ligand binding. Alcohols are a type of low-affinity drugs, and it remains unclear how water affects alcohol-protein interactions. Here, we present alcohol adsorption isotherms under controlled protein hydration using in situ NMR detection. As functions of hydration level, Gibbs free energy, enthalpy, and entropy of binding were determined from the temperature dependence of isotherms. Two types of alcohol binding were found. The dominant type is low-affinity nonspecific binding, which is strongly dependent on temperature and the level of hydration. At low hydration levels, this nonspecific binding only occurs above a threshold of alcohol vapor pressure. An increased hydration level reduces this threshold, with it finally disappearing at a hydration level of h ≈ 0.2 (g water/g protein), gradually shifting alcohol binding from an entropy-driven to an enthalpy-driven process. Water at charged and polar groups on the protein surface was found to be particularly important in enabling this binding. Although further increase in hydration has smaller effects on the changes of binding enthalpy and entropy, it results in a significant negative change in Gibbs free energy due to unmatched enthalpy-entropy compensation. These results show the crucial role of water-protein interplay in alcohol binding.
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Affiliation(s)
- Yuan Chong
- †Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27599-3255, United States
| | - Alfred Kleinhammes
- †Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27599-3255, United States
| | | | | | - Yue Wu
- †Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27599-3255, United States
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31
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32
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Impact of trifluoroethanol-induced structural changes on luciferase cleavage sites. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 144:1-7. [DOI: 10.1016/j.jphotobiol.2015.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 01/11/2015] [Accepted: 01/12/2015] [Indexed: 11/22/2022]
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33
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Enyedi KN, Czajlik A, Knapp K, Láng A, Majer Z, Lajkó E, Kőhidai L, Perczel A, Mező G. Development of cyclic NGR peptides with thioether linkage: structure and dynamics determining deamidation and bioactivity. J Med Chem 2015; 58:1806-17. [PMID: 25646854 DOI: 10.1021/jm501630j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NGR peptides that recognize CD13 receptors in tumor neovasculature are of high interest, in particular due to their potential applications in drug targeting. Here we report the synthesis and structural analysis of novel thioether bond-linked cyclic NGR peptides. Our results show that their chemostability (resistance against spontaneous decomposition forming isoAsp and Asp derivatives) strongly depends on both sample handling conditions and structural properties. A significant correlation was found between chemostability and structural measures, such as NH(Gly)-CO(Asn-sc) distances. The side-chain orientation of Asn is a key determining factor; if it is turned away from HN(Gly), the chemostability increases. Structure stabilizing factors (e.g., H-bonds) lower their internal dynamics, and thus biomolecules become even more resistant against spontaneous decomposition. The effect of cyclic NGR peptides on cell adhesion was examined in A2058 melanoma cell lines. It was found that some of the investigated peptides gradually increased cell adhesion with long-term characteristics, indicating time-dependent formation of integrin binding isoAsp derivatives that are responsible for the adhesion-inducing effect.
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Affiliation(s)
- Kata Nóra Enyedi
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences,▽MTA-ELTE Protein Modelling Research Group, Hungarian Academy of Sciences, ∥Laboratory for Chiroptical Structure Analysis, Institute of Chemistry, and ⊥Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University , Pázmány P. sétány 1/A, 1117 Budapest, Hungary
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34
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Wang Z, Han X, He N, Chen Z, Brooks CL. Environmental Effect on Surface Immobilized Biological Molecules. J Phys Chem B 2014; 118:12176-85. [DOI: 10.1021/jp508550d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Zunliang Wang
- State
Key Laboratory of Bioelectronics, School of Biological Science and
Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xiaofeng Han
- State
Key Laboratory of Bioelectronics, School of Biological Science and
Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China
| | - Nongyue He
- State
Key Laboratory of Bioelectronics, School of Biological Science and
Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China
| | - Zhan Chen
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L. Brooks
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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35
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Angelani CR, Curto LM, Cabanas IS, Caramelo JJ, Uversky VN, Delfino JM. Toward a common aggregation mechanism for a β-barrel protein family: Insights derived from a stable dimeric species. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1599-607. [DOI: 10.1016/j.bbapap.2014.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/30/2014] [Accepted: 06/02/2014] [Indexed: 10/25/2022]
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36
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Lawrence AD, Frank S, Newnham S, Lee MJ, Brown IR, Xue WF, Rowe ML, Mulvihill DP, Prentice MB, Howard MJ, Warren MJ. Solution structure of a bacterial microcompartment targeting peptide and its application in the construction of an ethanol bioreactor. ACS Synth Biol 2014; 3:454-465. [PMID: 24933391 DOI: 10.1021/sb4001118] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Targeting of proteins to bacterial microcompartments (BMCs) is mediated by an 18-amino-acid peptide sequence. Herein, we report the solution structure of the N-terminal targeting peptide (P18) of PduP, the aldehyde dehydrogenase associated with the 1,2-propanediol utilization metabolosome from Citrobacter freundii. The solution structure reveals the peptide to have a well-defined helical conformation along its whole length. Saturation transfer difference and transferred NOE NMR has highlighted the observed interaction surface on the peptide with its main interacting shell protein, PduK. By tagging both a pyruvate decarboxylase and an alcohol dehydrogenase with targeting peptides, it has been possible to direct these enzymes to empty BMCs in vivo and to generate an ethanol bioreactor. Not only are the purified, redesigned BMCs able to transform pyruvate into ethanol efficiently, but the strains containing the modified BMCs produce elevated levels of alcohol.
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Affiliation(s)
- Andrew D. Lawrence
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Stefanie Frank
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Sarah Newnham
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Matthew J. Lee
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Ian R. Brown
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Wei-Feng Xue
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Michelle L. Rowe
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Daniel P. Mulvihill
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | | | - Mark J. Howard
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
| | - Martin J. Warren
- School
of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, U.K
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37
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Thomas J, Jäger W, Xu Y. Chirality Induction and Amplification in the 2,2,2‐Trifluoroethanol⋅⋅⋅Propylene Oxide Adduct. Angew Chem Int Ed Engl 2014; 53:7277-80. [DOI: 10.1002/anie.201403838] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 05/07/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Javix Thomas
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada)
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada)
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada)
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38
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Thomas J, Xu Y. Structure and tunneling dynamics in a model system of peptide co-solvents: Rotational spectroscopy of the 2,2,2-trifluoroethanol⋯water complex. J Chem Phys 2014; 140:234307. [DOI: 10.1063/1.4883518] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Thomas J, Xu Y. Chirality Synchronization in Trifluoroethanol Dimer Revisited: The Missing Heterochiral Dimer. J Phys Chem Lett 2014; 5:1850-1855. [PMID: 26273864 DOI: 10.1021/jz500718f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chirality self-recognition in the dimer of transient chiral 2,2,2-trifluoroethanol (TFE) is studied using chirped pulse and cavity-based Fourier transform microwave spectroscopy with the aid of ab initio calculations. The broad-band and extreme high-resolution capabilities enable us to assign rotational spectra of the most stable homo- and heterochiral dimers and analyze their structural and dynamical properties in detail. A strong preference for the homochiral over the heterochiral diastereomers is observed. The current study unambiguously identifies the structure of the most stable homochiral dimer and supports the identification by the previous low-resolution infrared study. More importantly, it also indisputably detects the so far elusive, most stable heterochiral dimer.
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Affiliation(s)
- Javix Thomas
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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40
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Thomas J, Jäger W, Xu Y. Chirality Induction and Amplification in the 2,2,2‐Trifluoroethanol⋅⋅⋅Propylene Oxide Adduct. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403838] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Javix Thomas
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada)
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada)
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada)
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41
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Shao Q. Methanol Concentration Dependent Protein Denaturing Ability of Guanidinium/Methanol Mixed Solution. J Phys Chem B 2014; 118:6175-85. [DOI: 10.1021/jp500280v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Qiang Shao
- Drug Discovery and Design
Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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42
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Arthur EJ, King JT, Kubarych KJ, Brooks CL. Heterogeneous preferential solvation of water and trifluoroethanol in homologous lysozymes. J Phys Chem B 2014; 118:8118-27. [PMID: 24823618 PMCID: PMC4216199 DOI: 10.1021/jp501132z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
![]()
Cytoplasmic
osmolytes can significantly alter the thermodynamic
and kinetic properties of proteins relative to those under dilute
solution conditions. Spectroscopic experiments of lysozymes in cosolvents
indicate that such changes may arise from the heterogeneous, site-specific
hydrophobic interactions between protein surface residues and individual
solvent molecules. In pursuit of an accurate and predictive model
for explaining biomolecular interactions, we study the averaged structural
characteristics of mixed solvents with homologous lysozyme solutes
using all-atom molecular dynamics. By observing the time-averaged
densities of different aqueous solutions of trifluoroethanol, we deduce
trends in the heterogeneous solvent interactions over each protein’s
surface, and investigate how the homology of protein structure does
not necessarily translate to similarities in solvent structure and
composition—even when observing identical side chains.
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Affiliation(s)
- Evan J Arthur
- Department of Chemistry and ‡Biophysics Program, University of Michigan , 930 N. University Avenue , Ann Arbor, Michigan 48109-1055, USA
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43
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Comparison of the Efficacy of Alpha-Lactalbumin from Equine, Bovine, and Human Milk in the Growth of Intestinal IEC-6 Cells. Biosci Biotechnol Biochem 2014; 76:843-6. [DOI: 10.1271/bbb.110896] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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44
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Rostamnia S, Doustkhah E. A mesoporous silica/fluorinated alcohol adduct: an efficient metal-free, three-component synthesis of indazolophthalazinetrione heterocycles using a reusable nanoporous/trifluoroethanol adduct (SBA-15/TFE). Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.03.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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45
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Hexafluoroisopropanol dispersed into the nanoporous SBA-15 (HFIP/SBA-15) as a rapid, metal-free, highly reusable and suitable combined catalyst for domino cyclization process in chemoselective preparation of alkyl rhodanines. J Fluor Chem 2013. [DOI: 10.1016/j.jfluchem.2013.05.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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46
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Jain R, Sharma D, Kumar R. Effects of alcohols on the stability and low-frequency local motions that control the slow changes in structural dynamics of ferrocytochrome c. J Biochem 2013; 154:341-54. [DOI: 10.1093/jb/mvt059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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47
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Controlled Enzymatic Hydrolysis: A New Strategy for the Discovery of Antimicrobial Peptides. Probiotics Antimicrob Proteins 2013; 5:176-86. [DOI: 10.1007/s12602-013-9138-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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48
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Eichenberger AP, van Gunsteren WF, Smith LJ. Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data. JOURNAL OF BIOMOLECULAR NMR 2013; 55:339-353. [PMID: 23494634 DOI: 10.1007/s10858-013-9717-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 02/17/2013] [Indexed: 06/01/2023]
Abstract
Various experimental studies of hen egg white lysozyme (HEWL) in water and TFE/water clearly indicate structural differences between the native state and TFE state of HEWL, e.g. the helical content of the protein in the TFE state is much higher than in the native state. However, the available detailed NMR studies were not sufficient to determine fully a structure of HEWL in the TFE state. Different molecular dynamics (MD) simulations, i.e. at room temperature, at increased temperature and using proton-proton distance restraints derived from NMR NOE data, have been used to generate configurational ensembles corresponding to the TFE state of HEWL. The configurational ensemble obtained at room temperature using atom-atom distance restraints measured for HEWL in TFE/water solution satisfies the experimental data and has the lowest protein energy. In this ensemble residues 50-58, which are part of the β-sheet in native HEWL, adopt fluctuating α-helical secondary structure.
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Affiliation(s)
- Andreas P Eichenberger
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zurich, Switzerland
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49
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Samanta SR, Levere ME, Percec V. SET-LRP of hydrophobic and hydrophilic acrylates in trifluoroethanol. Polym Chem 2013. [DOI: 10.1039/c3py00289f] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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50
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King J, Arthur E, Brooks C, Kubarych K. Hydrophobic hydration of globular proteins studied with 2D-IR spectroscopy. EPJ WEB OF CONFERENCES 2013. [DOI: 10.1051/epjconf/20134106008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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