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Li R, Singh R, Kashav T, Yang C, Sharma RD, Lynn AM, Prasad R, Prakash A, Kumar V. Computational Insights of Unfolding of N-Terminal Domain of TDP-43 Reveal the Conformational Heterogeneity in the Unfolding Pathway. Front Mol Neurosci 2022; 15:822863. [PMID: 35548668 PMCID: PMC9083116 DOI: 10.3389/fnmol.2022.822863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/22/2022] [Indexed: 02/05/2023] Open
Abstract
TDP-43 proteinopathies is a disease hallmark that characterizes amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). The N-terminal domain of TDP-43 (NTD) is important to both TDP-43 physiology and TDP-43 proteinopathy. However, its folding and dimerization process is still poorly characterized. In the present study, we have investigated the folding/unfolding of NTD employing all-atom molecular dynamics (MD) simulations in 8 M dimethylsulfoxide (DMSO) at high temperatures. The MD results showed that the unfolding of the NTD at high temperature evolves through the formation of a number of conformational states differing in their stability and free energy. The presence of structurally heterogeneous population of intermediate ensembles was further characterized by the different extents of solvent exposure of Trp80 during unfolding. We suggest that these non-natives unfolded intermediate ensembles may facilitate NTD oligomerization and subsequently TDP-43 oligomerization, which might lead to the formation of irreversible pathological aggregates, characteristics of disease pathogenesis.
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Affiliation(s)
- Ruiting Li
- School of Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Ruhar Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Tara Kashav
- Department of Life Science, Central University of South Bihar, Gaya, India
| | - ChunMin Yang
- School of Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Ravi Datta Sharma
- Amity Institute of Biotechnology, Amity University Haryana, Gurgaon, India
| | - Andrew M. Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rajendra Prasad
- Amity Institute of Biotechnology, Amity University Haryana, Gurgaon, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health (AIISH), Amity University Haryana, Gurgaon, India
- *Correspondence: Vijay Kumar Amresh Prakash
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences (AINN), Amity University, Noida, India
- *Correspondence: Vijay Kumar Amresh Prakash
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52
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Acidic and basic self-assembling peptide and peptide-graphene oxide hydrogels: characterisation and effect on encapsulated nucleus pulposus cells. Acta Biomater 2022; 143:145-158. [PMID: 35196554 DOI: 10.1016/j.actbio.2022.02.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 12/28/2022]
Abstract
Extracellular pH can have a profound effect on cell metabolism, gene and protein expression. Nucleus pulposus (NP) cells, for example, under acidic conditions accelerate the production of degradative enzymes and pro-inflammatory cytokines, leading ultimately to intervertebral disc degeneration, a major cause of back pain. Self-assembling peptide hydrogels constitute a well-established class of biomaterials that could be exploited as pH-tunable platform to investigate cell behaviour under normal and non-physiological pH. In this paper we formulated acidic (pH = 4) and basic (pH = 9) hydrogels, from the same octapeptide FEFKFEFK (F8) (F = phenyalanine, E = glutamic acid, K = lysine), to test the effect of non-physiological pH on encapsulated NP cells. Similarly, graphene oxide-containing F8 hydrogels (GO-F8) were formulated as stiffer analogues. Acidic and basic hydrogels showed peculiar morphologies and rheological properties, with all systems able to buffer within 30 minutes of exposure to cell culture media. NP cells seeded in acidic F8 hydrogels showed a more catabolic phenotype compared to basic hydrogels, with increased gene expression of degradative enzymes (MMP-3, ADAMTS-4), neurotrophic factors (NGF and BDNF) and NF-κB p65 phosphorylation. Acidic GO-F8 hydrogels also induced a catabolic response, although milder than basic counterparts and with the highest gene expression of characteristic NP-matrix components, aggrecan and collagen II. In all systems, the cellular response had a peak within 3 days of encapsulation, thereafter decreasing over 7 days, suggesting a 'transitory' effect of hydrogel pH on encapsulated cells. This work gives an insight on the effect of pH (and pH buffering) on encapsulated NP cells and offers new designs of low and high pH peptide hydrogels for 3D cell culture studies. STATEMENT OF SIGNIFICANCE: We have recently shown the potential of graphene oxide - self-assembling peptide hybrid hydrogels for NP cell culture and regeneration. Alongside cell carrier, self-assembling peptide hydrogels actually provide a versatile pH-tunable platform for biological studies. In this work we decided to explore the effect of non-physiological pH (and pH buffering) on encapsulated NP cells. Our approach allows the formulation of both acidic and basic hydrogels, starting from the same peptide sequence. We showed that the initial pH of the scaffold does not affect significantly cell response to encapsulation, but the presence of GO results in lower inflammatory levels and higher NP matrix protein production. This platform could be exploited to study the effect of pH on different cell types whose behaviour can be pH-dependent.
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53
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Samanta D, Govil T, Saxena P, Gadhamshetty V, Krumholz LR, Salem DR, Sani RK. Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b. Biomolecules 2022; 12:560. [PMID: 35454149 PMCID: PMC9024549 DOI: 10.3390/biom12040560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 02/05/2023] Open
Abstract
Particulate methane monooxygenase (pMMO), a membrane-bound enzyme having three subunits (α, β, and γ) and copper-containing centers, is found in most of the methanotrophs that selectively catalyze the oxidation of methane into methanol. Active sites in the pMMO of Methylosinus trichosporium OB3b were determined by docking the modeled structure with ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene. The docking energy between the modeled pMMO structure and ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene was -5.2, -5.7, -4.2, and -3.8 kcal/mol, respectively, suggesting the existence of more than one active site within the monomeric subunits due to the presence of multiple binding sites within the pMMO monomer. The evaluation of tunnels and cavities of the active sites and the docking results showed that each active site is specific to the radius of the substrate. To increase the catalysis rates of methane in the pMMO of M. trichosporium OB3b, selected amino acid residues interacting at the binding site of ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene were mutated. Based on screening the strain energy, docking energy, and physiochemical properties, five mutants were downselected, B:Leu31Ser, B:Phe96Gly, B:Phe92Thr, B:Trp106Ala, and B:Tyr110Phe, which showed the docking energy of -6.3, -6.7, -6.3, -6.5, and -6.5 kcal/mol, respectively, as compared to the wild type (-5.2 kcal/mol) with ethylbenzene. These results suggest that these five mutants would likely increase methane oxidation rates compared to wild-type pMMO.
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Affiliation(s)
- Dipayan Samanta
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (D.S.); (T.G.); (P.S.); (D.R.S.)
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (V.G.); (L.R.K.)
| | - Tanvi Govil
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (D.S.); (T.G.); (P.S.); (D.R.S.)
- Composite and Nanocomposite Advanced Manufacturing-Biomaterials Center, Rapid City, SD 57701, USA
| | - Priya Saxena
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (D.S.); (T.G.); (P.S.); (D.R.S.)
| | - Venkata Gadhamshetty
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (V.G.); (L.R.K.)
- Department of Civil and Environmental Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Lee R. Krumholz
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (V.G.); (L.R.K.)
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - David R. Salem
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (D.S.); (T.G.); (P.S.); (D.R.S.)
- Composite and Nanocomposite Advanced Manufacturing-Biomaterials Center, Rapid City, SD 57701, USA
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (D.S.); (T.G.); (P.S.); (D.R.S.)
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (V.G.); (L.R.K.)
- Composite and Nanocomposite Advanced Manufacturing-Biomaterials Center, Rapid City, SD 57701, USA
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54
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Hsieh PH, Huang WY, Wang HC, Kuan CH, Shiue TY, Chen Y, Wang TW. Dual-responsive polypeptide nanoparticles attenuate tumor-associated stromal desmoplasia and anticancer through programmable dissociation. Biomaterials 2022; 284:121469. [PMID: 35344799 DOI: 10.1016/j.biomaterials.2022.121469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/02/2022] [Accepted: 03/11/2022] [Indexed: 12/22/2022]
Affiliation(s)
- Pei-Hsuan Hsieh
- Department of Materials Science and Engineering, National Tsing Hua University, Taiwan; Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
| | - Wei-Yuan Huang
- Department of Materials Science and Engineering, National Tsing Hua University, Taiwan
| | - Huan-Chih Wang
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taiwan; College of Biological Science and Technology, National Chiao Tung University, Taiwan
| | - Chen-Hsiang Kuan
- Division of Plastic Surgery, Department of Surgery, National Taiwan University Hospital, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taiwan
| | - Ting-Yun Shiue
- Institute of Biomedical Engineering, National Tsing Hua University, Taiwan
| | - Yunching Chen
- Institute of Biomedical Engineering, National Tsing Hua University, Taiwan
| | - Tzu-Wei Wang
- Department of Materials Science and Engineering, National Tsing Hua University, Taiwan.
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55
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Dorne JLCM, Cirlini M, Louisse J, Pedroni L, Galaverna G, Dellafiora L. A Computational Understanding of Inter-Individual Variability in CYP2D6 Activity to Investigate the Impact of Missense Mutations on Ochratoxin A Metabolism. Toxins (Basel) 2022; 14:207. [PMID: 35324704 PMCID: PMC8950366 DOI: 10.3390/toxins14030207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023] Open
Abstract
Cytochrome P-450 (CYP) enzymes have a key role in the metabolism of xenobiotics of food origin, and their highly polymorphic nature concurs with the diverse inter-individual variability in the toxicokinetics (TK) and toxicodynamics (TD) of food chemicals. Ochratoxin A is a well-known mycotoxin which contaminates a large variety of food and is associated with food safety concerns. It is a minor substrate of CYP2D6, although the effects of CYP2D6 polymorphisms on its metabolism may be overlooked. Insights on this aspect would provide a useful mechanistic basis for a more science-based hazard assessment, particularly to integrate inter-individual differences in CYP2D6 metabolism. This work presents a molecular modelling approach for the analysis of mechanistic features with regard to the metabolic capacity of CYP2D6 variants to oxidise a number of substrates. The outcomes highlighted that a low-frequency CYP2D6 variant (CYP2D6*110) is likely to enhance ochratoxin A oxidation with possible consequences on TK and TD. It is therefore recommended to further analyse such TK and TD consequences. Generally speaking, we propose the identification of mechanistic features and parameters that could provide a semi-quantitative means to discriminate ligands based on the likelihood to undergo transformation by CYP2D6 variants. This would support the development of a fit-for-purpose pipeline which can be extended to a tool allowing for the bulk analysis of a large number of compounds. Such a tool would ultimately include inter-phenotypic differences of polymorphic xenobiotic-metabolising enzymes in the hazard assessment and risk characterisation of food chemicals.
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Affiliation(s)
- Jean Lou C. M. Dorne
- Scientific Committee and Emerging Risks Unit, European Food Safety Authority, Via Carlo Magno 1A, 43124 Parma, Italy;
| | - Martina Cirlini
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (L.P.); (G.G.)
| | - Jochem Louisse
- Wageningen Food Safety Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands;
| | - Lorenzo Pedroni
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (L.P.); (G.G.)
| | - Gianni Galaverna
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (L.P.); (G.G.)
| | - Luca Dellafiora
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (L.P.); (G.G.)
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56
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Mass OA, Wilson CK, Barcenas G, Terpetschnig EA, Obukhova OM, Kolosova OS, Tatarets AL, Li L, Yurke B, Knowlton WB, Pensack RD, Lee J. Influence of Hydrophobicity on Excitonic Coupling in DNA-Templated Indolenine Squaraine Dye Aggregates. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:3475-3488. [PMID: 35242270 PMCID: PMC8883467 DOI: 10.1021/acs.jpcc.1c08981] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/15/2022] [Indexed: 06/01/2023]
Abstract
Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA HJ). Indolenine squaraines were chosen for their excellent spectral properties, stability, and diversity of chemical modifications. Six squaraines of varying hydrophobicity from highly hydrophobic to highly hydrophilic were assembled in two dimer configurations and a tetramer. In general, the examined squaraines demonstrated a propensity toward face-to-face aggregation behavior observed via steady-state absorption, fluorescence, and circular dichroism spectroscopies. Modeling based on the Kühn-Renger-May approach quantified the strength of excitonic coupling in the squaraine aggregates. The strength of excitonic coupling strongly correlated with squaraine hydrophobic region. Dimer aggregates of dichloroindolenine squaraine were found to exhibit the strongest coupling strength of 132 meV (1065 cm-1). In addition, we identified the sites for dye attachment in the DNA HJ that promote the closest spacing between the dyes in their dimers. The extracted aggregate geometries, and the role of electrostatic and steric effects in squaraine aggregation are also discussed. Taken together, these findings provide a deeper insight into how dye structures influence excitonic coupling in dye aggregates covalently templated via DNA, and guidance in design rules for exciton-based materials and devices.
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Affiliation(s)
- Olga A. Mass
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Christopher K. Wilson
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - German Barcenas
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | | | - Olena M. Obukhova
- State
Scientific Institution “Institute for Single Crystals”
of National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Olga S. Kolosova
- State
Scientific Institution “Institute for Single Crystals”
of National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Anatoliy L. Tatarets
- State
Scientific Institution “Institute for Single Crystals”
of National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Lan Li
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Center
for Advanced Energy Studies, Idaho
Falls, Idaho 83401, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Ryan. D. Pensack
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Chemistry and Biochemistry, Boise State
University, Boise, Idaho 83725, United
States
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57
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Brzeski J. The influence of tetrel bonds on the acidities of group 14 tetrafluoride - inorganic acid complexes. J Comput Chem 2022; 43:611-618. [PMID: 35147239 DOI: 10.1002/jcc.26822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 12/12/2022]
Abstract
Ab initio methods were used to determine the influence of tetrel bond formation on the acidity. The systems composed of inorganic acids and tetrafluorides of 14 group elements have been tested - HA/EF4 , where HA = H2 O, NH3 , HF, HCN, HNC, HCNO, HOCN and E = C, Si, Ge, Sn or Pb. It turns out that the electron density flow involved with formation of tetrel bond to carbon-based systems leads to negligible increase in acidity. In the case of the acceptor compounds based on the remaining 14 group elements however, the effect is much more apparent, as most of those compounds may be considered a Brønsted superacids. The electronic stability of anions formed after the deprotonation of aforementioned complexes has been investigated. Vast majority of the anions were found to exhibit significant electron binding energies.
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Affiliation(s)
- Jakub Brzeski
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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58
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Ansari A, Ibrahim F, Haider MS, Aman A. In vitro application of bacteriocin produced by
Lactiplantibacillus plantarum
for the biopreservation of meat at refrigeration temperature. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Asma Ansari
- The Karachi Institute of Biotechnology & Genetic Engineering (KIBGE) University of Karachi Karachi Pakistan
| | - Fariha Ibrahim
- Department of Biomedical Engineering Ziauddin University Karachi Pakistan
| | - Muhammad Samee Haider
- Food and Marine Resources Research Centre (FMRRC), Pakistan Council of Scientific and Industrial Research (PCSIR) Karachi Pakistan
| | - Afsheen Aman
- The Karachi Institute of Biotechnology & Genetic Engineering (KIBGE) University of Karachi Karachi Pakistan
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59
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Zou Y, Guan L. Unraveling the Influence of K280 Acetylation on the Conformational Features of Tau Core Fragment: A Molecular Dynamics Simulation Study. Front Mol Biosci 2021; 8:801577. [PMID: 34966788 PMCID: PMC8710698 DOI: 10.3389/fmolb.2021.801577] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/22/2021] [Indexed: 01/16/2023] Open
Abstract
Abnormal aggregation of the microtubule-associated protein Tau is closely associated with tauopathies, including Alzheimer's disease and chronic traumatic encephalopathy. The hexapeptide 275VQIINK280 (PHF6*), a fibril-nucleating core motif of Tau, has been shown to play a vital role in the aggregation of Tau. Mounting experiment evidence demonstrated the acetylation of a single-lysine residue K280 in the PHF6* was a critical event for the formation of pathological Tau amyloid deposits. However, the underlying mechanisms by which K280 acetylation affects Tau aggregation at the atomic level remain elusive. In this work, we performed replica exchange molecular dynamics simulations to investigate the influence of acetylation of K280 on the aggregation of PHF6*. Our simulations show that acetylation of K280 not only enhances the self-assembly capability of PHF6* peptides but also increases the β-sheet structure propensity of the PHF6*. The inter-molecular interactions among PHF6* peptides are strengthened by the acetylation of K280, resulting in an increased ordered β-sheet-rich conformations of the PHF6* assemblies along with a decrease of the structural diversity. The residue-pairwise contact frequency analysis shows that K280 acetylation increases the interactions among the hydrophobic chemical groups from PHF6* peptides, which promotes the aggregation of PHF6*. This study offers mechanistic insights into the effects of acetylation on the aggregation of PHF6*, which will be helpful for an in-depth understanding of the relationship between acetylation and Tau aggregation at the molecular level.
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Affiliation(s)
- Yu Zou
- Department of Sport and Exercise Science, College of Education, Zhejiang University, Hangzhou, China
| | - Lulu Guan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, Hangzhou, China
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60
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Learning the local landscape of protein structures with convolutional neural networks. J Biol Phys 2021; 47:435-454. [PMID: 34751854 DOI: 10.1007/s10867-021-09593-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022] Open
Abstract
One fundamental problem of protein biochemistry is to predict protein structure from amino acid sequence. The inverse problem, predicting either entire sequences or individual mutations that are consistent with a given protein structure, has received much less attention even though it has important applications in both protein engineering and evolutionary biology. Here, we ask whether 3D convolutional neural networks (3D CNNs) can learn the local fitness landscape of protein structure to reliably predict either the wild-type amino acid or the consensus in a multiple sequence alignment from the local structural context surrounding site of interest. We find that the network can predict wild type with good accuracy, and that network confidence is a reliable measure of whether a given prediction is likely going to be correct or not. Predictions of consensus are less accurate and are primarily driven by whether or not the consensus matches the wild type. Our work suggests that high-confidence mis-predictions of the wild type may identify sites that are primed for mutation and likely targets for protein engineering.
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61
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Fabbrizzi L. Beyond the Molecule: Intermolecular Forces from Gas Liquefaction to X-H⋅⋅⋅π Hydrogen Bonds. Chempluschem 2021; 87:e202100243. [PMID: 34730880 DOI: 10.1002/cplu.202100243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/04/2021] [Indexed: 11/11/2022]
Abstract
Interest toward molecule-molecule interactions developed during the first half of the 19th century with studies on gas liquefaction. In 1869, Andrews carried out the first accurate study on the effects of temperature and pressure on the behaviour of real gases, and in 1873, van der Waals formulated an equation capable of accounting for critical phenomena of each individual gas The nature of the intermolecular forces responsible for aggregation of gases was investigated in the early 20th century by Keesom and Debye (electrostatic interactions between dipoles) and by London (interaction between instantaneous dipoles, studied by quantum mechanics). The hydrogen bond theory, a particular case of dipolar interaction, originated in the 1920s in Berkeley in the institute directed by G. N. Lewis. Later it was made clear that hydrogen bonding is responsible for the aggregation of most biological systems, from proteins to nucleic acids. This Perspective describes the most significant steps through which the science of intermolecular interactions has progressed over the last two centuries, revisiting classical experiments and theoretical formulations, which led to the complex state of art of today.
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Affiliation(s)
- Luigi Fabbrizzi
- Dipartimento di Chimica, Università di Pavia, via Taramelli 12, 27100, Pavia, Italy
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62
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Muraoka T. Amphiphilic Peptides with Flexible Chains for Tuning Supramolecular Morphologies, Macroscopic Properties and Biological Functions. J SYN ORG CHEM JPN 2021. [DOI: 10.5059/yukigoseikyokaishi.79.1033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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63
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Joseph JA, Reinhardt A, Aguirre A, Chew PY, Russell KO, Espinosa JR, Garaizar A, Collepardo-Guevara R. Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy. NATURE COMPUTATIONAL SCIENCE 2021; 1:732-743. [PMID: 35795820 PMCID: PMC7612994 DOI: 10.1038/s43588-021-00155-3] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/08/2021] [Indexed: 05/10/2023]
Abstract
Various physics- and data-driven sequence-dependent protein coarse-grained models have been developed to study biomolecular phase separation and elucidate the dominant physicochemical driving forces. Here, we present Mpipi, a multiscale coarse-grained model that describes almost quantitatively the change in protein critical temperatures as a function of amino-acid sequence. The model is parameterised from both atomistic simulations and bioinformatics data and accounts for the dominant role of π-π and hybrid cation-π/π-π interactions and the much stronger attractive contacts established by arginines than lysines. We provide a comprehensive set of benchmarks for Mpipi and seven other residue-level coarse-grained models against experimental radii of gyration and quantitative in-vitro phase diagrams; Mpipi predictions agree well with experiment on both fronts. Moreover, it can account for protein-RNA interactions, correctly predicts the multiphase behaviour of a charge-matched poly-arginine/poly-lysine/RNA system, and recapitulates experimental LLPS trends for sequence mutations on FUS, DDX4 and LAF-1 proteins.
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Affiliation(s)
- Jerelle A. Joseph
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Anne Aguirre
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Kieran O. Russell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Jorge R. Espinosa
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Adiran Garaizar
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
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64
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Effects of hydrophobic solute on water normal modes. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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65
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Li J, Hou C, Ma X, Guo S, Zhang H, Shi L, Liao C, Zheng B, Ye L, Yang L, He X. Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. Int J Mol Sci 2021; 22:9653. [PMID: 34502559 PMCID: PMC8431812 DOI: 10.3390/ijms22179653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 12/16/2022] Open
Abstract
Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.
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Affiliation(s)
- Jiacheng Li
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Chengyu Hou
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Hongchi Zhang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Chenchen Liao
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Bing Zheng
- Key Laboratory of Functional Inorganic Material Chemistry (Ministry of Education), School of Chemistry and Materials Science, Heilongjiang University, Harbin 150001, China;
| | - Lin Ye
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
- Shenzhen STRONG Advanced Materials Research Institute Co., Ltd., Shenzhen 518035, China
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66
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Ahmad Sajid T, Jamal MA, Saeed M, Atta-ul-Haq, Muneer M. Elucidation of molecular interactions between amino acid and imidazolium based ionic liquid in an aqueous system: Volumetric and acoustic studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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67
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The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference? Life (Basel) 2021; 11:life11080773. [PMID: 34440517 PMCID: PMC8398314 DOI: 10.3390/life11080773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
The genetic code was evolved, to some extent, to minimize the effects of mutations. The effects of mutations depend on the amino acid repertoire, the structure of the genetic code and frequencies of amino acids in proteomes. The amino acid compositions of proteins and corresponding codon usages are still under selection, which allows us to ask what kind of environment the standard genetic code is adapted to. Using simple computational models and comprehensive datasets comprising genomic and environmental data from all three domains of Life, we estimate the expected severity of non-synonymous genomic mutations in proteins, measured by the change in amino acid physicochemical properties. We show that the fidelity in these physicochemical properties is expected to deteriorate with extremophilic codon usages, especially in thermophiles. These findings suggest that the genetic code performs better under non-extremophilic conditions, which not only explains the low substitution rates encountered in halophiles and thermophiles but the revealed relationship between the genetic code and habitat allows us to ponder on earlier phases in the history of Life.
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68
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Kharbikar BN, Chendke GS, Desai TA. Modulating the foreign body response of implants for diabetes treatment. Adv Drug Deliv Rev 2021; 174:87-113. [PMID: 33484736 PMCID: PMC8217111 DOI: 10.1016/j.addr.2021.01.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/30/2020] [Accepted: 01/10/2021] [Indexed: 02/06/2023]
Abstract
Diabetes Mellitus is a group of diseases characterized by high blood glucose levels due to patients' inability to produce sufficient insulin. Current interventions often require implants that can detect and correct high blood glucose levels with minimal patient intervention. However, these implantable technologies have not reached their full potential in vivo due to the foreign body response and subsequent development of fibrosis. Therefore, for long-term function of implants, modulating the initial immune response is crucial in preventing the activation and progression of the immune cascade. This review discusses the different molecular mechanisms and cellular interactions involved in the activation and progression of foreign body response (FBR) and fibrosis, specifically for implants used in diabetes. We also highlight the various strategies and techniques that have been used for immunomodulation and prevention of fibrosis. We investigate how these general strategies have been applied to implants used for the treatment of diabetes, offering insights on how these devices can be further modified to circumvent FBR and fibrosis.
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Affiliation(s)
- Bhushan N Kharbikar
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gauree S Chendke
- University of California Berkeley - University of California San Francisco Graduate Program in Bioengineering, San Francisco, CA 94143, USA
| | - Tejal A Desai
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; University of California Berkeley - University of California San Francisco Graduate Program in Bioengineering, San Francisco, CA 94143, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA.
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69
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Jani V, Sonavane U, Joshi R. Destabilization potential of beta sheet breaker peptides on Abeta fibril structure: an insight from molecular dynamics simulation study. RSC Adv 2021; 11:23557-23573. [PMID: 35479797 PMCID: PMC9036544 DOI: 10.1039/d1ra03609b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/29/2021] [Indexed: 02/02/2023] Open
Abstract
Alzheimer's disease is characterized by amyloid-β aggregation. Currently, all the approved medications are to treat the symptoms but there is no clinically approved treatment for the cure or to prevent the progression of Alzheimer's disease (AD). Earlier reports suggest the use of small molecules and peptides to target and destabilize the amyloid fibril. The use of Beta Sheet Breaker (BSB) peptides seems to be a promising and attractive therapeutic approach as it can strongly bind and destabilize the preformed amyloid fibril. There are experimental studies describing the destabilization role of various BSB peptides, but the exact mechanism remains elusive. In the current work, an attempt is made to study the destabilization mechanism of different BSB peptides on preformed amyloid protofibril using molecular docking and simulations. Molecular docking of eight different BSB peptides of varying length (5-mer to 10-mer) on the Abeta protofibril was done. Docking was followed by multiple sets of molecular simulations for the Abeta protofibril–BSB peptide complex for each of the top ranked poses of the eight BSB peptides. As a control, multiple sets of simulations for the Abeta protofibril (APO) were also carried out. An increase in the RMSD, decrease in the number of interchain hydrogen bonds, destabilization of important salt bridge interactions (D23–K28), and destabilization of interchain hydrophobic interactions suggested the destabilization of Abeta protofibril by BSB peptides. The MM-GBSA free energy of binding for each of the BSB peptides was calculated to measure the binding affinity of BSB peptides to Abeta protofibril. Further residue wise contribution of free energy of binding was also calculated. The study showed that 7-mer peptides tend to bind strongly to Abeta protofibril as compared to other BSB peptides. The KKLVFFA peptide showed better destabilization potential as compared to the other BSB peptides. The details about the destabilization mechanism of BSB peptides will help in the design of other peptides for the therapeutic intervention for AD. Destabilzation of Abeta protofibril by Beta Sheet Breaker (BSB) peptides.![]()
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Affiliation(s)
- Vinod Jani
- Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
| | - Uddhavesh Sonavane
- Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
| | - Rajendra Joshi
- Centre for Development of Advanced Computing (C-DAC) Panchavati, Pashan Pune India
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70
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Design and synthesis of polyacrylic acid/deoxycholic acid-modified chitosan copolymer and a close inspection of human growth hormone-copolymer interactions: An experimental and computational study. Colloids Surf B Biointerfaces 2021; 206:111956. [PMID: 34218011 DOI: 10.1016/j.colsurfb.2021.111956] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/17/2021] [Accepted: 06/25/2021] [Indexed: 11/22/2022]
Abstract
Despite efforts to achieve a long-acting formulation for human growth hormone (hGH), daily injections are still prescribed for children with growth hormone deficiency. To grapple with the issue, acquiring a deep knowledge of the protein and understanding its interaction mechanism with the carrier can be beneficial. Herein, we designed and synthesized a novel chitosan-based copolymer and investigated its interaction with hGH using a combination of experimental and computational strategies. To construct the amphiphilic triblock copolymers (CDP), we grafted deoxycholic acid (DCA) and polyacrylic acid (PAA) onto the chitosan chains, and Fourier-transform infrared (FTIR) analysis confirmed the proper formation of CDP. Circular dichroism (CD) demonstrated the preservation of the secondary structure of hGH interacting with CDP, and, further, fluorescence spectroscopy proved the stability of the tertiary structure of the protein. Applying molecular dynamics simulation (MD), we examined the dynamics and integrity of hGH in the presence of the copolymer and compared its behavior with the protein in aquatic environments. Additionally, energy and contact analysis illustrated that the residues involved in the interaction were located predominantly in the connecting loops, and van der Waals (vdW) and electrostatic interactions were the main driving forces of the polymer-protein complex formation. This research's main aim was to trace the protein-polymer interaction's mechanism. We anticipate that the utility of the copolymer can address the challenges of fabricating a new sustained-release delivery platform for therapeutic proteins.
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71
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Pan J, Gao L, Sun W, Wang S, Shi X. Length Effects of Short Alkyl Side Chains on Phase-Separated Structure and Dynamics of Hydrophobic Association Hydrogels. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00471] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Jiageng Pan
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, China
| | - Liang Gao
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, China
| | - Weixiang Sun
- School of Material Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Shuting Wang
- School of Material Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Xuetao Shi
- School of Material Science and Engineering, South China University of Technology, Guangzhou 510640, China
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72
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Phylogenetic analysis of mutational robustness based on codon usage supports that the standard genetic code does not prefer extreme environments. Sci Rep 2021; 11:10963. [PMID: 34040064 PMCID: PMC8154912 DOI: 10.1038/s41598-021-90440-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/10/2021] [Indexed: 02/04/2023] Open
Abstract
The mutational robustness of the genetic code is rarely discussed in the context of biological diversity, such as codon usage and related factors, often considered as independent of the actual organism's proteome. Here we put the living beings back to picture and use distortion as a metric of mutational robustness. Distortion estimates the expected severities of non-synonymous mutations measuring it by amino acid physicochemical properties and weighting for codon usage. Using the biological variance of codon frequencies, we interpret the mutational robustness of the standard genetic code with regards to their corresponding environments and genomic compositions (GC-content). Employing phylogenetic analyses, we show that coding fidelity in physicochemical properties can deteriorate with codon usages adapted to extreme environments and these putative effects are not the artefacts of phylogenetic bias. High temperature environments select for codon usages with decreased mutational robustness of hydrophobic, volumetric, and isoelectric properties. Selection at high saline concentrations also leads to reduced fidelity in polar and isoelectric patterns. These show that the genetic code performs best with mesophilic codon usages, strengthening the view that LUCA or its ancestors preferred lower temperature environments. Taxonomic implications, such as rooting the tree of life, are also discussed.
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73
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Yaguchi A, Hiramatsu H, Ishida A, Oshikawa M, Ajioka I, Muraoka T. Hydrogel-Stiffening and Non-Cell Adhesive Properties of Amphiphilic Peptides with Central Alkylene Chains. Chemistry 2021; 27:9295-9301. [PMID: 33871881 DOI: 10.1002/chem.202100739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 12/17/2022]
Abstract
Amphiphilic peptides bearing terminal alkyl tails form supramolecular nanofibers that are increasingly used as biomaterials with multiple functionalities. Insertion of alkylene chains in peptides can be designed as another type of amphiphilic peptide, yet the influence of the internal alkylene chains on self-assembly and biological properties remains poorly defined. Unlike the terminal alkyl tails, the internal alkylene chains can affect not only the hydrophobicity but also the flexibility and packing of the peptides. Herein, we demonstrate the supramolecular and biological effects of the central alkylene chain length inserted in a peptide. Insertion of the alkylene chain at the center of the peptide allowed for strengthened β-sheet hydrogen bonds and modulation of the packing order, and consequently the amphiphilic peptide bearing C2 alkylene chain formed a hydrogel with the highest stiffness. Interestingly, the amphiphilic peptides bearing internal alkylene chains longer than C2 showed a diminished cell-adhesive property. This study offers a novel molecular design to tune mechanical and biological properties of peptide materials.
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Affiliation(s)
- Atsuya Yaguchi
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Hirotsugu Hiramatsu
- Department of Applied Chemistry and Institute of Molecular Science, National Yang Ming Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu, 30010, Taiwan.,Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu, 30010, Taiwan
| | - Atsuya Ishida
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Mio Oshikawa
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.,Kanagawa Institute of Industrial Science and Technology, 705-1 Shimoimaizumi, Ebina, Kanagawa, 243-0435, Japan
| | - Itsuki Ajioka
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.,Kanagawa Institute of Industrial Science and Technology, 705-1 Shimoimaizumi, Ebina, Kanagawa, 243-0435, Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu-shi, Tokyo, 183-8538, Japan
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74
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Takase Y, Yamazaki Y, Hayashi Y, Toma-Fukai S, Kamikubo H. Structure elements can be predicted using the contact volume among protein residues. Biophys Physicobiol 2021; 18:50-59. [PMID: 33954082 PMCID: PMC8049775 DOI: 10.2142/biophysico.bppb-v18.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/15/2021] [Indexed: 12/01/2022] Open
Abstract
Previously, the structure elements of dihydrofolate reductase (DHFR) were determined using comprehensive Ala-insertion mutation analysis, which is assumed to be a kind of protein “building blocks.” It is hypothesized that our comprehension of the structure elements could lead to understanding how an amino acid sequence dictates its tertiary structure. However, the comprehensive Ala-insertion mutation analysis is a time- and cost-consuming process and only a set of the DHFR structure elements have been reported so far. Therefore, developing a computational method to predict structure elements is an urgent necessity. We focused on intramolecular residue–residue contacts to predict the structure elements. We introduced a simple and effective parameter: the overlapped contact volume (CV) among the residues and calculated the CV along the DHFR sequence using the crystal structure. Our results indicate that the CV profile can recapitulate its precipitate ratio profile, which was used to define the structure elements in the Ala-insertion mutation analysis. The CV profile allowed us to predict structure elements like the experimentally determined structure elements. The strong correlation between the CV and precipitate ratio profiles indicates the importance of the intramolecular residue–residue contact in maintaining the tertiary structure. Additionally, the CVs between the structure elements are considerably more than those between a structure element and a linker or two linkers, indicating that the structure elements play a fundamental role in increasing the intramolecular adhesion. Thus, we propose that the structure elements can be considered a type of “building blocks” that maintain and dictate the tertiary structures of proteins.
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Affiliation(s)
- Yasumichi Takase
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yoichi Yamazaki
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yugo Hayashi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Sachiko Toma-Fukai
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Hironari Kamikubo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.,Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
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75
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Andlinger DJ, Röscheisen P, Hengst C, Kulozik U. Influence of pH, Temperature and Protease Inhibitors on Kinetics and Mechanism of Thermally Induced Aggregation of Potato Proteins. Foods 2021; 10:foods10040796. [PMID: 33917748 PMCID: PMC8068184 DOI: 10.3390/foods10040796] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 01/07/2023] Open
Abstract
Understanding aggregation in food protein systems is essential to control processes ranging from the stabilization of colloidal dispersions to the formation of macroscopic gels. Patatin rich potato protein isolates (PPI) have promising techno-functionality as alternatives to established proteins from egg white or milk. In this work, the influence of pH and temperature on the kinetics of PPI denaturation and aggregation was investigated as an option for targeted functionalization. At a slightly acidic pH, rates of denaturation and aggregation of the globular patatin in PPI were fast. These aggregates were shown to possess a low amount of disulfide bonds and a high amount of exposed hydrophobic amino acids (S0). Gradually increasing the pH slowed down the rate of denaturation and aggregation and alkaline pH levels led to an increased formation of disulfide bonds within these aggregates, whereas S0 was reduced. Aggregation below denaturation temperature (Td) favored aggregation driven by disulfide bridge formation. Aggregation above Td led to fast unfolding, and initial aggregation was less determined by disulfide bridge formation. Inter-molecular disulfide formation occurred during extended heating times. Blocking different protein interactions revealed that the formation of disulfide bond linked aggregation is preceded by the formation of non-covalent bonds. Overall, the results help to control the kinetics, morphology, and interactions of potato protein aggregation for potential applications in food systems.
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76
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Sharma A, Sharma P, Roy S. Elastin-inspired supramolecular hydrogels: a multifaceted extracellular matrix protein in biomedical engineering. SOFT MATTER 2021; 17:3266-3290. [PMID: 33730140 DOI: 10.1039/d0sm02202k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The phenomenal advancement in regenerative medicines has led to the development of bioinspired materials to fabricate a biomimetic artificial extracellular matrix (ECM) to support cellular survival, proliferation, and differentiation. Researchers have diligently developed protein polymers consisting of functional sequences of amino acids evolved in nature. Nowadays, certain repetitive bioinspired polymers are treated as an alternative to synthetic polymers due to their unique properties like biodegradability, easy scale-up, biocompatibility, and non-covalent molecular associations which imparts tunable supramolecular architecture to these materials. In this direction, elastin has been identified as a potential scaffold that renders extensibility and elasticity to the tissues. Elastin-like polypeptides (ELPs) are artificial repetitive polymers that exhibit lower critical solution temperature (LCST) behavior in a particular environment than synthetic polymers and hence have gained extensive interest in the fabrication of stimuli-responsive biomaterials. This review discusses in detail the unique structural aspects of the elastin and its soluble precursor, tropoelastin. Furthermore, the versatility of elastin-like peptides is discussed through numerous examples that bolster the significance of elastin in the field of regenerative medicines such as wound care, cardiac tissue engineering, ocular disorders, bone tissue regeneration, etc. Finally, the review highlights the importance of exploring short elastin-mimetic peptides to recapitulate the structural and functional aspects of elastin for advanced healthcare applications.
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Affiliation(s)
- Archita Sharma
- Institute of Nano Science and Technology (INST), Sector 81, Knowledge City, Mohali, 140306, Punjab, India.
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77
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Fogalli GB, Line SRP. Estimating the Influence of Physicochemical and Biochemical Property Indexes on Selection for Amino Acids Usage in Eukaryotic Cells. J Mol Evol 2021; 89:257-268. [PMID: 33760966 DOI: 10.1007/s00239-021-10003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 03/10/2021] [Indexed: 11/26/2022]
Abstract
Proteins can evolve by accumulating changes on amino acid sequences. These changes are mainly caused by missense mutations on its DNA coding sequences. Mutations with neutral or positive effects on fitness can be maintained while deleterious mutations tend to be eliminated by natural selection. Amino acid changes are influenced by the biophysical, chemical, and biological properties of amino acids. There is a multiplicity of amino acid properties that can influence the function and expression of proteins. Amino acid properties can be expressed into numerical indexes, which can help to predict functional and structural aspects of proteins and allow statistical inferences of selection pressure on amino acid usage. The accuracy of these analyses may be compromised by the existence of several numerical indexes that measure the same amino acid property, and the lack of objective parameters to determine the most accurate and biologically relevant index. In the present study, the gradient consistency test was used in order to estimate the magnitude of directional selection imparted by amino acid biochemical and biophysical properties on protein evolution.
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Affiliation(s)
- Giovani B Fogalli
- Department of Biosciences, Piracicaba Dental School, University of Campinas, Campinas, Brazil
| | - Sergio R P Line
- Department of Biosciences, Piracicaba Dental School, University of Campinas, Campinas, Brazil.
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78
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Wang C, Biok NA, Nayani K, Wang X, Yeon H, Derek Ma CK, Gellman SH, Abbott NL. Cationic Side Chain Identity Directs the Hydrophobically Driven Self-Assembly of Amphiphilic β-Peptides in Aqueous Solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3288-3298. [PMID: 33683138 DOI: 10.1021/acs.langmuir.0c03255] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Hydrophobic interactions mediated by nonpolar molecular fragments in water are influenced by local chemical and physical contexts in ways that are not yet fully understood. Here, we use globally amphiphilic (GA) β-peptides (GA-Lys and GA-Arg) with stable conformations to explore if replacement of β3-homolysine (βLys) with β3-homoarginine (βArg) influences the hydrophobically driven assembly of these peptides in bulk aqueous solution. The studies were conducted in 10 mM triethanolamine buffer at pH 7, where both βLys (ammonium) and βArg (guanidinium) side chains are substantially protonated. Comparisons of light scattering measurements and cryo-electron micrographs before and after the addition of 60 vol% MeOH indicate very different outcomes of the hydrophobically driven assembly of AcY-GA-Lys versus AcY-GA-Arg (AcY denotes an N-acetylated-β3-homotyrosine (βTyr) at each N-terminus). Nuclear magnetic resonance and analytical ultracentrifugation confirm that AcY-GA-Lys assembles into large aggregates in aqueous buffer, whereas AcY-GA-Arg at comparable concentrations forms only small oligomers. Titration of AcY-GA-Arg into aqueous solutions of AcY-GA-Lys reveals that the driving force for AcY-GA-Lys association is far stronger than that for AcY-GA-Arg association. We discuss these results in the light of past experimental observations involving single molecule force measurements with GA β-peptides and hydrophobically driven dimerization of conventional peptides that form a GA α-helix upon dimerization (but do not display the Lys versus Arg trend predicted by extrapolating from the earlier AFM studies with β-peptides). Overall, our results establish that the identity of proximal cationic groups, ammonium versus guanidinium, profoundly modulates the hydrophobically driven self-assembly of conformationally stable β-peptides in bulk aqueous solution.
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Affiliation(s)
- Chenxuan Wang
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
- Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Naomi A Biok
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
| | - Karthik Nayani
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca14853, New York, United States
| | - Xiaoguang Wang
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Hongseung Yeon
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Chi-Kuen Derek Ma
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
| | - Nicholas L Abbott
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca14853, New York, United States
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79
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Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun 2021; 12:1085. [PMID: 33597515 PMCID: PMC7889641 DOI: 10.1038/s41467-021-21181-9] [Citation(s) in RCA: 223] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/08/2021] [Indexed: 01/31/2023] Open
Abstract
Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.
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80
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Krainer G, Welsh TJ, Joseph JA, Espinosa JR, Wittmann S, de Csilléry E, Sridhar A, Toprakcioglu Z, Gudiškytė G, Czekalska MA, Arter WE, Guillén-Boixet J, Franzmann TM, Qamar S, George-Hyslop PS, Hyman AA, Collepardo-Guevara R, Alberti S, Knowles TPJ. Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun 2021; 12:1085. [PMID: 33597515 DOI: 10.1101/2020.05.04.076299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/08/2021] [Indexed: 05/26/2023] Open
Abstract
Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.
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Affiliation(s)
- Georg Krainer
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jerelle A Joseph
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Jorge R Espinosa
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Sina Wittmann
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Ella de Csilléry
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Akshay Sridhar
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Zenon Toprakcioglu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Giedre Gudiškytė
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Magdalena A Czekalska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka, 44/52 01-224, Warsaw, Poland
| | - William E Arter
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jordina Guillén-Boixet
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Titus M Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Seema Qamar
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Peter St George-Hyslop
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
- Division of Neurology, Department of Medicine, University of Toronto and University Health Network, Toronto, Ontario, Canada.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
| | - Rosana Collepardo-Guevara
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany.
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.
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81
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Schalck T, den Bergh BV, Michiels J. Increasing Solvent Tolerance to Improve Microbial Production of Alcohols, Terpenoids and Aromatics. Microorganisms 2021; 9:249. [PMID: 33530454 PMCID: PMC7912173 DOI: 10.3390/microorganisms9020249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Fuels and polymer precursors are widely used in daily life and in many industrial processes. Although these compounds are mainly derived from petrol, bacteria and yeast can produce them in an environment-friendly way. However, these molecules exhibit toxic solvent properties and reduce cell viability of the microbial producer which inevitably impedes high product titers. Hence, studying how product accumulation affects microbes and understanding how microbial adaptive responses counteract these harmful defects helps to maximize yields. Here, we specifically focus on the mode of toxicity of industry-relevant alcohols, terpenoids and aromatics and the associated stress-response mechanisms, encountered in several relevant bacterial and yeast producers. In practice, integrating heterologous defense mechanisms, overexpressing native stress responses or triggering multiple protection pathways by modifying the transcription machinery or small RNAs (sRNAs) are suitable strategies to improve solvent tolerance. Therefore, tolerance engineering, in combination with metabolic pathway optimization, shows high potential in developing superior microbial producers.
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Affiliation(s)
- Thomas Schalck
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Bram Van den Bergh
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Jan Michiels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
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82
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Lin Y, Fichou Y, Longhini AP, Llanes LC, Yin P, Bazan GC, Kosik KS, Han S. Liquid-Liquid Phase Separation of Tau Driven by Hydrophobic Interaction Facilitates Fibrillization of Tau. J Mol Biol 2021; 433:166731. [PMID: 33279579 PMCID: PMC7855949 DOI: 10.1016/j.jmb.2020.166731] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022]
Abstract
Amyloid aggregation of tau protein is implicated in neurodegenerative diseases, yet its facilitating factors are poorly understood. Recently, tau has been shown to undergo liquid liquid phase separation (LLPS) both in vivo and in vitro. LLPS was shown to facilitate tau amyloid aggregation in certain cases, while being independent of aggregation in other cases. It is therefore important to understand the differentiating properties that resolve this apparent conflict. We report on a model system of hydrophobically driven LLPS induced by high salt concentration (LLPS-HS), and compare it to electrostatically driven LLPS represented by tau-RNA/heparin complex coacervation (LLPS-ED). We show that LLPS-HS promotes tau protein dehydration, undergoes maturation and directly leads to canonical tau fibrils, while LLPS-ED is reversible, remains hydrated and does not promote amyloid aggregation. We show that the nature of the interaction driving tau condensation is a differentiating factor between aggregation-prone and aggregation-independent LLPS.
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Affiliation(s)
- Yanxian Lin
- Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Yann Fichou
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States
| | - Andrew P Longhini
- Molecular, Cell and Developmental Biology, University of California, Santa Barbara, CA 93106, United States
| | - Luana C Llanes
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States; Center for Polymers and Organic Solids, University of California, Santa Barbara, CA 93106, United States
| | - Pengyi Yin
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States
| | - Guillermo C Bazan
- Departments of Chemistry and Chemical Engineering, National University of Singapore, 117543, Singapore
| | - Kenneth S Kosik
- Molecular, Cell and Developmental Biology, University of California, Santa Barbara, CA 93106, United States; Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, United States
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States; Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States.
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83
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Pham P, Oliver S, Wong EHH, Boyer C. Effect of hydrophilic groups on the bioactivity of antimicrobial polymers. Polym Chem 2021. [DOI: 10.1039/d1py01075a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Antimicrobial polymers have recently been investigated as potential treatments to combat multidrug-resistant pathogens.
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Affiliation(s)
- Phuong Pham
- Australian Centre for NanoMedicine and Cluster for Advanced Macromolecular Design (CAMD), School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Susan Oliver
- Australian Centre for NanoMedicine and Cluster for Advanced Macromolecular Design (CAMD), School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Edgar H. H. Wong
- Australian Centre for NanoMedicine and Cluster for Advanced Macromolecular Design (CAMD), School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Cyrille Boyer
- Australian Centre for NanoMedicine and Cluster for Advanced Macromolecular Design (CAMD), School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
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84
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Percástegui E, Ronson TK, Nitschke JR. Design and Applications of Water-Soluble Coordination Cages. Chem Rev 2020; 120:13480-13544. [PMID: 33238092 PMCID: PMC7760102 DOI: 10.1021/acs.chemrev.0c00672] [Citation(s) in RCA: 238] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Indexed: 12/23/2022]
Abstract
Compartmentalization of the aqueous space within a cell is necessary for life. In similar fashion to the nanometer-scale compartments in living systems, synthetic water-soluble coordination cages (WSCCs) can isolate guest molecules and host chemical transformations. Such cages thus show promise in biological, medical, environmental, and industrial domains. This review highlights examples of three-dimensional synthetic WSCCs, offering perspectives so as to enhance their design and applications. Strategies are presented that address key challenges for the preparation of coordination cages that are soluble and stable in water. The peculiarities of guest binding in aqueous media are examined, highlighting amplified binding in water, changing guest properties, and the recognition of specific molecular targets. The properties of WSCC hosts associated with biomedical applications, and their use as vessels to carry out chemical reactions in water, are also presented. These examples sketch a blueprint for the preparation of new metal-organic containers for use in aqueous solution, as well as guidelines for the engineering of new applications in water.
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Affiliation(s)
- Edmundo
G. Percástegui
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Instituto
de Química, Ciudad UniversitariaUniversidad
Nacional Autónoma de México, Ciudad de México 04510, México
- Centro
Conjunto de Investigación en Química Sustentable, UAEM-UNAM, Carretera Toluca-Atlacomulco Km 14.5, Toluca, 50200 Estado de México, México
| | - Tanya K. Ronson
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Jonathan R. Nitschke
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
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85
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Blum MM, Richter A, Siegert M, Thiermann H, John H. Adduct of the blistering warfare agent sesquimustard with human serum albumin and its mass spectrometric identification for biomedical verification of exposure. Anal Bioanal Chem 2020; 412:7723-7737. [PMID: 32902690 PMCID: PMC7550388 DOI: 10.1007/s00216-020-02917-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/07/2020] [Accepted: 08/25/2020] [Indexed: 11/24/2022]
Abstract
Apart from the well-known sulfur mustard (SM), additional sulfur-containing blistering chemical warfare agents exist. Sesquimustard (Q) is one of them and five times more blistering than SM. It is a common impurity in mustard mixtures and regularly found in old munitions but can also be used in pure form. Compared to the extensive literature on SM, very little experimental data is available on Q and no protein biomarkers of exposure have been reported. We herein report for the first time the adduct of Q with the nucleophilic Cys34 residue of human serum albumin (HSA) formed in vitro and introduce two novel bioanalytical procedures for detection. After proteolysis of this HSA adduct catalyzed either by pronase or by proteinase K, two biomarkers were identified by high-resolution tandem mass spectrometry (MS/HR MS), namely a dipeptide and a tripeptide, both alkylated at their Cys residue, which we refer to as HETETE-CP and HETETE-CPF. HETETE represents the Q-derived thio-alkyl moiety bearing a terminal hydroxyl group: "hydroxyethylthioethylthioethyl." Targeting both peptide markers from plasma, a micro liquid chromatography-electrospray ionization tandem mass spectrometry method working in the selected reaction monitoring mode (μLC-ESI MS/MS SRM) was developed and validated as well suited for the verification of exposure to Q. Fulfilling the quality criteria defined by the Organisation for the Prohibition of Chemical Weapons, the novel methods enable the detection of exposure to Q alone or in mixtures with SM. We further report on the relative reactivity of Q compared to SM. Based on experiments making use of partially deuterated Q as the alkylating agent, we rule out a major role for six-membered ring sulfonium ions as relevant reactive species in the alkylation of Cys34. Furthermore, the results of molecular dynamics simulations are indicative that the protein environment around Cys34 allows adduct formation with elongated but not bulky molecules such as Q, and identify important hydrogen bonding interactions and hydrophobic contacts. Graphical abstract.
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Affiliation(s)
- Marc-Michael Blum
- Blum - Scientific Services, Björnsonweg 70d, 22587, Hamburg, Germany
| | - Annika Richter
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Markus Siegert
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany
| | - Horst Thiermann
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany
| | - Harald John
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany.
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86
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Na J, Hwang E, Choi JS, Ji MJ, Noh Y, Lim YB, Choi HJ. A Three-Dimensional Sensor to Recognize Amyloid-β in Blood Plasma of Patients. ACS OMEGA 2020; 5:27295-27303. [PMID: 33134692 PMCID: PMC7594136 DOI: 10.1021/acsomega.0c03578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Detecting amyloid beta (Aβ) in unpurified blood to diagnose Alzheimer's disease (AD) is challenging owing to low concentrations of Aβ and the presence of many other substances in the blood. Here, we propose a 3D sensor for AD diagnosis using blood plasma, with pairs of 3D silicon micropillar electrodes with a comprehensive circuit configuration. The sensor is developed with synthesized artificial peptide and impedance analysis based on a maximum signal-to-noise ratio. Its sensitivity and selectivity were verified using an in vitro test based on samples of human blood serum, which showed its feasibility for application in diagnosis of AD by testing blood plasma of the AD patient. The 3D sensor is designed to improve reliability by checking the impedance of each pair multiple times via constructing a reference pair and a working pair on the same sensor. Therefore, we demonstrate the ability of the 3D sensor to recognize cases of AD using blood plasma and introduce its potential as a self-health care sensor for AD patients.
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Affiliation(s)
- Jukwan Na
- Department
of Materials Science and Engineering, Yonsei
University, Seoul 03722, Republic of Korea
| | - Euimin Hwang
- Department
of Materials Science and Engineering, Yonsei
University, Seoul 03722, Republic of Korea
| | - Jun Shik Choi
- Department
of Materials Science and Engineering, Yonsei
University, Seoul 03722, Republic of Korea
| | - Min-Jin Ji
- Department
of Health Science and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea
| | - Young Noh
- Department
of Health Science and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea
- Department
of Neurology, Gil Medical Center, Gachon
University College of Medicine, Incheon 21565, Republic of Korea
| | - Yong-beom Lim
- Department
of Materials Science and Engineering, Yonsei
University, Seoul 03722, Republic of Korea
| | - Heon-Jin Choi
- Department
of Materials Science and Engineering, Yonsei
University, Seoul 03722, Republic of Korea
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87
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Mallajosyula VVA, Swaroop S, Varadarajan R. Influenza Hemagglutinin Head Domain Mimicry by Rational Design. Protein J 2020; 39:434-448. [PMID: 33068234 DOI: 10.1007/s10930-020-09930-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 02/07/2023]
Abstract
Despite diligent vaccination efforts, influenza virus infection remains a major cause for respiratory-related illness across the globe. The less-than-optimal immunity conferred by the currently prescribed seasonal vaccines and protracted production times warrant the development of novel vaccines. Induction of an epitope-focused antibody response targeting known neutralization epitopes is a viable strategy to enhance the breadth of protection against rapidly evolving infectious viruses. We report the development of a design framework to mimic the hemagglutinin (HA) head fragment of H1-subtype viruses by delineating the interaction network of invariant residues lining the receptor binding site (RBS); a site targeted by cross-reactive neutralizing antibodies. The incorporation of multiple sequence alignment information in our algorithm to fix the construct termini and engineer rational mutations facilitates the facile extension of the design to heterologous (subtype-specific) influenza strains. We evaluated our design protocol by generating head fragments from divergent influenza A H1N1 A/Puerto Rico/8/34 and pH1N1 A/California/07/2009 strains that share a sequence identity of only 74.4% within the HA1 subunit. The designed immunogens exhibited characteristics of a well-ordered protein, and bound conformation-specific RBS targeting antibodies with high affinity, a desirable feature for putative vaccine candidates. Additionally, the bacterial expression of these immunogens provides a low-cost, rapidly scalable alternative.
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Affiliation(s)
| | - Shiv Swaroop
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.,Department of Biochemistry, Central University of Rajasthan, Kishangarh, Ajmer, 305817, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
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88
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New insights on human IRE1 tetramer structures based on molecular modeling. Sci Rep 2020; 10:17490. [PMID: 33060689 PMCID: PMC7567888 DOI: 10.1038/s41598-020-74347-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/29/2020] [Indexed: 11/29/2022] Open
Abstract
Inositol-Requiring Enzyme 1α (IRE1α; hereafter IRE1) is a transmembrane kinase/ribonuclease protein related with the unfolded protein response (UPR) signaling. Experimental evidence suggests that IRE1 forms several three dimensional (3D) structural variants: dimers, tetramers and higher order oligomers, where each structural variant can contain different IRE1 conformers in different arrangements. For example, studies have shown that two sets of IRE1 dimers exist; a face-to-face dimer and a back-to-back dimer, with the latter considered the important unit for UPR signaling propagation. However, the structural configuration and mechanistic details of the biologically important IRE1 tetramers are limited. Here, we combine protein–protein docking with molecular dynamics simulations to derive human IRE1 tetramer models and identify a molecular mechanism of IRE1 activation. To validate the derived models of the human IRE1 tetramer, we compare the dynamic behavior of the models with the yeast IRE1 tetramer crystallographic structure. We show that IRE1 tetramer conformational changes could be linked to the initiation of the unconventional splicing of mRNA encoding X-box binding protein-1 (XBP1), which allows for the expression of the transcription factor XBP1s (XBP1 spliced). The derived IRE1 tetrameric models bring new mechanistic insights about the IRE1 molecular activation mechanism by describing the IRE1 tetramers as active protagonists accommodating the XBP1 substrate.
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89
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Zhao L, Wang S, Yang Z, Tian L, Gao L, Shi X. Structural evolution of dispersed hydrophobic association in a hydrogel analyzed by the tensile behavior. SOFT MATTER 2020; 16:8245-8253. [PMID: 32803214 DOI: 10.1039/d0sm01211d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The use of dispersed cross-links with different levels of strength is one of the most successful strategies for toughening a hydrogel. By using a model hydrogel having dispersed association of single-component short alkyl chains, this work demonstrates that the differential modulus-elongation relation derived from tensile curves can reflect the structural evolution of dispersed cross-links at a molecular level. This analysis method allows for decoupling the mechanical contribution of strong and weak hydrophobic clusters, which serve as the minor and major cross-links in our system, respectively. At small deformation, the weak hydrophobic associations majorly determine the stiffness, and their rupture releases folded partial chains to endow deformation capacity. At large deformation, the strength ratio of strong and weak hydrophobic association should be balanced to achieve the optimal strength. Furthermore, the structural parameters of these partial chains, including the Kuhn number, the Kuhn length and the chain conformation, are determined based on scaling theory of extensibility. These results allow for correlating the apparent mechanics to the structural parameters of the dispersed hydrophobic association, paving the way for customized mechanics for specific applications.
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Affiliation(s)
- Liang Zhao
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Shuting Wang
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Zican Yang
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Luming Tian
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Liang Gao
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Xuetao Shi
- National Engineering Research Centre for Tissue Restoration and Reconstruction and School of Material Science and Engineering, South China University of Technology, Guangzhou, 510640, P. R. China.
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90
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Ou X, Xue B, Lao Y, Wutthinitikornkit Y, Tian R, Zou A, Yang L, Wang W, Cao Y, Li J. Structure and sequence features of mussel adhesive protein lead to its salt-tolerant adhesion ability. SCIENCE ADVANCES 2020; 6:6/39/eabb7620. [PMID: 32978166 PMCID: PMC7518861 DOI: 10.1126/sciadv.abb7620] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/12/2020] [Indexed: 05/11/2023]
Abstract
Mussels can strongly adhere to hydrophilic minerals in sea habitats by secreting adhesive proteins. The adhesion ability of these proteins is often attributed to the presence of Dopa derived from posttranslational modification of Tyr, whereas the contribution of structural feature is overlooked. It remains largely unknown how adhesive proteins overcome the surface-bound water layer to establish underwater adhesion. Here, we use molecular dynamics simulations to probe the conformations of adhesive protein Pvfp-5β and its salt-tolerant underwater adhesion on superhydrophilic mica. Dopa and positively charged basic residues form pairs, in this intrinsically disordered protein, and these residue pairs can lead to firm surface binding. Our simulations further suggest that the unmodified Tyr shows similar functions on surface adhesion by forming pairing structure with a positively charged residue. We confirm the presence of these residue pairs and verify the strong binding ability of unmodified proteins using nuclear magnetic resonance spectroscopy and lap shear tests.
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Affiliation(s)
- Xinwen Ou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yichong Lao
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Yanee Wutthinitikornkit
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Ranran Tian
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Aodong Zou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Lingyun Yang
- iHuman Institute, Shanghai Tech University, 393 Hua Xia Zhong Road, Shanghai 201210, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China.
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China.
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91
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Khanppnavar B, Roy A, Chandra K, Uversky VN, Maiti NC, Datta S. Deciphering the structural intricacy in virulence effectors for proton-motive force mediated unfolding in type-III protein secretion. Int J Biol Macromol 2020; 159:18-33. [DOI: 10.1016/j.ijbiomac.2020.04.266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 10/24/2022]
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92
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Liu J, Lu G, Cui Y, Wei S, An T, Shen G, Chen Z. An insight into the transmission role of insect vectors based on the examination of gene characteristics of African swine fever virus originated from non-blood sucking flies in pig farm environments. BMC Vet Res 2020; 16:227. [PMID: 32615970 PMCID: PMC7331130 DOI: 10.1186/s12917-020-02420-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/08/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Insect vector transmitted pathogens from contaminated environments are a key potential risk for public health. Meanwhile, transmission by non-blood sucking flies needs to be considered. Sequencing and phylogenetic tree analyses were used to study African swine fever virus (ASFV) genes derived from flies collected from pig farms that were infected with ASFV. The major differential genes were analyzed the encoded proteins, particularly their conformation, physico-chemical features, and interactions identified by immunophenotyping. RESULTS Results showed that the ASFV p72 and D117L genes from these non-blood sucking flies identified by morphology have high sequence similarity from ASFV genotype II strains, however, A179L is found in an independent cluster, with five amino acid substitutions; four of which are in a continuous sequence. Moreover, the binding of a BH3 peptide into a surface groove formed by α-helices of ASFV A179L from the non-blood sucking flies is consistent with that of representative ASFV genotype II strains, Georgia/2007.They only differ in the direction of spatial interaction of six conserved amino residues. Many hydrophilic amino residues are located at the canonical ligand-binding groove of A179L from flies, with hydrophobic amino residues located at the corresponding positions in A179L of the Georgia/2007.Furthermore, analysis of protein interactions by immunophenotyping revealed that both A179Ls have similar roles in regulating autophagy and apoptosis. CONCLUSIONS In conclusion, the main genes that differ between ASFV from flies and Georgia/2007 were similar in structure and protein interaction, while exhibiting differences in physico-chemical features and amino acid variations. Understanding the mechanical transmission characteristics of non-blood sucking flies is important.
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Affiliation(s)
- Jinling Liu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, No.120, Dongling Road, Shenhe District, Shenyang, 110866, PR China
| | - Gen Lu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, No.120, Dongling Road, Shenhe District, Shenyang, 110866, PR China
| | - Yuesong Cui
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, No.120, Dongling Road, Shenhe District, Shenyang, 110866, PR China
| | - Shu Wei
- The Preventive Center of Animal Disease of Liaoning Province, No.95, Renhe Road, Shenbei District, Shenyang, 110164, PR China
| | - Tongqing An
- Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, No. 678, Haping road, Xiangfang district, Harbin, 150069, PR China
| | - Guoshun Shen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, No.120, Dongling Road, Shenhe District, Shenyang, 110866, PR China.
| | - Zeliang Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, No.120, Dongling Road, Shenhe District, Shenyang, 110866, PR China.
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, PR China.
- Brucellosis Prevention and Treatment Engineering Technology Research Center of Inner Mongolia Autonomous region, Inner Mongolia University for Nationalities, Tongliao, 028000, PR China.
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93
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Trehalose Effect on the Aggregation of Model Proteins into Amyloid Fibrils. Life (Basel) 2020; 10:life10050060. [PMID: 32414105 PMCID: PMC7281244 DOI: 10.3390/life10050060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
Protein aggregation into amyloid fibrils is a phenomenon that attracts attention from a wide and composite part of the scientific community. Indeed, the presence of mature fibrils is associated with several neurodegenerative diseases, and in addition these supramolecular aggregates are considered promising self-assembling nanomaterials. In this framework, investigation on the effect of cosolutes on protein propensity to aggregate into fibrils is receiving growing interest, and new insights on this aspect might represent valuable steps towards comprehension of highly complex biological processes. In this work we studied the influence exerted by the osmolyte trehalose on fibrillation of two model proteins, that is, lysozyme and insulin, investigated during concomitant variation of the solution ionic strength due to NaCl. In order to monitor both secondary structures and the overall tridimensional conformations, we have performed UV spectroscopy measurements with Congo Red, Circular Dichroism, and synchrotron Small Angle X-ray Scattering. For both proteins we describe the effect of trehalose in changing the fibrillation pattern and, as main result, we observe that ionic strength in solution is a key factor in determining trehalose efficiency in slowing down or blocking protein fibrillation. Ionic strength reveals to be a competitive element with respect to trehalose, being able to counteract its inhibiting effects toward amyloidogenesis. Reported data highlight the importance of combining studies carried out on cosolutes with valuation of other physiological parameters that may affect the aggregation process. Also, the obtained experimental results allow to hypothesize a plausible mechanism adopted by the osmolyte to preserve protein surface and prevent protein fibrillation.
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94
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Thevendran R, Sarah S, Tang TH, Citartan M. Strategies to bioengineer aptamer-driven nanovehicles as exceptional molecular tools for targeted therapeutics: A review. J Control Release 2020; 323:530-548. [PMID: 32380206 DOI: 10.1016/j.jconrel.2020.04.051] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 02/06/2023]
Abstract
Aptamers are a class of folded nucleic acid strands capable of binding to different target molecules with high affinity and selectivity. Over the years, they have gained a substantial amount of interest as promising molecular tools for numerous medical applications, particularly in targeted therapeutics. However, only the different treatment approaches and current developments of aptamer-drug therapies have been discussed so far, ignoring the crucial technical and functional aspects of constructing a therapeutically effective aptamer-driven drug delivery system that translates to improved in-vivo performance. Hence, this paper provides a comprehensive review of the strategies used to improve the therapeutic performance of aptamer-guided delivery systems. We focus on the different functional features such as drug deployment, payload capacity, in-vivo stability and targeting efficiency to further our knowledge in enhancing the cell-specific delivery of aptamer-drug conjugates. Each reported strategy is critically discussed to emphasize both the benefits provided in comparison with other similar techniques and to outline their potential drawbacks with respect to the molecular properties of the aptamers, the drug and the system to be designed. The molecular architecture and design considerations for an efficient aptamer-based delivery system are also briefly elaborated.
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Affiliation(s)
- Ramesh Thevendran
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Shigdar Sarah
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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95
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Nagpal U, Kamalesh D, Raghuraman P, Ramireddy S, Sudandiradoss C. Delineating the folding perturbations and molecular mechanisms of Thr-Ala 642 mutation in Rab-GTPase activating protein Akt substrate of 160kDa and its impact on the aetiology of diabetes. J Biomol Struct Dyn 2020; 39:409-420. [DOI: 10.1080/07391102.2020.1726814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Utkarsh Nagpal
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India
| | - D. Kamalesh
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India
| | - P. Raghuraman
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India
| | - Sriroopreddy Ramireddy
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India
| | - C. Sudandiradoss
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India
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96
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Przeradzka MA, Freato N, Boon-Spijker M, van Galen J, van der Zwaan C, Mertens K, van den Biggelaar M, Meijer AB. Unique surface-exposed hydrophobic residues in the C1 domain of factor VIII contribute to cofactor function and von Willebrand factor binding. J Thromb Haemost 2020; 18:364-372. [PMID: 31675465 DOI: 10.1111/jth.14668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/29/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND The identity of the amino acid regions of factor VIII (FVIII) that contribute to factor IXa (FIXa) and von Willebrand factor (VWF) binding has not been fully resolved. Previously, we observed that replacing the FVIII C1 domain for the one of factor V (FV) markedly reduces VWF binding and cofactor function. Compared to the FV C1 domain, this implies that the FVIII C1 domain comprises unique surface-exposed elements involved in VWF and FIXa interaction. OBJECTIVE The aim of this study is to identify residues in the FVIII C1 domain that contribute to VWF and FIXa binding. METHODS Structures and primary sequences of FVIII and FV were compared to identify surface-exposed residues unique to the FVIII C1 domain. The identified residues were replaced with alanine residues to identify their role in FIXa and VWF interaction. This role was assessed employing surface plasmon resonance analysis studies and enzyme kinetic assays. RESULTS Five surface-exposed hydrophobic residues unique to the FVIII C1 domain, ie, F2035, F2068, F2127, V2130, I2139 were identified. Functional analysis indicated that residues F2068, V2130, and especially F2127 contribute to VWF and/or FIXa interaction. Substitution into alanine of the also surface-exposed V2125, which is spatially next to F2127, affected only VWF binding. CONCLUSION The surface-exposed hydrophobic residues in C1 domain contribute to cofactor function and VWF binding. These findings provide novel information on the fundamental role of the C1 domain in FVIII life cycle.
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Affiliation(s)
- Małgorzata A Przeradzka
- Department of Molecular and Cellular Hemostasis, Sanquin Research, Amsterdam, the Netherlands
| | - Nadia Freato
- Department of Molecular and Cellular Hemostasis, Sanquin Research, Amsterdam, the Netherlands
| | - Mariëtte Boon-Spijker
- Department of Molecular and Cellular Hemostasis, Sanquin Research, Amsterdam, the Netherlands
| | - Josse van Galen
- Department of Molecular and Cellular Hemostasis, Sanquin Research, Amsterdam, the Netherlands
| | - Carmen van der Zwaan
- Department of Molecular and Cellular Hemostasis, Sanquin Research, Amsterdam, the Netherlands
| | - Koen Mertens
- Department of Molecular and Cellular Hemostasis, Sanquin Research, Amsterdam, the Netherlands
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, the Netherlands
| | | | - Alexander B Meijer
- Department of Molecular and Cellular Hemostasis, Sanquin Research, Amsterdam, the Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, the Netherlands
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97
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In silico analysis of caprine superoxide dismutase 1 (SOD1) gene. Genomics 2020; 112:212-217. [DOI: 10.1016/j.ygeno.2019.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 01/22/2019] [Indexed: 01/18/2023]
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98
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Gupta S, Dasmahapatra AK. Destabilization potential of phenolics on Aβ fibrils: mechanistic insights from molecular dynamics simulation. Phys Chem Chem Phys 2020; 22:19643-19658. [DOI: 10.1039/d0cp02459g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ellagic acid from pomegranate and walnuts is found to destabilize Aβ fibrils. It can be a potential drug to treat AD.
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Affiliation(s)
- Shivani Gupta
- Department of Chemical Engineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Ashok Kumar Dasmahapatra
- Department of Chemical Engineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
- Center for Nanotechnology
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99
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Swain LL, Mishra C, Sahoo SS, Nayak G, Pradhan SK, Mishra SR, Dige M. An in vivo and in silico analysis of novel variation in TMBIM6 gene affecting cardiopulmonary traits of Indian goats. J Therm Biol 2019; 88:102491. [PMID: 32125979 DOI: 10.1016/j.jtherbio.2019.102491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/30/2019] [Accepted: 12/23/2019] [Indexed: 01/17/2023]
Abstract
Transmembrane Bax Inhibitor Motif-containing 6 (TMBIM6) gene acts as calcium leak channel and negatively regulates autophagy and autophagosome formation. The TMBIM6 gene was amplified and searched for variation in three different goat populations (i.e. Black Bengal, Ganjam and Raighar) of Odisha state of the India. The result indicated two substitutions i.e. 55th position (C55T) and 95th position (C95A) in the amplified region of the gene resulting in change of amino acids (Leu > Phe and Thr > Asn). The identified SNPs were combined to form haplotypes and animals were grouped accordingly. Structural analysis showed minor changes (5%) in between mutant and wild TMBIM6 protein structures. However, any functional variation could not be identified with respect to the calcium ligand and open pore state. But an alteration of calcium binding site was found. The binding interaction of calcium with the TMBIM6 protein was hydrophobic in nature in closed state whereas hydrophilic in open pore stage. The stress releasing function was the result of calcium leakage controlled by amino acids coded by exon 4 and exon 5 regions of TMBIM6 gene. The effect of breed and haplotype on cardiopulmonary traits was studied. The data on cardiopulmonary traits of body i.e. rectal temperature, skin temperature, heart rate and respiration rate were recorded when ambient temperature usually remained the highest. The statistical analysis showed, significant difference in rectal temperature, skin temperature and respiration rate among these goat populations. The haplotypes (CC and TA) were found to have a significant (P < 0.05) effect on rectal temperature, skin temperature and respiration rate. However, any such significant effect could not be identified in recorded heart rate. The objective of the present study to identify the genetic variations in TMBIM6 gene having significant effect on cardiopulmonary traits which can be further uses as the molecular markers to improve heat tolerance mechanism in goats.
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Affiliation(s)
- Lipi Lekha Swain
- Department of Animal Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India.
| | - Chinmoy Mishra
- Department of Animal Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India.
| | - Siddhant Sekhar Sahoo
- Department of Animal Breeding and Genetics, National Dairy Research Institute, Karnal, India.
| | - Gangadhar Nayak
- Department of Animal Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar, India.
| | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, India.
| | - Smruti Ranjan Mishra
- Department of Veterinary Physiology, Orissa University of Agriculture and Technology, Bhubaneswar, India.
| | - Mahesh Dige
- Department of Animal Genetics, Central Institute for Research on Goats, Makhdoom, Mathura, India.
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100
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Singh R, Meena NK, Das T, Sharma RD, Prakash A, Lynn AM. Delineating the conformational dynamics of intermediate structures on the unfolding pathway of β-lactoglobulin in aqueous urea and dimethyl sulfoxide. J Biomol Struct Dyn 2019; 38:5027-5036. [PMID: 31744390 DOI: 10.1080/07391102.2019.1695669] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The funnel shaped energy landscape model of the protein folding suggests that progression of folding proceeds through multiple pathways, having the multiple intermediates which leads to multidimensional free-energy surface. Herein, we applied all-atom MD simulation to conduct a comparative study on the structure of β-lactoglobulin (β-LgA) in aqueous mixture of 8 M urea and 8 M dimethyl sulfoxide (DMSO), at different temperatures. The cumulative results of multiple simulations suggest a common unfolding pathway of β-LgA, occurred through the stable and meta-stable intermediates (I), in both urea and DMSO. However, the free-energy landscape (FEL) analyses show that the structural transitions of I-states are energetically different. In urea, FEL shows distinct ensemble of intermediates, I1 and I2, separated by the energy barrier of ∼3.0 kcal mol-1. Similarly, we find the population of two distinct I1 and I2 states in DMSO, however, the I1 appeared transiently around ∼30-35 ns and is short-lived. But, the I2 ensemble is observed structurally compact and long-lived (∼50-150 ns) as compared to unfolding in urea. Furthermore, the I1 and I2 are separated through a high energy barrier of ∼6.0 kcal mol-1. Thus, our results provide the structural insights of intermediates which essentially bear the signature of a different unfolding pathway of β-LgA in urea and DMSO.Abbreviationsβ-LgAβ-lactoglobulinDMSOdimethyl sulfoxideFELfree-energy landscapeGdmClguanidinium chlorideIintermediate stateMGmolten globule statePMEparticle mesh EwaldQfraction of native contactsRMSDroot mean square deviationRMSFroot mean square fluctuationRgradius of gyrationSASAsolvent Accessible Surface AreascSASAthe side chain SASATrptryptophanCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ruhar Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naveen Kumar Meena
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Trishala Das
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Datta Sharma
- Amity Institute of Integrative Sciences and Health, Amity University, Haryana, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University, Haryana, India
| | - Andrew M Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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