1
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Robang A, Wong KM, Leisen J, Liu R, Radford WL, Rao Sudarshan T, Hudalla GA, Paravastu AK. Parallel β-Sheet Structure and Structural Heterogeneity Detected within Q11 Self-Assembling Peptide Nanofibers. J Phys Chem B 2024; 128:5387-5396. [PMID: 38787393 PMCID: PMC11163420 DOI: 10.1021/acs.jpcb.4c00825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/26/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Q11 peptide nanofibers are used as a biomaterial for applications such as antigen presentation and tissue engineering, yet detailed knowledge of molecular-level structure has not been reported. The Q11 peptide sequence was designed using heuristics-based patterning of hydrophobic and polar amino acids with oppositely charged amino acids placed at opposite ends of the sequence to promote antiparallel β-sheet formation. In this work, we employed solid-state nuclear magnetic resonance spectroscopy (NMR) to evaluate whether the molecular organization within Q11 self-assembled peptide nanofibers is consistent with the expectations of the peptide designers. We discovered that Q11 forms a distribution of molecular structures. NMR data from two-dimensional (2D) 13C-13C dipolar-assisted rotational resonance indicate that the K3 and E9 residues between Q11 β-strands are spatially proximate (within ∼0.6 nm). Frequency-selective rotational echo double resonance (fsREDOR) on K3 Nζ and E9 Cδ-labeled sites showed that approximately 9% of the sites are close enough for salt bridge formation to occur. Surprisingly, dipolar recoupling measurements revealed that Q11 peptides do not assemble into antiparallel β-sheets as expected, and structural analysis using Fourier-transform infrared spectroscopy and 2D NMR alone can be misleading. 13C PITHIRDS-CT dipolar recoupling measurements showed that the most abundant structure consists of parallel β-sheets, in contrast to the expected antiparallel β-sheet structure. Structural heterogeneity was detected from 15N{13C} REDOR measurements, with approximately 22% of β-strands having antiparallel nearest neighbors. We cannot propose a complete structural model of Q11 nanofibers because of the complexity involved when examining structurally heterogeneous samples using NMR. Altogether, our results show that while heuristics-based patterning is effective in promoting β-sheet formation, designing a peptide sequence to form a targeted β-strand arrangement remains challenging.
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Affiliation(s)
- Alicia
S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Kong M. Wong
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Johannes Leisen
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Renjie Liu
- J. Crayton
Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Walker L. Radford
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Tarunya Rao Sudarshan
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gregory A. Hudalla
- J. Crayton
Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Anant K. Paravastu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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2
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Liu Z, Xu M, Zhou S, Wang J, Huang Z. Enhancing the Thermal Stability of Zein Particle-Stabilized Aeratable Emulsions Through Genipin-Protein Cross-Linking and Its Possible Mechanism of Action. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3707-3718. [PMID: 38268446 DOI: 10.1021/acs.jafc.3c07770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Protein particle-stabilized emulsions often lack thermal stability, impacting their industrial use. This study investigated the effects of genipin (GP)-zein cross-linked particles with varying GP-to-protein weight ratios (0/0.02/0.1:1) on emulsion thermal stability. Enhanced stability was observed at the GP level of 0.1. Heat treatment increased the covalent cross-linking in raw particles and emulsions. Isolated particles from heated emulsions grew in size (micrometer scale) with higher GP levels, unlike heated raw particles (nanoscale). GP-protein cross-linking reduced the droplet-droplet and particle-emulsifier interactions in the heated emulsion. Spectroscopic analysis and electrophoresis revealed that GP-zein cross-linking increased protein structural stability and inhibited nondisulfide and non-GP cross-linking reactions in heated emulsions. The GP-zein bridges between particles at the oil-water interface create strong connections in the particle layer (shell), referred to as "particle-shell locking", enhancing the thermal stability of emulsion significantly. This insight aids the future design of protein-particle-based emulsions, preserving properties like aeratability during thermal processing.
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Affiliation(s)
- Zelong Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology and Business University, Beijing 100048, China
| | - Meiyu Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology and Business University, Beijing 100048, China
| | - Sumei Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology and Business University, Beijing 100048, China
| | - Jing Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology and Business University, Beijing 100048, China
| | - Zhaoxian Huang
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
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3
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Smith CS, Álvarez Z, Qiu R, Sasselli IR, Clemons T, Ortega JA, Vilela-Picos M, Wellman H, Kiskinis E, Stupp SI. Enhanced Neuron Growth and Electrical Activity by a Supramolecular Netrin-1 Mimetic Nanofiber. ACS NANO 2023; 17:19887-19902. [PMID: 37793046 DOI: 10.1021/acsnano.3c04572] [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] [Indexed: 10/06/2023]
Abstract
Neurotrophic factors are essential not only for guiding the organization of the developing nervous system but also for supporting the survival and growth of neurons after traumatic injury. In the central nervous system (CNS), inhibitory factors and the formation of a glial scar after injury hinder the functional recovery of neurons, requiring exogenous therapies to promote regeneration. Netrin-1, a neurotrophic factor, can initiate axon guidance, outgrowth, and branching, as well as synaptogenesis, through activation of deleted in colorectal cancer (DCC) receptors. We report here the development of a nanofiber-shaped supramolecular mimetic of netrin-1 with monomers that incorporate a cyclic peptide sequence as the bioactive component. The mimetic structure was found to activate the DCC receptor in primary cortical neurons using low molar ratios of the bioactive comonomer. The supramolecular nanofibers enhanced neurite outgrowth and upregulated maturation as well as pre- and postsynaptic markers over time, resulting in differences in electrical activity similar to neurons treated with the recombinant netrin-1 protein. The results suggest the possibility of using the supramolecular structure as a therapeutic to promote regenerative bioactivity in CNS injuries.
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Affiliation(s)
- Cara S Smith
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Zaida Álvarez
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- Department of Medicine, Northwestern University, Chicago, Illinois 60611, United States
- Biomaterials for Neural Regeneration, Institute for Bioengineering of Catalonia (IBEC), Barcelona 08028, Spain
| | - Ruomeng Qiu
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Ivan R Sasselli
- Centro de Fisica de Materiales (CFM), CSIC-UPV/EHU, San Sebastián 20018, Spain
| | - Tristan Clemons
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - J Alberto Ortega
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- The Ken & Ruth Davee Department of Neurology, Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
- Department of Pathology and Experimental Therapeutics, Institute of Neurosciences, University of Barcelona, L'Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Marcos Vilela-Picos
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Haley Wellman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Evangelos Kiskinis
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- The Ken & Ruth Davee Department of Neurology, Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
| | - Samuel I Stupp
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Medicine, Northwestern University, Chicago, Illinois 60611, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
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4
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Zhao T, Pan Y. An evaluation of the effect of hydrofluoric acid (HF) treatment on keratins. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:377-384. [PMID: 36002950 DOI: 10.1002/jez.b.23173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 06/26/2022] [Accepted: 07/28/2022] [Indexed: 06/09/2023]
Abstract
Hydrofluoric acid (HF) is commonly used in geological and paleontological research to extract organic fossils for morphological and chemical studies. However, during HF treatment, organic matter can also be altered, which raises concerns that HF-treated organic matter may not be representative of the original organic matter. To provide reference data for protein studies on fossils, herein, we use Fourier transform infrared (FTIR) spectroscopy to investigate the effect of HF (21.3 M) treatment on keratins, with treatment durations ranging from 2 to 48 h. Results show that the FTIR spectra of HF-treated samples are overall similar to that of the untreated sample, while curve fitting shows that HF treatment has led to alteration of the secondary structure in all the HF-treated samples and the effect is time-dependent. The 2- and 4-h treatment mainly reduced the content of the random coils, α-helix, and intermolecular β-sheet. From 8h onwards, the content of random coils greatly increased at the expense of other structures. Our results imply that for protein detection in fossils using FTIR spectroscopy, the negative effect of HF treatment is not substantial, as the bands characteristic of proteins, that is, amide A, amide B, amide I, amide II, and amide III, are still present after the 48-h treatment. If the target is a secondary structure, the effect of HF treatment should be considered. When HF treatment is necessary, limiting the treatment duration to less than 4h may be a choice.
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Affiliation(s)
- Tao Zhao
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Centre for Research and Education on Biological Evolution and Environment and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Yanhong Pan
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Centre for Research and Education on Biological Evolution and Environment and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
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5
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Whippable emulsions co-stabilized by protein particles and emulsifiers: The effect of emulsifier type. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2022.108379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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6
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Li H, Cornel EJ, Fan Z, Du J. Chirality-controlled polymerization-induced self-assembly. Chem Sci 2022; 13:14179-14190. [PMID: 36540815 PMCID: PMC9728572 DOI: 10.1039/d2sc05695j] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/17/2022] [Indexed: 09/21/2023] Open
Abstract
Recent studies have shown that biodegradable nanoparticles can be efficiently prepared with polymerization of N-carboxyanhydrides-induced self-assembly (NCA-PISA). However, thus far, the effect of chiral monomer ratio on such NCA-PISA formulations and the resulting nanoparticles has not yet been fully explored. Herein, we show, for the first time, that the morphology, secondary structure, and biodegradation rate of PISA nanoparticles can be controlled by altering the chiral ratio of the core-forming monomers. This chirality-controlled PISA (CC-PISA) method allowed the preparation of nanoparticles that are more adjustable and applicable for future biomedical applications. Additionally, the complex secondary peptide structure (ratio of α-helix to β-sheet) and π-π stacking affect the polymer self-assembly process. More specifically, a PEG45 macro-initiator was chain-extended with l- and d-phenylalanine (l- and d-Phe-NCA) in various molar ratios in dry THF at 15 wt%. This ring-opening polymerization (ROP) allowed the preparation of homo- and hetero-chiral Phe-peptide block copolymers that self-assembled in situ into nanoparticles. For homo-chiral formulations, polymers self-assembled into vesicles once a sufficiently high phenylalanine degree of polymerization (DP) was obtained. Hetero-chiral formulations formed larger nanoparticles with various morphologies and, much to our surprise, using an equal enantiomer ratio inhibited PISA and led to a polymer solution instead. Finally, it was shown that the enzymatic biodegradation rate of such PISA particles is greatly affected by the polymer chirality. This PISA approach could be of great value to fabricate nanoparticles that exploit chirality in disease treatment.
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Affiliation(s)
- Haolan Li
- Department of Polymeric Materials, School of Materials Science and Engineering, Tongji University 4800 Caoan Road Shanghai 201804 China
| | - Erik Jan Cornel
- Department of Polymeric Materials, School of Materials Science and Engineering, Tongji University 4800 Caoan Road Shanghai 201804 China
| | - Zhen Fan
- Department of Polymeric Materials, School of Materials Science and Engineering, Tongji University 4800 Caoan Road Shanghai 201804 China
| | - Jianzhong Du
- Department of Polymeric Materials, School of Materials Science and Engineering, Tongji University 4800 Caoan Road Shanghai 201804 China
- Department of Gynaecology and Obstetrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University Shanghai 200434 China
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7
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Xiao X, Robang AS, Sarma S, Le JV, Helmicki ME, Lambert MJ, Guerrero-Ferreira R, Arboleda-Echavarria J, Paravastu AK, Hall CK. Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides. PNAS NEXUS 2022; 1:pgac263. [PMID: 36712347 PMCID: PMC9802472 DOI: 10.1093/pnasnexus/pgac263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Screening amino acid sequence space via experiments to discover peptides that self-assemble into amyloid fibrils is challenging. We have developed a computational peptide assembly design (PepAD) algorithm that enables the discovery of amyloid-forming peptides. Discontinuous molecular dynamics (DMD) simulation with the PRIME20 force field combined with the FoldAmyloid tool is used to examine the fibrilization kinetics of PepAD-generated peptides. PepAD screening of ∼10,000 7-mer peptides resulted in twelve top-scoring peptides with two distinct hydration properties. Our studies revealed that eight of the twelve in silico discovered peptides spontaneously form amyloid fibrils in the DMD simulations and that all eight have at least five residues that the FoldAmyloid tool classifies as being aggregation-prone. Based on these observations, we re-examined the PepAD-generated peptides in the sequence pool returned by PepAD and extracted five sequence patterns as well as associated sequence signatures for the 7-mer amyloid-forming peptides. Experimental results from Fourier transform infrared spectroscopy (FTIR), thioflavin T (ThT) fluorescence, circular dichroism (CD), and transmission electron microscopy (TEM) indicate that all the peptides predicted to assemble in silico assemble into antiparallel β-sheet nanofibers in a concentration-dependent manner. This is the first attempt to use a computational approach to search for amyloid-forming peptides based on customized settings. Our efforts facilitate the identification of β-sheet-based self-assembling peptides, and contribute insights towards answering a fundamental scientific question: "What does it take, sequence-wise, for a peptide to self-assemble?".
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Affiliation(s)
| | | | | | - Justin V Le
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Michael E Helmicki
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Matthew J Lambert
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ricardo Guerrero-Ferreira
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Johana Arboleda-Echavarria
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University School of Medicine, Atlanta, GA 30322, USA
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8
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Siri M, Herrera M, Moyano AJ, Celej MS. Influence of the macromolecular crowder alginate in the fibrillar organization of the functional amyloid FapC from Pseudomonas aeruginosa. Arch Biochem Biophys 2021; 713:109062. [PMID: 34688606 DOI: 10.1016/j.abb.2021.109062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/03/2021] [Accepted: 10/15/2021] [Indexed: 11/28/2022]
Abstract
Bacterial biofilms are an alternative lifestyle in which communities of bacteria are embedded in an extracellular matrix manly composed by polysaccharides, nucleic acids and proteins, being the hallmark of bacterial survival in a variety of ecological niches. Amyloid fibrils are one of the proteinaceous components of such extracellular crowded environments. FapC is the main component of the functional amyloid recently discovered in Pseudomonas species, including the opportunistic pathogen P. aeruginosa, which is a major cause of nosocomial infections and contamination of medical devices. Considering that several functional roles have been attributed to this bacterial amyloid, FapC emerged as a novel target to control Pseudomonas biofilm formation and to design new treatments against chronic infections. In this study, we used complementary biophysical techniques to evaluate conformational signatures of FapC amyloids formed in the presence of alginate, the major exopolysaccharide associated with the mucoid phenotype of P. aeruginosa strains isolated from cystic fibrosis patients. We found that the this naturally occurring macromolecular crowder leads to morphological similar yet polymorphic FapC fibrils, highlighting the importance of considering the complexity of the extracellular matrix in order to improve our understanding of microbial functional amyloids.
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Affiliation(s)
- Macarena Siri
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Melisa Herrera
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Alejandro J Moyano
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - M Soledad Celej
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.
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9
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De Meutter J, Goormaghtigh E. Protein Structural Denaturation Evaluated by MCR-ALS of Protein Microarray FTIR Spectra. Anal Chem 2021; 93:13441-13449. [PMID: 34592098 DOI: 10.1021/acs.analchem.1c01416] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The loss of native structure is common in proteins. Among others, aggregation is one structural modification of particular importance as it is a major concern for the efficiency and safety of biotherapeutic proteins. Yet, recognizing the structural features associated with intermolecular bridging in a high-throughput manner remains a challenge. We combined here the use of protein microarrays spotted at a density of ca 2500 samples per cm2 and Fourier transform infrared (FTIR) imaging to analyze structural modifications in a set of 85 proteins characterized by widely different secondary structure contents, submitted or not to mild denaturing conditions. Multivariate curve resolution alternating least squares (MCR-ALS) was used to model a new spectral component appearing in the protein set subject to denaturing conditions. In the native protein set, 6 components were found to be sufficient to obtain good modeling of the spectra. Furthermore, their shape allowed them to be assigned to α-helix, β-sheet, and other structures. Their content in each protein was correlated with the known secondary structure, confirming these assignments. In the denatured proteins, a new component was necessary and modeled by MCR-ALS. This new component could be assigned to the intermolecular β-sheet, bridging protein molecules. MCR-ALS, therefore, unveiled a potential spectroscopic marker of protein aggregation and allowed a semiquantitative evaluation of its content. Insight into other structural rearrangements was also obtained.
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Affiliation(s)
- Joëlle De Meutter
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Campus Plaine, Université Libre de Bruxelles CP206/2, B1050 Brussels, Belgium
| | - Erik Goormaghtigh
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Campus Plaine, Université Libre de Bruxelles CP206/2, B1050 Brussels, Belgium
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10
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Shaheen A, Ismat F, Iqbal M, Haque A, Ul-Haq Z, Mirza O, De Zorzi R, Walz T, Rahman M. Characterization of the multidrug efflux transporter styMdtM from Salmonella enterica serovar Typhi. Proteins 2021; 89:1193-1204. [PMID: 33983672 PMCID: PMC8338744 DOI: 10.1002/prot.26141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/14/2021] [Accepted: 05/07/2021] [Indexed: 11/09/2022]
Abstract
Salmonellae are foodborne pathogens and the major cause of gastroenteritis in humans. Salmonellae express multidrug efflux transporters that play a key role in their drug resistance, which is becoming an increasing problem for therapeutic intervention. Despite their biomedical importance, the mechanisms underlying substrate transport by multidrug efflux transporters remain poorly understood. Here, we describe the first characterization of a multidrug transporter belonging to the major facilitator superfamily from the genus Salmonella. We show that several clinical Salmonella Typhi (S. Typhi) isolates constitutively express the styMdtM (STY4874) gene, which encodes a known multidrug-resistance (MDR) transporter. Guided by the structure of the Escherichia coli (E. coli) homolog, we studied two residues critical for substrate transport, Asp25 and Arg111. Mutation of Asp25 to glutamate did not affect the transport function of styMdtM, whereas mutation to alanine reduced its transport activity, suggesting that a negative charge at this position is critical for substrate translocation across the membrane. Substrate-affinity measurements by intrinsic fluorescence spectroscopy showed that the Asp25Ala mutant retained its capacity to bind substrate, albeit at a lower level. Mutation of Arg111 to alanine resulted in a decrease in secondary structure content of the transporter, and mutation to lysine completely destabilized the structure of the transporter. A homology model of styMdtM suggests that Arg111 is important for stabilizing the transmembrane domain by mediating necessary interactions between neighboring helices. Together, our studies provide new structural and mechanistic insights into the Salmonella MDR transporter styMdtM.
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Affiliation(s)
- Aqsa Shaheen
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus, Gujrat, Pakistan
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Fouzia Ismat
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Mazhar Iqbal
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Abdul Haque
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Akhuwat First University, 250 R.B, Bardakay, Near Abbaspur Railway Station, University Park, Faisalabad, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rita De Zorzi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Current address: Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri, 1 – 34127 Trieste, Italy
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Current address: Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, NY 10065, USA
| | - Moazur Rahman
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- School of Biological Sciences, University of the Punjab, Lahore
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11
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Pankova SM, Sakibaev FA, Holyavka MG, Vyshkvorkina YM, Lukin AN, Artyukhov VG. Studies of the Processes of the Trypsin Interactions with Ion Exchange Fibers and Chitosan. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021030146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Abstract
FTIR spectroscopy has been widely used to characterize biopharmaceuticals for many years, in particular to analyze protein structure. More recently, it was demonstrated to be a useful tool to study and compare protein samples in terms of glycosylation. Based on a spectral region specific to carbohydrate absorption, we present here a detailed protocol to compare the FTIR spectra of glycoproteins in terms of global glycosylation level and in terms of glycan composition. This FTIR information is compared to MS information. Both approaches yield consistent results but it appears FTIR analysis is easier and more rapid to perform comparisons.
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13
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Saidani H, Léonetti M, Kmita H, Homblé F. The Open State Selectivity of the Bean Seed VDAC Depends on Stigmasterol and Ion Concentration. Int J Mol Sci 2021; 22:ijms22063034. [PMID: 33809742 PMCID: PMC8002290 DOI: 10.3390/ijms22063034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 11/16/2022] Open
Abstract
The voltage-dependent anion channel (VDAC) is the major pathway for metabolites and ions transport through the mitochondrial outer membrane. It can regulate the flow of solutes by switching to a low conductance state correlated with a selectivity reversal, or by a selectivity inversion of its open state. The later one was observed in non-plant VDACs and is poorly characterized. We aim at investigating the selectivity inversion of the open state using plant VDAC purified from Phaseolus coccineus (PcVDAC) to evaluate its physiological role. Our main findings are: (1) The VDAC selectivity inversion of the open state occurs in PcVDAC, (2) Ion concentration and stigmasterol affect the occurrence of the open state selectivity inversion and stigmasterol appears to interact directly with PcVDAC. Interestingly, electrophysiological data concerning the selectivity inversion of the PcVDAC open state suggests that the phenomenon probably does not have a significant physiological effect in vivo.
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Affiliation(s)
- Hayet Saidani
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 206/2, B-1050 Bruxelles, Belgium;
- Laboratory of Functional Neurophysiology and Pathology, Research Unit, UR/11ES09, Department of Biological Sciences, Faculty of Science of Tunis, University Tunis El Manar, 1068 Tunis, Tunisia
| | - Marc Léonetti
- Université de. Grenoble Alpes, CNRS, LRP, 38000 Grenoble, France;
| | - Hanna Kmita
- Department of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland;
| | - Fabrice Homblé
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 206/2, B-1050 Bruxelles, Belgium;
- Correspondence: ; Tel.: +32-2-650-5383
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14
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Abstract
In this chapter, we describe how Fourier transform infrared spectroscopy (FTIR) can be applied in cryobiological research to study: structure and thermal properties of biomolecules in cells and tissues, physical properties of cryopreservation and freeze-drying formulations, and permeation of molecules into cells and tissues. An infrared spectrum gives information about characteristic molecular vibrations of specific groups in molecules, whereas the temperature dependence of specific infrared bands may reveal information about conformational and phase changes. Infrared spectroscopy is minimally invasive and does not require labeling, whereas spectra can be recorded in any physical state of a sample. Data acquisition and spectral processing procedures are described to study phase state changes of protective formulations, cell membrane phase behavior during freezing and drying, protein denaturation during heating, and permeation of protective molecules into tissues. The latter can be used to estimate incubation times needed to load tissues with sufficient amounts of protective agents for cryopreservation or freeze-drying.
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15
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De Meutter J, Goormaghtigh E. FTIR Imaging of Protein Microarrays for High Throughput Secondary Structure Determination. Anal Chem 2021; 93:3733-3741. [PMID: 33577285 DOI: 10.1021/acs.analchem.0c03677] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The paper introduces a new method designed for high-throughput protein structure determination. It is based on spotting proteins as microarrays at a density of ca. 2000-4000 samples per cm2 and recording Fourier transform infrared (FTIR) spectra by FTIR imaging. It also introduces a new protein library, called cSP92, which contains 92 well-characterized proteins. It has been designed to cover as well as possible the structural space, both in terms of secondary structures and higher level structures. Ascending stepwise linear regression (ASLR), partial least square (PLS) regression, and support vector machine (SVM) have been used to correlate spectral characteristics to secondary structure features. ASLR generally provides better results than PLS and SVM. The observation that secondary structure prediction is as good for protein microarray spectra as for the reference attenuated total reflection spectra recorded on the same samples validates the high throughput microarray approach. Repeated double cross-validation shows that the approach is suitable for the high accuracy determination of the protein secondary structure with root mean square standard error in the cross-validation of 4.9 ± 1.1% for α-helix, 4.6 ± 0.8% for β-sheet, and 6.3 ± 2.2% for the "other" structures when using ASLR.
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Affiliation(s)
- Joëlle De Meutter
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Campus Plaine, Université Libre de Bruxelles, CP206/2, B1050 Brussels, Belgium
| | - Erik Goormaghtigh
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Campus Plaine, Université Libre de Bruxelles, CP206/2, B1050 Brussels, Belgium
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16
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Liu Q, Wan K, Shang Y, Wang ZG, Zhang Y, Dai L, Wang C, Wang H, Shi X, Liu D, Ding B. Cofactor-free oxidase-mimetic nanomaterials from self-assembled histidine-rich peptides. NATURE MATERIALS 2021; 20:395-402. [PMID: 33257794 DOI: 10.1038/s41563-020-00856-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/14/2020] [Indexed: 05/21/2023]
Abstract
Natural oxidases mainly rely on cofactors and well-arranged amino acid residues for catalysing electron-transfer reactions but suffer from non-recovery of their activity upon externally induced protein unfolding. However, it remains unknown whether residues at the active site can catalyse similar reactions in the absence of the cofactor. Here, we describe a series of self-assembling, histidine-rich peptides, as short as a dipeptide, with catalytic function similar to that of haem-dependent peroxidases. The histidine residues of the peptide chains form periodic arrays that are able to catalyse H2O2 reduction reactions efficiently through the formation of reactive ternary complex intermediates. The supramolecular catalyst exhibiting the highest activity could be switched between inactive and active states without loss of activity for ten cycles of heating/cooling or acidification/neutralization treatments, demonstrating the reversible assembly/disassembly of the active residues. These findings may aid the design of advanced biomimetic catalytic materials and provide a model for primitive cofactor-free enzymes.
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Affiliation(s)
- Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
| | - Kaiwei Wan
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Laboratory of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing, China.
| | - Yiyang Zhang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, China
| | - Luru Dai
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
| | - Chen Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China.
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China.
- University of the Chinese Academy of Sciences, Beijing, People's Republic of China.
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17
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Amino acid side chain contribution to protein FTIR spectra: impact on secondary structure evaluation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:641-651. [PMID: 33558954 PMCID: PMC8189991 DOI: 10.1007/s00249-021-01507-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/13/2021] [Accepted: 01/25/2021] [Indexed: 01/25/2023]
Abstract
Prediction of protein secondary structure from FTIR spectra usually relies on the absorbance in the amide I–amide II region of the spectrum. It assumes that the absorbance in this spectral region, i.e., roughly 1700–1500 cm−1 is solely arising from amide contributions. Yet, it is accepted that, on the average, about 20% of the absorbance is due to amino acid side chains. The present paper evaluates the contribution of amino acid side chains in this spectral region and the potential to improve secondary structure prediction after correcting for their contribution. We show that the β-sheet content prediction is improved upon subtraction of amino acid side chain contributions in the amide I–amide II spectral range. Improvement is relatively important, for instance, the error of prediction of β-sheet content decreases from 5.42 to 4.97% when evaluated by ascending stepwise regression. Other methods tested such as partial least square regression and support vector machine have also improved accuracy for β-sheet content evaluation. The other structures such as α-helix do not significantly benefit from side chain contribution subtraction, in some cases prediction is even degraded. We show that co-linearity between secondary structure content and amino acid composition is not a main limitation for improving secondary structure prediction. We also show that, even though based on different criteria, secondary structures defined by DSSP and XTLSSTR both arrive at the same conclusion: only the β-sheet structure clearly benefits from side chain subtraction. It must be concluded that side chain contribution subtraction benefit for the evaluation of other secondary structure contents is limited by the very rough description of side chain absorbance which does not take into account the variations related to their environment. The study was performed on a large protein set. To deal with the large number of proteins present, we worked on protein microarrays deposited on BaF2 slides and FTIR spectra were acquired with an imaging system.
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18
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Evaluation of protein secondary structure from FTIR spectra improved after partial deuteration. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:613-628. [PMID: 33534058 PMCID: PMC8189984 DOI: 10.1007/s00249-021-01502-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 11/11/2022]
Abstract
FTIR spectroscopy has become a major tool to determine protein secondary structure. One of the identified obstacle for reaching better predictions is the strong overlap of bands assigned to different secondary structures. Yet, while for instance disordered structures and α-helical structures absorb almost at the same wavenumber, the absorbance bands are differentially shifted upon deuteration, in part because exchange is much faster for disordered structures. We recorded the FTIR spectra of 85 proteins at different stages of hydrogen/deuterium exchange process using protein microarrays and infrared imaging for high throughput measurements. Several methods were used to relate spectral shape to secondary structure content. While in absolute terms, β-sheet is always better predicted than α-helix content, results consistently indicate an improvement of secondary structure predictions essentially for the α-helix and the category called “Others” (grouping random, turns, bends, etc.) after 15 min of exchange. On the contrary, the β-sheet fraction is better predicted in non-deuterated conditions. Using partial least square regression, the error of prediction for the α-helix content is reduced after 15-min deuteration. Further deuteration degrades the prediction. Error on the prediction for the “Others” structures also decreases after 15-min deuteration. Cross-validation or a single 25-protein test set result in the same overall conclusions.
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19
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De Meutter J, Goormaghtigh E. Searching for a Better Match between Protein Secondary Structure Definitions and Protein FTIR Spectra. Anal Chem 2021; 93:1561-1568. [PMID: 33332103 DOI: 10.1021/acs.analchem.0c03943] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Obtaining protein secondary structure content from high-resolution structures requires definitions and thresholds for the various parameters involved, typically hydrogen bond energy or length/angle and backbone φ/ψ angles. Several definitions are currently used and can have a profound impact on secondary structure content. Fourier transform infrared (FTIR) spectroscopy has its own sensitivity to molecular geometry. It is, therefore, important to select a set of definitions that matches this sensitivity. Here, we used a new protein set consisting of 92 proteins designed for the calibration of spectroscopic methods. Spectra have been obtained from protein microarrays in a high throughput process. The potential for improving secondary structure predictions from FTIR spectra has been tested using 71 structures determined according to different definitions. The paper demonstrates that different secondary structure definitions result in large variations in secondary structure content that are not equivalent in view of the protein FTIR spectra. The prediction quality factor ζ can be improved by ca. 20-50% by selecting an adequate definition set. The results also indicate that the dictionary of secondary structure of proteins (DSSP) algorithm, which is currently widely used to evaluate protein secondary structure content, is a good choice when dealing with FTIR spectra.
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Affiliation(s)
- Joëlle De Meutter
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Université Libre de Bruxelles, Campus Plaine CP206/2, B1050 Brussels, Belgium
| | - Erik Goormaghtigh
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Université Libre de Bruxelles, Campus Plaine CP206/2, B1050 Brussels, Belgium
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20
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Bernier SC, Millette MA, Roy S, Cantin L, Coutinho A, Salesse C. Structural information and membrane binding of truncated RGS9-1 Anchor Protein and its C-terminal hydrophobic segment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183566. [PMID: 33453187 DOI: 10.1016/j.bbamem.2021.183566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/22/2020] [Accepted: 01/10/2021] [Indexed: 01/19/2023]
Abstract
Visual phototransduction takes place in photoreceptor cells. Light absorption by rhodopsin leads to the activation of transducin as a result of the exchange of its GDP for GTP. The GTP-bound ⍺-subunit of transducin then activates phosphodiesterase (PDE), which in turn hydrolyzes cGMP leading to photoreceptor hyperpolarization. Photoreceptors return to the dark state upon inactivation of these proteins. In particular, PDE is inactivated by the protein complex R9AP/RGS9-1/Gβ5. R9AP (RGS9-1 anchor protein) is responsible for the membrane anchoring of this protein complex to photoreceptor outer segment disk membranes most likely by the combined involvement of its C-terminal hydrophobic domain as well as other types of interactions. This study thus aimed to gather information on the structure and membrane binding of the C-terminal hydrophobic segment of R9AP as well as of truncated R9AP (without its C-terminal domain, R9AP∆TM). Circular dichroism and infrared spectroscopic measurements revealed that the secondary structure of R9AP∆TM mainly includes ⍺-helical structural elements. Moreover, intrinsic fluorescence measurements of native R9AP∆TM and individual mutants lacking one tryptophan demonstrated that W79 is more buried than W173 but that they are both located in a hydrophobic environment. This method also revealed that membrane binding of R9AP∆TM does not involve regions near its tryptophan residues, while infrared spectroscopy validated its binding to lipid vesicles. Additional fluorescence measurements showed that the C-terminal segment of R9AP is membrane embedded. Maximum insertion pressure and synergy data using Langmuir monolayers suggest that interactions with specific phospholipids could be involved in the membrane binding of R9AP∆TM.
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Affiliation(s)
- Sarah C Bernier
- CUO-Recherche, Centre de recherche du CHU de Québec and Département d'ophtalmologie, Faculté de Médecine, and Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Marc-Antoine Millette
- CUO-Recherche, Centre de recherche du CHU de Québec and Département d'ophtalmologie, Faculté de Médecine, and Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Sarah Roy
- CUO-Recherche, Centre de recherche du CHU de Québec and Département d'ophtalmologie, Faculté de Médecine, and Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Line Cantin
- CUO-Recherche, Centre de recherche du CHU de Québec and Département d'ophtalmologie, Faculté de Médecine, and Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada
| | - Ana Coutinho
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Department of Chemistry and Biochemistry, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Christian Salesse
- CUO-Recherche, Centre de recherche du CHU de Québec and Département d'ophtalmologie, Faculté de Médecine, and Regroupement Stratégique PROTEO, Université Laval, Québec, Québec, Canada.
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21
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Wang Y, Wang X, Yu L, Tian Y, Li S, Leng F, Ma J, Chen J. Effects of Sr 2 + on the preparation of Escherchia coli DH5α competent cells and plasmid transformation. PeerJ 2020. [DOI: 10.7717/peerj.9480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial gene transformation used with Escherichia coli as a desired microorganism is one of the important techniques in genetic engineering. In this study, the preparation of E. coli DH5α competent cells treated with SrCl2 and transformation by heat-shock with pUC19 plasmid was optimized by Response Surface Methodology (RSM). Other five E. coli strains including BL21 (DE3), HB-101, JM109, TOP10 and TG1, three different sizes plasmids (pUC19, pET32a, pPIC9k) were used to verify the protocol, respectively. The transformation mechanism was explored by scanning electron microscope combined with energy dispersive spectrometer (SEM-EDS), atomic absorption spectroscopy (AAS) and Fourier-transform infrared spectroscopy (FT-IR). An equation of regression model was obtained, and the ideal parameters were Sr2 + ions of 90 mM, heat-shock time of 90 s and 9 ng of plasmid. Under this conditions, the transformation efficiency could almost reach to 106 CFU/µg DNA. A small change of the cell surface structure has been observed between E. coli DH5α strain and competent cells by abovementioned spectrum technologies, which implied that a strict regulation mechanism involved in the formation of competent cells and transformation of plasmids. An equation of regression model for the competent cells preparation and plasmid transformation could be applied in gene cloning technology
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Affiliation(s)
- Yonggang Wang
- School of Energy and Power Engineering, Lanzhou University of Technology, Lan Zhou, Gansu, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Xinjian Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Linmiao Yu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Yuan Tian
- Lhasa National Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modelling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Shaowei Li
- Lhasa National Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modelling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Feifan Leng
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Jianzhong Ma
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Jixiang Chen
- School of Energy and Power Engineering, Lanzhou University of Technology, Lan Zhou, Gansu, China
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
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22
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De Meutter J, Goormaghtigh E. A convenient protein library for spectroscopic calibrations. Comput Struct Biotechnol J 2020; 18:1864-1876. [PMID: 32728409 PMCID: PMC7369421 DOI: 10.1016/j.csbj.2020.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/14/2022] Open
Abstract
While several Raman, CD or FTIR spectral libraries are available for well-characterized proteins of known structure, proteins themselves are usually very difficult to acquire, preventing a convenient calibration of new instruments and new recording methods. The problem is particularly critical in the field of FTIR spectroscopy where numerous new methods are becoming available on the market. The present papers reports the construction of a protein library (cSP92) including commercially available products, that are well characterized experimentally for their purity and solubility in conditions compatible with the recording of FTIR spectra and whose high-resolution structure is available. Overall, 92 proteins were selected. These proteins cover well the CATH space at the level of classes and architectures. In terms of secondary structure content, an analysis of their high-resolution structure by DSSP shows that the mean content in the different secondary structures present in cSP92 is very similar to the mean content found in the PDB. The 92-protein set is analyzed in details for the distribution of helix length, number of strands in β- sheets, length of β-strands and amino acid content, all features that may be important for the interpretation of FTIR spectra.
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Affiliation(s)
- Joëlle De Meutter
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Campus Plaine CP206/02, Brussels, Belgium
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23
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Singh A, Upadhyay V, Singh A, Panda AK. Structure-Function Relationship of Inclusion Bodies of a Multimeric Protein. Front Microbiol 2020; 11:876. [PMID: 32457730 PMCID: PMC7225587 DOI: 10.3389/fmicb.2020.00876] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 04/15/2020] [Indexed: 12/17/2022] Open
Abstract
High level expression of recombinant proteins in bacteria often results in their aggregation into inclusion bodies. Formation of inclusion bodies poses a major bottleneck in high-throughput recovery of recombinant protein. These aggregates have amyloid-like nature and can retain biological activity. Here, effect of expression temperature on the quality of Escherichia coli asparaginase II (a tetrameric protein) inclusion bodies was evaluated. Asparaginase was expressed as inclusion bodies at different temperatures. Purified inclusion bodies were checked for biological activities and analyzed for structural properties in order to establish a structure-activity relationship. Presence of activity in inclusion bodies showed the existence of properly folded asparaginase tetramers. Expression temperature affected the properties of asparaginase inclusion bodies. Inclusion bodies expressed at higher temperatures were characterized by higher biological activity and less amyloid content as evident by Thioflavin T binding and Fourier Transform Infrared (FTIR) spectroscopy. Complex kinetics of proteinase K digestion of asparaginase inclusion bodies expressed at higher temperatures indicate higher extent of conformational heterogeneity in these aggregates.
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Affiliation(s)
- Anupam Singh
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Vaibhav Upadhyay
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Akansha Singh
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Amulya K Panda
- Product Development Cell, National Institute of Immunology, New Delhi, India
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24
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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25
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McGivney E, Cederholm L, Barth A, Hakkarainen M, Hamacher-Barth E, Ogonowski M, Gorokhova E. Rapid Physicochemical Changes in Microplastic Induced by Biofilm Formation. Front Bioeng Biotechnol 2020; 8:205. [PMID: 32266235 PMCID: PMC7103643 DOI: 10.3389/fbioe.2020.00205] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/02/2020] [Indexed: 11/23/2022] Open
Abstract
Risk assessment of microplastic (MP) pollution requires understanding biodegradation processes and related changes in polymer properties. In the environment, there are two-way interactions between the MP properties and biofilm communities: (i) microorganisms may prefer some surfaces, and (ii) MP surface properties change during the colonization and weathering. In a 2-week experiment, we studied these interactions using three model plastic beads (polyethylene [PE], polypropylene [PP], and polystyrene [PS]) exposed to ambient bacterioplankton assemblage from the Baltic Sea; the control beads were exposed to bacteria-free water. For each polymer, the physicochemical properties (compression, crystallinity, surface chemistry, hydrophobicity, and surface topography) were compared before and after exposure under controlled laboratory conditions. Furthermore, we characterized the bacterial communities on the MP surfaces using 16S rRNA gene sequencing and correlated community diversity to the physicochemical properties of the MP. Significant changes in PE crystallinity, PP stiffness, and PS maximum compression were observed as a result of exposure to bacteria. Moreover, there were significant correlations between bacterial diversity and some physicochemical characteristics (crystallinity, stiffness, and surface roughness). These changes coincided with variation in the relative abundance of unique OTUs, mostly related to the PE samples having significantly higher contribution of Sphingobium, Novosphingobium, and uncultured Planctomycetaceae compared to the other test materials, whereas PP and PS samples had significantly higher abundance of Sphingobacteriales and Alphaproteobacteria, indicating possible involvement of these taxa in the initial biodegradation steps. Our findings demonstrate measurable signs of MP weathering under short-term exposure to environmentally relevant microbial communities at conditions resembling those in the water column. A systematic approach for the characterization of the biodegrading capacity in different systems will improve the risk assessment of plastic litter in aquatic environments.
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Affiliation(s)
- Eric McGivney
- Department of Environmental Science, Stockholm University, Stockholm, Sweden
| | - Linnea Cederholm
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Minna Hakkarainen
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Martin Ogonowski
- Department of Environmental Science, Stockholm University, Stockholm, Sweden
| | - Elena Gorokhova
- Department of Environmental Science, Stockholm University, Stockholm, Sweden
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Zafar M, Shah MA, Shehzad A, Tariq A, Habib M, Muddassar M, Shah MS, Iqbal M, Hemmatzadeh F, Rahman M. Characterization of the highly immunogenic VP2 protrusion domain as a diagnostic antigen for members of Birnaviridae family. Appl Microbiol Biotechnol 2020; 104:3391-3402. [PMID: 32088761 PMCID: PMC7222154 DOI: 10.1007/s00253-020-10458-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/31/2020] [Accepted: 02/10/2020] [Indexed: 11/13/2022]
Abstract
Birnaviridae is a family of viruses (birnaviruses) which consists of four genera, members of which cause diseases in fish, birds, mollusks, and insects. The genome of birnaviruses encodes the highly immunogenic VP2 capsid protein. In order to demonstrate that the VP2 protein can be exploited as a diagnostic antigen for birnaviruses, we developed a lateral flow assay based on the surface-exposed VP2 protrusion domain of a representative birnavirus, infectious bursal disease virus (IBDV) of serotype 1 which causes the highly devastating infectious bursal disease in chickens. The biophysical characterization of the purified domain reveals that the domain predominantly consists of β-sheets, exists in a trimeric form, and remains folded at high temperatures, making it suitable for diagnostic purposes. Owing to its highly immunogenic nature and excellent biophysical properties, we employed the VP2 protrusion domain in a gold nanoparticle-based lateral flow assay for rapid detection of anti-IBDV antibodies in serum samples of infected chickens. Our results indicate that the domain binds anti-IBDV antibodies with high specificity during laboratory testing and on-site testing. The lateral flow assay reported here yields comparable results in a qualitative manner as obtained through a commercial enzyme-linked immunosorbent assay (ELISA). As VP2 is a common capsid protein of birnaviruses, the lateral flow assay can be generalized for other birnaviruses, and members of Tetraviridae and Nodaviridae families which contain homologous VP2 capsid proteins.
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Affiliation(s)
- Maryam Zafar
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), P.O. Nilore, Islamabad, Pakistan.,School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, South Australia,, 5371, Australia
| | - Majid Ali Shah
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), P.O. Nilore, Islamabad, Pakistan
| | - Aamir Shehzad
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), P.O. Nilore, Islamabad, Pakistan
| | - Anam Tariq
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), P.O. Nilore, Islamabad, Pakistan
| | - Mudasser Habib
- Vaccine Development Group, Animal Sciences Division, NIAB, Faisalabad, Pakistan
| | - Muhammad Muddassar
- Department of Biosciences, COMSATS-University Islamabad, Park Road, Islamabad, Pakistan
| | | | - Mazhar Iqbal
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), P.O. Nilore, Islamabad, Pakistan
| | - Farhid Hemmatzadeh
- School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, South Australia,, 5371, Australia.
| | - Moazur Rahman
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan. .,Pakistan Institute of Engineering and Applied Sciences (PIEAS), P.O. Nilore, Islamabad, Pakistan. .,School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, South Australia,, 5371, Australia.
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Ullah R, Shehzad A, Shah MA, March MD, Ismat F, Iqbal M, Onesti S, Rahman M, McPherson MJ. C-Terminal Domain of the Human Zinc Transporter hZnT8 Is Structurally Indistinguishable from Its Disease Risk Variant (R325W). Int J Mol Sci 2020; 21:ijms21030926. [PMID: 32023808 PMCID: PMC7037036 DOI: 10.3390/ijms21030926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/17/2020] [Accepted: 01/19/2020] [Indexed: 02/07/2023] Open
Abstract
The human zinc transporter 8 (hZnT8) plays important roles in the storage of insulin in the secretory vesicles of pancreatic β cells. hZnT8 consists of a transmembrane domain, with its N- and C-termini protruding into the cytoplasm. Interestingly, the exchange of arginine to tryptophan at position 325 in the C-terminal domain (CTD) increases the risk of developing type 2 diabetes mellitus (T2D). In the present study, the CTDs of hZnT8 (the wild-type (WT) and its disease risk variant (R325W)) were expressed, purified, and characterized in their native forms by biophysical techniques. The data reveal that the CTDs form tetramers which are stabilized by zinc binding, and exhibit negligible differences in their secondary structure content and zinc-binding affinities in solution. These findings provide the basis for conducting further structural studies aimed at unravelling the molecular mechanism underlying the increased susceptibility to develop T2D, which is modulated by the disease risk variant.
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Affiliation(s)
- Raheem Ullah
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 44000, Pakistan; (R.U.); (A.S.); (M.A.S.); (F.I.); (M.I.)
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (M.D.M.); (S.O.)
| | - Aamir Shehzad
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 44000, Pakistan; (R.U.); (A.S.); (M.A.S.); (F.I.); (M.I.)
| | - Majid Ali Shah
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 44000, Pakistan; (R.U.); (A.S.); (M.A.S.); (F.I.); (M.I.)
| | - Matteo De March
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (M.D.M.); (S.O.)
| | - Fouzia Ismat
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 44000, Pakistan; (R.U.); (A.S.); (M.A.S.); (F.I.); (M.I.)
| | - Mazhar Iqbal
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 44000, Pakistan; (R.U.); (A.S.); (M.A.S.); (F.I.); (M.I.)
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (M.D.M.); (S.O.)
| | - Moazur Rahman
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 44000, Pakistan; (R.U.); (A.S.); (M.A.S.); (F.I.); (M.I.)
- Correspondence: (M.R.); (M.J.M.); Tel.: +92-41-920-1407 (M.R.); +44-113-343-2595 (M.J.M.)
| | - Michael J. McPherson
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
- Correspondence: (M.R.); (M.J.M.); Tel.: +92-41-920-1407 (M.R.); +44-113-343-2595 (M.J.M.)
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28
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Sharma V, Srinivasan A, Roychoudhury A, Rani K, Tyagi M, Dev K, Nikolajeff F, Kumar S. Characterization of protein extracts from different types of human teeth and insight in biomineralization. Sci Rep 2019; 9:9314. [PMID: 31249316 PMCID: PMC6597790 DOI: 10.1038/s41598-019-44268-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/09/2019] [Indexed: 12/20/2022] Open
Abstract
The present study describes an efficient method for isolation and purification of protein extracts from four types of human teeth i.e. molar, premolar, canine, and incisor. Detailed structural characterization of these protein extracts was done by Fourier transform infrared spectroscopy (FTIR) and circular dichroism (CD) which showed that a major fraction of the proteins present are unstructured in nature including primarily random coils in addition to the other structures like extended beta (β) structure, poly-l-proline-type II (PPII) helix, turns, with only a small fraction constituting of ordered structures like alpha (α) helix and β sheets. These resultant labile structures give the proteins the necessary flexibility that they require to interact with a variety of substrates including different ions like calcium and phosphates and for other protein-protein interactions. We also did initial studies on the mineralization of calcium phosphate with the protein extracts. Nanoparticle tracking analysis (NTA) show an increase in the size of calcium phosphate accumulation in the presence of protein extracts. We propose that protein extracts elevate the crystallization process of calcium phosphate. Our current biophysical study provides novel insights into the structural characterization of proteins from human teeth and their implications in understanding the tooth biomineralization. As per our knowledge, this is the first report which focuses on the whole protein extraction from different types of human teeth as these extracts imitate the in vivo tooth mineralization.
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Affiliation(s)
- Vaibhav Sharma
- Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | | | - Ajoy Roychoudhury
- Department of Oral and Maxillofacial Surgery, Center for Dental Education and Research (CDER), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Komal Rani
- Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Mitali Tyagi
- Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Kapil Dev
- Department of Biotechnology, Jamia Milia Islamia, New Delhi, India
| | - Fredrik Nikolajeff
- Department of Engineering Science, Uppsala University, Uppsala, 75105, Sweden
| | - Saroj Kumar
- Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi, India.
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Kitjanukit S, Sasaki K, Okibe N. Production of highly catalytic, archaeal Pd(0) bionanoparticles using Sulfolobus tokodaii. Extremophiles 2019; 23:549-556. [PMID: 31218490 DOI: 10.1007/s00792-019-01106-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 06/09/2019] [Indexed: 01/25/2023]
Abstract
The thermo-acidophilic archaeon, Sulfolobus tokodaii, was utilized for the production of Pd(0) bionanoparticles from acidic Pd(II) solution. Use of active cells was essential to form well-dispersed Pd(0) nanoparticles located on the cell surface. The particle size could be manipulated by modifying the concentration of formate (as electron donor; e-donor) and by addition of enzymatic inhibitor (Cu2+) in the range of 14-63 nm mean size. Since robust Pd(II) reduction progressed in pre-grown S. tokodaii cells even in the presence of up to 500 mM Cl-, it was possible to conversely utilize the effect of Cl- to produce even finer and denser particles in the range of 8.7-15 nm mean size. This effect likely resulted from the increasing stability of anionic Pd(II)-chloride complex at elevated Cl- concentrations, eventually allowing involvement of greater number of initial Pd(0) crystal nucleation sites (enzymatic sites). The catalytic activity [evaluated based on Cr(VI) reduction reaction] of Pd(0) bionanoparticles of varying particle size formed under different conditions were compared. The finest Pd(0) bionanoparticles obtained at 50 mM Cl- (mean 8.7 nm; median 5.6 nm) exhibited the greatest specific Cr(VI) reduction rate, with four times higher catalytic activity compared to commercial Pd/C. The potential applicability of S. tokodaii cells in the recovery of highly catalytic Pd(0) nanoparticles from actual acidic chloride leachate was, thus, suggested.
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Affiliation(s)
- Santisak Kitjanukit
- Department of Earth Resource Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Keiko Sasaki
- Department of Earth Resource Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Naoko Okibe
- Department of Earth Resource Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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30
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Fezoua-Boubegtiten Z, Hastoy B, Scotti P, Milochau A, Bathany K, Desbat B, Castano S, Oda R, Lang J. The transmembrane domain of the SNARE protein VAMP2 is highly sensitive to its lipid environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:670-676. [DOI: 10.1016/j.bbamem.2018.12.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/15/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022]
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31
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Acikgoz E, Güler G, Camlar M, Oktem G, Aktug H. Glycogen synthase kinase-3 inhibition in glioblastoma multiforme cells induces apoptosis, cell cycle arrest and changing biomolecular structure. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 209:150-164. [PMID: 30388586 DOI: 10.1016/j.saa.2018.10.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/13/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
Glioblastoma multiforme (GBM) is the most malignant and aggressive primary human brain tumors. The regulatory pathways of apoptosis are altered in GBMs, leading to a survival advantage of the tumor cells. Thus, identification of target molecules, which are effective in triggering of the cell death mechanisms in GBM, is an essential strategy for therapeutic purposes. Glycogen synthase kinase-3 (GSK-3) plays an important role in apoptosis, proliferation and cell cycle. This study focused on the effect of GSK-3 inhibitor IX in the GBM cells. Apoptosis induction was determined by Annexin-V assay, multicaspase activity and immunofluorescence analyses. Concentration-dependent effects of GSK-3 inhibitor IX on the cell cycle were also evaluated. Moreover, the effect of GSK inhibitor on the cellular biomolecules was assessed by using ATR-FTIR spectroscopy. Our assay results indicated that GSK-3 inhibitor IX induces apoptosis, resulting in a significant increase in the expression of caspase-3 and caspase-8 proteins. Cell cycle analyses revealed that GSK-3 inhibitor IX leads to dose-dependent G2/M-phase cell cycle arrest. Based on the FTIR data, treatment of GBM cells causes dysregulation in the carbohydrate metabolism and induces apoptotic cell death which was characterized by the spectral alterations in nucleic acids, an increment in the lipid amount with disordering state and compositional changes in the cellular proteins. These findings suggest that GSK-3 inhibitor IX exhibits anti-cancer effects by inducing apoptosis and changing biomolecular structure of membrane lipids, carbohydrates, nucleic acids and proteins, and thus, may be further evaluated as a potential effective candidate agent for the GBM combination therapies.
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Affiliation(s)
- Eda Acikgoz
- Department of Histology and Embryology, Faculty of Medicine, Ege University, 35100 Izmir, Turkey; Department of Histology and Embryology, Faculty of Medicine, Yuzuncu Yil University, 65080 Van, Turkey.
| | - Günnur Güler
- Center for Drug Research & Development and Pharmacokinetic Applications (ARGEFAR), Ege University, 35100 Izmir, Turkey.
| | - Mahmut Camlar
- Department of Neurosurgery, Sağlık Bilimleri University Izmir Tepecik Education and Research Hospital, Izmir 35100, Turkey
| | - Gulperi Oktem
- Department of Histology and Embryology, Faculty of Medicine, Ege University, 35100 Izmir, Turkey
| | - Huseyin Aktug
- Department of Histology and Embryology, Faculty of Medicine, Ege University, 35100 Izmir, Turkey
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32
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Activation and conformational changes of chitinase induced by ultrasound. Food Chem 2019; 285:355-362. [PMID: 30797357 DOI: 10.1016/j.foodchem.2019.01.180] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/27/2018] [Accepted: 01/28/2019] [Indexed: 12/19/2022]
Abstract
This study investigated the effect of ultrasound on chitinase activity and conformational changes. Results revealed that ultrasound activated chitinase with a maximum enhancement of 19.17% compared with the untreated chitinase. Furthermore, an increase of Vmax and a decrease of Km after sonication were obtained, illustrating that the affinity between chitinase and substrate was intensified. No obvious effect on the tolerance to most metal ions was exhibited whether sonicated or not (p > 0.05). The conformational changes of chitinase were analyzed by circular dichroism (CD), Fourier transform infrared (FTIR), Raman and fluorescence spectroscopy. Results indicated that the activation of chitinase induced by ultrasound was presumably due to the decrease of tryptophan on the chitinase surface and the increase of β-sheet and random coil in chitinase secondary conformation. In brief, ultrasound is a possible way to activate chitinase to increase its application in food industry.
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Güldenhaupt J, Amaral M, Kötting C, Schartner J, Musil D, Frech M, Gerwert K. Zeitaufgelöst und markerfrei gemessene ligandeninduzierte Konformationsänderungen von HSP90 - hin zu einem Konformationsaktivitätsscreening für die Wirkstoffentwicklung. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jörn Güldenhaupt
- Lehrstuhl für Biophysik; Ruhr-Universität Bochum; 44780 Bochum Deutschland
| | - Marta Amaral
- Molecular Interactions and Biophysics; Merck KGaA; Frankfurter Straße 250 64293 Darmstadt Deutschland
- Derzeitige Adresse: Sanofi-Aventis (Deutschland) GmbH; Biologics Research/ Protein Therapeutics; Frankfurt am Main Deutschland
| | - Carsten Kötting
- Lehrstuhl für Biophysik; Ruhr-Universität Bochum; 44780 Bochum Deutschland
| | - Jonas Schartner
- Lehrstuhl für Biophysik; Ruhr-Universität Bochum; 44780 Bochum Deutschland
| | - Djordje Musil
- Molecular Interactions and Biophysics; Merck KGaA; Frankfurter Straße 250 64293 Darmstadt Deutschland
| | - Matthias Frech
- Molecular Interactions and Biophysics; Merck KGaA; Frankfurter Straße 250 64293 Darmstadt Deutschland
| | - Klaus Gerwert
- Lehrstuhl für Biophysik; Ruhr-Universität Bochum; 44780 Bochum Deutschland
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Güldenhaupt J, Amaral M, Kötting C, Schartner J, Musil D, Frech M, Gerwert K. Ligand-Induced Conformational Changes in HSP90 Monitored Time Resolved and Label Free-Towards a Conformational Activity Screening for Drug Discovery. Angew Chem Int Ed Engl 2018; 57:9955-9960. [PMID: 29772085 PMCID: PMC6099472 DOI: 10.1002/anie.201802603] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Indexed: 11/25/2022]
Abstract
Investigation of protein–ligand interactions is crucial during early drug‐discovery processes. ATR‐FTIR spectroscopy can detect label‐free protein–ligand interactions with high spatiotemporal resolution. Here we immobilized, as an example, the heat shock protein HSP90 on an ATR crystal. This protein is an important molecular target for drugs against several diseases including cancer. With our novel approach we investigated a ligand‐induced secondary structural change. Two specific binding modes of 19 drug‐like compounds were analyzed. Different binding modes can lead to different efficacy and specificity of different drugs. In addition, the kobs values of ligand dissociation were obtained. The results were validated by X‐ray crystallography for the structural change and by SPR experiments for the dissociation kinetics, but our method yields all data in a single and simple experiment.
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Affiliation(s)
- Jörn Güldenhaupt
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Marta Amaral
- Molecular Interactions and Biophysics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany.,Current address: Sanofi-Aventis (Deutschland) GmbH, Biologics Research/Protein Therapeutics, Frankfurt am Main, Germany
| | - Carsten Kötting
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Jonas Schartner
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Djordje Musil
- Molecular Interactions and Biophysics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Matthias Frech
- Molecular Interactions and Biophysics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Klaus Gerwert
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, 44780, Bochum, Germany
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Itkin A, Salnikov ES, Aisenbrey C, Raya J, Glattard E, Raussens V, Ruysschaert JM, Bechinger B. Structural Characterization of the Amyloid Precursor Protein Transmembrane Domain and Its γ-Cleavage Site. ACS OMEGA 2017; 2:6525-6534. [PMID: 31457253 PMCID: PMC6645296 DOI: 10.1021/acsomega.7b00619] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/16/2017] [Indexed: 06/10/2023]
Abstract
Alzheimer's disease is the most common form of dementia that affects about 50 million of sufferers worldwide. A major role for the initiation and progression of Alzheimer's disease has been associated with the amyloid β-peptide (Aβ), which is a protease cleavage product of the amyloid precursor protein. The amyloid precursor protein is an integral membrane protein with a single transmembrane domain. Here, we assessed the structural integrity of the transmembrane domain within oriented phosphatidylcholine lipid bilayers and determined the tilt angle distribution and dynamics of various subdomains using solid-state NMR and attenuated total reflectance Fourier transform infrared spectroscopies. Although the overall secondary structure of the transmembrane domain is α-helical, pronounced conformational and topological heterogeneities were observed for the γ- and, to a lesser extent, the ζ-cleavage site, with pronounced implications for the production of Aβ and related peptides, the development of the disease, and pharmaceutical innovation.
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Affiliation(s)
- Anna Itkin
- University
of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics
and NMR, 4, rue Blaise
Pascal, F-67070 Strasbourg, France
- Center
for Structural Biology and Bioinformatics, Laboratory of Structure
and Function of Biological Membranes, Université
Libre de Bruxelles, Campus
Plaine - Acces 2 - Batiment BC - Niveau 4, Boulevard du Triomphe -
CP 206/2, B-1050 Brussels, Belgium
| | - Evgeniy S. Salnikov
- University
of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics
and NMR, 4, rue Blaise
Pascal, F-67070 Strasbourg, France
| | - Christopher Aisenbrey
- University
of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics
and NMR, 4, rue Blaise
Pascal, F-67070 Strasbourg, France
| | - Jesus Raya
- University
of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics
and NMR, 4, rue Blaise
Pascal, F-67070 Strasbourg, France
| | - Elise Glattard
- University
of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics
and NMR, 4, rue Blaise
Pascal, F-67070 Strasbourg, France
| | - Vincent Raussens
- Center
for Structural Biology and Bioinformatics, Laboratory of Structure
and Function of Biological Membranes, Université
Libre de Bruxelles, Campus
Plaine - Acces 2 - Batiment BC - Niveau 4, Boulevard du Triomphe -
CP 206/2, B-1050 Brussels, Belgium
| | - Jean-Marie Ruysschaert
- Center
for Structural Biology and Bioinformatics, Laboratory of Structure
and Function of Biological Membranes, Université
Libre de Bruxelles, Campus
Plaine - Acces 2 - Batiment BC - Niveau 4, Boulevard du Triomphe -
CP 206/2, B-1050 Brussels, Belgium
| | - Burkhard Bechinger
- University
of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics
and NMR, 4, rue Blaise
Pascal, F-67070 Strasbourg, France
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36
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Schartner J, Nabers A, Budde B, Lange J, Hoeck N, Wiltfang J, Kötting C, Gerwert K. An ATR-FTIR Sensor Unraveling the Drug Intervention of Methylene Blue, Congo Red, and Berberine on Human Tau and Aβ. ACS Med Chem Lett 2017; 8:710-714. [PMID: 28740603 DOI: 10.1021/acsmedchemlett.7b00079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/09/2017] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease affects millions of human beings worldwide. The disease progression is characterized by the formation of plaques and neurofibrillary tangles in the brain, which are based on aggregation processes of the Aβ peptide and tau protein. Today there is no cure and even no in vitro assay available for the identification of drug candidates, which provides direct information concerning the protein secondary structure label-free. Therefore, we developed an attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) sensor, which uses surface bound antibodies to immobilize a desired target protein. The secondary structure of the protein can be evaluated based on the secondary structure sensitive frequency of the amide I band. Direct information about the effect of a drug candidate on the secondary structure distribution of the total target protein fraction within the respective body fluid can be detected by a frequency shift of the amide I band. Thereby, the extent of the amide I shift is indicative for the compound efficiency. The functionality of this approach was demonstrated by the quantification of the effect of the drug candidate methylene blue on the pathogenic misfolded tau protein as extracted from cerebrospinal fluid (CSF). Methylene blue induces a shift from pathogenic folded β-sheet dominated to the healthy monomeric state. A similar effect was observed for congo red on pathogenic Aβ isoforms from CSF. In addition, the effect of berberine on synthetic Aβ1-42 is studied. Berberine seems to decelerate the aggregation process of synthetic Aβ1-42 peptides.
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Affiliation(s)
- Jonas Schartner
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Andreas Nabers
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Brian Budde
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Julia Lange
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Nina Hoeck
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Jens Wiltfang
- Department
of Psychiatry and Psychotherapy, Georg-August-University Göttingen, University Medical
Center, 37099 Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 37099 Göttingen, Germany
- iBiMED,
Medical Sciences Department, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carsten Kötting
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Klaus Gerwert
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
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Shah MA, Ullah R, March MD, Shah MS, Ismat F, Habib M, Iqbal M, Onesti S, Rahman M. Overexpression and characterization of the 100K protein of Fowl adenovirus-4 as an antiviral target. Virus Res 2017; 238:218-225. [PMID: 28666898 DOI: 10.1016/j.virusres.2017.06.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/26/2017] [Accepted: 06/27/2017] [Indexed: 10/19/2022]
Abstract
100K is an important scaffolding protein of adenoviruses including fowl adenovirus serotype 4 (FAdV-4) that causes inclusion body hepatitis-hydropericardium syndrome (IBH-HPS) in poultry. 100K carries out the trimerization of the major capsid hexon protein of the virus for the generation of new virions inside the target host cells. Despite its critical role for FAdV-4, no structural study, in particular, has been conducted so far. Here, the overexpression of soluble 100K protein was successfully carried out in E. coli using various expression constructs and purification yield of 3mg per litre culture volume was obtained. Gel filtration chromatography suggested that 100K protein exists in trimeric form. Circular dichroism and Fourier transform infrared spectroscopy clearly reveal that 100K protein folds with a high content of α-helices. The 3-dimentional homology model of the 100K protein, refined with molecular dynamics tools also depicts higher α-helical content within the protein model. Moreover, overexpressed recombinant 100K protein could be used to differentiate vaccinated and FAdV-4 infected chickens on the basis of higher serum anti 100K antibody titres. Our work provides preliminary structural and functional results to study biological role of the 100K protein and for further investigations to develop 100K inhibitors to control IBH-HPS in poultry.
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Affiliation(s)
- Majid Ali Shah
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Basovizza 34149, Trieste, Italy; Pakistan Institute of Engineering and Applied Sciences, P.O. Nilore, Islamabad, Pakistan
| | - Raheem Ullah
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Basovizza 34149, Trieste, Italy; Pakistan Institute of Engineering and Applied Sciences, P.O. Nilore, Islamabad, Pakistan
| | - Matteo De March
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Basovizza 34149, Trieste, Italy
| | - Muhammad Salahuddin Shah
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Vaccine Development Group, Animal Sciences Division, NIAB, Faisalabad, Pakistan
| | - Fouzia Ismat
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences, P.O. Nilore, Islamabad, Pakistan
| | - Mudasser Habib
- Vaccine Development Group, Animal Sciences Division, NIAB, Faisalabad, Pakistan
| | - Mazhar Iqbal
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences, P.O. Nilore, Islamabad, Pakistan
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Basovizza 34149, Trieste, Italy
| | - Moazur Rahman
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences, P.O. Nilore, Islamabad, Pakistan.
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Mayans E, Casanovas J, Gil AM, Jiménez AI, Cativiela C, Puiggalí J, Alemán C. Diversity and Hierarchy in Supramolecular Assemblies of Triphenylalanine: From Laminated Helical Ribbons to Toroids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:4036-4048. [PMID: 28374591 DOI: 10.1021/acs.langmuir.7b00622] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microstructures from small phenylalanine-based peptides have attracted great attention lately because these compounds are considered to be a new class of tunable materials. In spite of the extensive studies on uncapped diphenylalanine and tetraphenylalanine peptides, studies on the self-assembly of uncapped triphenylananine (FFF) are very scarce and nonsystematic. In this work, we demonstrate that FFF assemblies can organize in a wide number of well-defined supramolecular structures, which include laminated helical-ribbons, leaflike dendrimers, doughnut-, needle-, and flower-shapes. These organizations are produced by the attractive or repulsive interactions between already formed assemblies and therefore can be controlled through the choice of solvents used as the incubation medium. Thus, the formation of the desired supramolecular structures is regulated through the protonation/deprotonation of the terminal groups, the polarity of the incubation medium, which affects both peptide···solvent interactions and the cavity solvation energy (i.e., solvent···solvent interactions), and the steric interactions between own assemblies that act as building blocks. Finally, the β-sheet disposition in the latter structural motifs has been examined using both theoretical calculations and Fourier transform infrared spectroscopy. Results indicate that FFF molecules can adopt both parallel and antiparallel β-sheets. However, the former one is the most energetically favored because of the formation of π-π stacking interactions between the aromatic rings of hydrogen-bonded strands.
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Affiliation(s)
- Enric Mayans
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya , Edifici I.2, C/Eduard Maristany, 10-14, 08019 Barcelona, Spain
- Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida , c/Jaume II no. 69, Lleida E-25001, Spain
| | - Ana M Gil
- Department of Organic Chemistry and Instituto de Síntesis Quimica y Catalisis Homogenea (ISQCH), Universidad de Zaragoza-CSIC , 50009 Zaragoza, Spain
| | - Ana I Jiménez
- Department of Organic Chemistry and Instituto de Síntesis Quimica y Catalisis Homogenea (ISQCH), Universidad de Zaragoza-CSIC , 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Department of Organic Chemistry and Instituto de Síntesis Quimica y Catalisis Homogenea (ISQCH), Universidad de Zaragoza-CSIC , 50009 Zaragoza, Spain
| | - Jordi Puiggalí
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya , Edifici I.2, C/Eduard Maristany, 10-14, 08019 Barcelona, Spain
- Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya , Edifici I.2, C/Eduard Maristany, 10-14, 08019 Barcelona, Spain
- Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, 08019 Barcelona, Spain
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39
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Mayans E, Fabregat G, Juárez R, Cativiela C, Puiggalí J, Alemán C. Surface Mediated Hierarchical Assemblies of Highly Hydrophobic Phenylalanine-Based Peptides. ChemistrySelect 2017. [DOI: 10.1002/slct.201601436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Enric Mayans
- Departament d'Enginyeria Química; ETSEIB, Universitat Politècnica de Catalunya; Diagonal 647 08028 Barcelona Spain
- Center for Research in Nano-Engineering; Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n; Barcelona E-08028 Spain
| | - Georgina Fabregat
- Departament d'Enginyeria Química; ETSEIB, Universitat Politècnica de Catalunya; Diagonal 647 08028 Barcelona Spain
- Center for Research in Nano-Engineering; Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n; Barcelona E-08028 Spain
| | - Ruben Juárez
- Departament d'Enginyeria Química; ETSEIB, Universitat Politècnica de Catalunya; Diagonal 647 08028 Barcelona Spain
| | - Carlos Cativiela
- Department of Organic Chemistry and Instituto de Síntesis Quimica y Catalisis Homogenea (ISQCH); University of Zaragoza-CSIC; 50009 Zaragoza Spain
| | - Jordi Puiggalí
- Departament d'Enginyeria Química; ETSEIB, Universitat Politècnica de Catalunya; Diagonal 647 08028 Barcelona Spain
- Center for Research in Nano-Engineering; Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n; Barcelona E-08028 Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química; ETSEIB, Universitat Politècnica de Catalunya; Diagonal 647 08028 Barcelona Spain
- Center for Research in Nano-Engineering; Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n; Barcelona E-08028 Spain
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40
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Srour B, Bruechert S, Andrade SLA, Hellwig P. Secondary Structure Determination by Means of ATR-FTIR Spectroscopy. Methods Mol Biol 2017; 1635:195-203. [PMID: 28755370 DOI: 10.1007/978-1-4939-7151-0_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Specialized infrared spectroscopic techniques have been developed that allow studying the secondary structure of membrane proteins and the influence of crucial parameters like lipid content and detergent. Here, we focus on an ATR-FTIR spectroscopic study of Af-Amt1 and the influence of LDAO/glycerol on its structural integrity. Our results clearly indicate that infrared spectroscopy can be used to identify the adapted sample conditions.
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Affiliation(s)
- Batoul Srour
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, Strasbourg, France
| | - Stefan Bruechert
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Susana L A Andrade
- BIOSS Centre for Biological Signalling Studies, Schänzlestr. 1, 79104, Freiburg, Germany
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Petra Hellwig
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, Strasbourg, France.
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41
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Gemma A, Mayans E, Ballano G, Torras J, Díaz A, Jiménez AI, Puiggalí J, Cativiela C, Alemán C. Self-assembly of diphenylalanine with preclick components as capping groups. Phys Chem Chem Phys 2017; 19:27038-27051. [DOI: 10.1039/c7cp03792a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Alkyne and azide, which are commonly used in the cycloaddition reaction recognized as “click chemistry”, have been used as capping groups of two engineered diphenylalanine (FF) derivatives due to their ability to form weak intermolecular interactions (i.e. dipole–π and π–π stacking).
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Affiliation(s)
- Andrea Gemma
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya
- Barcelona
- Spain
| | - Enric Mayans
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya
- Barcelona
- Spain
- Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya
- Barcelona
| | - Gema Ballano
- Departmento de Química Orgánica and Instituto de Síntesis Quimica y Catalisis Homogenea (ISQCH), Universidad de Zaragoza–CSIC
- Zaragoza
- Spain
| | - Juan Torras
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya
- Barcelona
- Spain
| | - Angélica Díaz
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya
- Barcelona
- Spain
- Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya
- Barcelona
| | - Ana I. Jiménez
- Departmento de Química Orgánica and Instituto de Síntesis Quimica y Catalisis Homogenea (ISQCH), Universidad de Zaragoza–CSIC
- Zaragoza
- Spain
| | - Jordi Puiggalí
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya
- Barcelona
- Spain
- Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya
- Barcelona
| | - Carlos Cativiela
- Departmento de Química Orgánica and Instituto de Síntesis Quimica y Catalisis Homogenea (ISQCH), Universidad de Zaragoza–CSIC
- Zaragoza
- Spain
| | - Carlos Alemán
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya
- Barcelona
- Spain
- Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya
- Barcelona
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42
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Jung H, Pena-Francesch A, Saadat A, Sebastian A, Kim DH, Hamilton RF, Albert I, Allen BD, Demirel MC. Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins. Proc Natl Acad Sci U S A 2016; 113:6478-83. [PMID: 27222581 PMCID: PMC4988609 DOI: 10.1073/pnas.1521645113] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Many globular and structural proteins have repetitions in their sequences or structures. However, a clear relationship between these repeats and their contribution to the mechanical properties remains elusive. We propose a new approach for the design and production of synthetic polypeptides that comprise one or more tandem copies of a single unit with distinct amorphous and ordered regions. Our designed sequences are based on a structural protein produced in squid suction cups that has a segmented copolymer structure with amorphous and crystalline domains. We produced segmented polypeptides with varying repeat number, while keeping the lengths and compositions of the amorphous and crystalline regions fixed. We showed that mechanical properties of these synthetic proteins could be tuned by modulating their molecular weights. Specifically, the toughness and extensibility of synthetic polypeptides increase as a function of the number of tandem repeats. This result suggests that the repetitions in native squid proteins could have a genetic advantage for increased toughness and flexibility.
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Affiliation(s)
- Huihun Jung
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802; Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802
| | - Abdon Pena-Francesch
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802; Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802
| | - Alham Saadat
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802; The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
| | - Aswathy Sebastian
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802; The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802; Bioinformatics Consulting Center, Pennsylvania State University, University Park, PA 16802
| | - Dong Hwan Kim
- Department of Biology, Pennsylvania State University, University Park, PA 16802
| | - Reginald F Hamilton
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802; Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802; The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802; Bioinformatics Consulting Center, Pennsylvania State University, University Park, PA 16802
| | - Benjamin D Allen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802; The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802;
| | - Melik C Demirel
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802; Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802; The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802;
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43
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Gallea JI, Sarroukh R, Yunes-Quartino P, Ruysschaert JM, Raussens V, Celej MS. Structural remodeling during amyloidogenesis of physiological Nα-acetylated α-synuclein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:501-10. [DOI: 10.1016/j.bbapap.2016.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 12/24/2022]
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44
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Guzman-Puyol S, Heredia-Guerrero JA, Ceseracciu L, Hajiali H, Canale C, Scarpellini A, Cingolani R, Bayer IS, Athanassiou A, Mele E. Low-Cost and Effective Fabrication of Biocompatible Nanofibers from Silk and Cellulose-Rich Materials. ACS Biomater Sci Eng 2016; 2:526-534. [DOI: 10.1021/acsbiomaterials.5b00500] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
| | | | | | - Hadi Hajiali
- DIBRIS, University of Genoa, Via Opera Pia, 13, Genova 16145, Italy
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45
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Mid-infrared spectroscopy for protein analysis: potential and challenges. Anal Bioanal Chem 2016; 408:2875-89. [PMID: 26879650 DOI: 10.1007/s00216-016-9375-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/22/2016] [Accepted: 01/28/2016] [Indexed: 12/11/2022]
Abstract
Mid-infrared (MIR) spectroscopy investigates the interaction of MIR photons with both organic and inorganic molecules via the excitation of vibrational and rotational modes, providing inherent molecular selectivity. In general, infrared (IR) spectroscopy is particularly sensitive to protein structure and structural changes via vibrational resonances originating from the polypeptide backbone or side chains; hence information on the secondary structure of proteins can be obtained in a label-free fashion. In this review, the challenges for IR spectroscopy for protein analysis are discussed as are the potential and limitations of different IR spectroscopic techniques enabling protein analysis. In particular, the amide I spectral range has been widely used to study protein secondary structure, conformational changes, protein aggregation, protein adsorption, and the formation of amyloid fibrils. In addition to representative examples of the potential of IR spectroscopy in various fields related to protein analysis, the potential of protein analysis taking advantage of miniaturized MIR systems, including waveguide-enhanced MIR sensors, is detailed.
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46
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Ambroggio EE, Caruso B, Villarreal MA, Raussens V, Fidelio GD. Reversing the peptide sequence impacts on molecular surface behaviour. Colloids Surf B Biointerfaces 2015; 139:25-32. [PMID: 26700230 DOI: 10.1016/j.colsurfb.2015.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/20/2015] [Accepted: 12/02/2015] [Indexed: 01/01/2023]
Abstract
The protein's primary structure has all the information for specific protein/peptide folding and, in many cases, can define specific amphiphilic regions along molecules that are important for interaction with membranes. In order to shed light on how peptide sequence is important for the surface properties of amphiphilic peptides, we designed three pairs of peptides with the following characteristics: (1) all molecules have the same hydrophobic residues; (2) the couples differ from each other in their hydrophilic amino acids: positively, negatively and non-charged; (3) each pair has the same residues (same global molecular hydrophobicity) but the primary structure is reversed in comparison to its partner (retro-isomer), giving a molecule with a hydrophilic N or C-terminus and a hydrophobic C or N-terminus. Using the Langmuir monolayer approach, we observed that sequence reversal has a central role in the lateral stability of peptide monolayers, in the ability of the molecules to partition into the air-water interface and in the rheological properties of peptide films, whereas the peptide's secondary structure, determined by ATR-FTIR, was the same for all peptides. Reversing the sequence also gives a differential way of peptide/lipid interaction when peptides are in the presence of POPC lipid bilayers. Our results show how sequence inversion confers a distinctive peptide surface behaviour and lipid interaction for molecules with a similar structure.
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Affiliation(s)
- Ernesto E Ambroggio
- CIQUIBIC, CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina.
| | - Benjamín Caruso
- CIQUIBIC, CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina
| | - Marcos A Villarreal
- Instituto de Investigaciones en Físico-Química de Córdoba (INFIQC), CONICET, Departamento de Matemática y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Vincent Raussens
- Centre for Structural Biology and Bioinformatics, Laboratory for Structure and Function of Biological Membranes, Universit é Libre de Bruxelles, CP 206/02, Blvd. du Triomphe, B-1050 Brussels, Belgium
| | - Gerardo D Fidelio
- CIQUIBIC, CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina
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47
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Herrera MG, Benedini LA, Lonez C, Schilardi PL, Hellweg T, Ruysschaert JM, Dodero VI. Self-assembly of 33-mer gliadin peptide oligomers. SOFT MATTER 2015; 11:8648-60. [PMID: 26376290 DOI: 10.1039/c5sm01619c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The 33-mer gliadin peptide, LQLQPF(PQPQLPY)3PQPQPF, is a highly immunogenic peptide involved in celiac disease and probably in other immunopathologies associated with gliadin. Herein, dynamic light scattering measurements showed that 33-mer, in the micromolar concentration range, forms polydisperse nano- and micrometer range particles in aqueous media. This behaviour is reminiscent of classical association of colloids and we hypothesized that the 33-mer peptide self-assembles into micelles that could be the precursors of 33-mer oligomers in water. Deposition of 33-mer peptide aqueous solution on bare mica generated nano- and microstructures with different morphologies as revealed by atomic force microscopy. At 6 μM, the 33-mer is organised in isolated and clusters of spherical nanostructures. In the 60 to 250 μM concentration range, the spherical oligomers associated mainly in linear and annular arrangements and structures adopting a "sheet" type morphology appeared. At higher concentrations (610 μM), mainly filaments and plaques immersed in a background of nanospherical structures were detected. The occurrence of different morphologies of oligomers and finally the filaments suggests that the unique specific geometry of the 33-mer oligomers has a crucial role in the subsequent condensation and organization of their fractal structures into the final filaments. The self-assembly process on mica is described qualitatively and quantitatively by a fractal diffusion limited aggregation (DLA) behaviour with the fractal dimension in the range of 1.62 ± 0.02 to 1.73 ± 0.03. Secondary structure evaluation of the oligomers by Attenuated Total Reflection FTIR spectroscopy (ATR-FTIR) revealed the existence of a conformational equilibrium of self-assembled structures, from an extended conformation to a more folded parallel beta elongated structures. Altogether, these findings provide structural and morphological information about supramolecular organization of the 33-mer peptide, which might offer new perspectives for the understanding and treatment of gliadin intolerance disorders.
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Affiliation(s)
- M G Herrera
- Departamento de Química-INQUISUR, Universidad Nacional del Sur-CONICET, Av. Alem 1253, 8000 Bahía Blanca, Argentina.
| | - L A Benedini
- Departamento de Química-INQUISUR, Universidad Nacional del Sur-CONICET, Av. Alem 1253, 8000 Bahía Blanca, Argentina.
| | - C Lonez
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, CB30ES, UK.
| | - P L Schilardi
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), CONICET - Departamento de Química, Facultad de Ciencias Exactas, UNLP, CC16, Suc. 4(1900) La Plata, Buenos Aires, Argentina.
| | - T Hellweg
- Universität Bielefeld, Fakultät für Chemie, Physikalische und Biophysikalische Chemie, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - J-M Ruysschaert
- Structure and Function of Biological Membranes, Université Libre de Bruxelles, Belgium.
| | - V I Dodero
- Departamento de Química-INQUISUR, Universidad Nacional del Sur-CONICET, Av. Alem 1253, 8000 Bahía Blanca, Argentina.
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48
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Güler G, Gärtner RM, Ziegler C, Mäntele W. Lipid-Protein Interactions in the Regulated Betaine Symporter BetP Probed by Infrared Spectroscopy. J Biol Chem 2015; 291:4295-307. [PMID: 26592930 DOI: 10.1074/jbc.m114.621979] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Indexed: 11/06/2022] Open
Abstract
The Na(+)-coupled betaine symporter BetP senses changes in the membrane state and increasing levels of cytoplasmic K(+) during hyperosmotic stress latter via its C-terminal domain and regulates transport activity according to both stimuli. This intriguing sensing and regulation behavior of BetP was intensively studied in the past. It was shown by several biochemical studies that activation and regulation depends crucially on the lipid composition of the surrounding membrane. In fact, BetP is active and regulated only when negatively charged lipids are present. Recent structural studies have revealed binding of phosphatidylglycerol lipids to functional important parts of BetP, suggesting a functional role of lipid interactions. However, a regulatory role of lipid interactions could only be speculated from the snapshot provided by the crystal structure. Here, we investigate the nature of lipid-protein interactions of BetP reconstituted in closely packed two-dimensional crystals of negatively charged lipids and probed at the molecular level with Fourier transform infrared (FTIR) spectroscopy. The FTIR data indicate that K(+) binding weakens the interaction of BetP especially with the anionic lipid head groups. We suggest a regulation mechanism in which lipid-protein interactions, especially with the C-terminal domain and the functional important gating helices transmembrane helice 3 (TMH3) and TMH12, confine BetP to its down-regulated transport state. As BetP is also activated by changes in the physical state of the membrane, our results point toward a more general mechanism of how active transport can be modified by dynamic lipid-protein interactions.
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Affiliation(s)
- Günnur Güler
- From the Goethe-University, Institute of Biophysics, Max-von-Laue-Strasse 1, D-60438, Frankfurt am Main, Germany
| | - Rebecca M Gärtner
- Max Planck Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Strasse 3, D-60438, Frankfurt am Main, Germany, and
| | - Christine Ziegler
- Max Planck Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Strasse 3, D-60438, Frankfurt am Main, Germany, and University of Regensburg, Faculty of Biology and Preclinical Medicine, Universitätsstrasse 31, D-93051, Regensburg, Germany
| | - Werner Mäntele
- From the Goethe-University, Institute of Biophysics, Max-von-Laue-Strasse 1, D-60438, Frankfurt am Main, Germany,
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Disruption of secondary structure by oxidative stress alters the cross-linking pattern of myosin by microbial transglutaminase. Meat Sci 2015; 108:97-105. [DOI: 10.1016/j.meatsci.2015.05.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 05/23/2015] [Accepted: 05/25/2015] [Indexed: 11/19/2022]
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Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an “Elephant and Blind Men” Situation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:215-60. [DOI: 10.1007/978-3-319-20164-1_7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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