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From molecular dynamics to quantum mechanics of misfolded proteins and amyloid-like macroaggregates applied to neurodegenerative diseases. J Mol Graph Model 2021; 110:108046. [PMID: 34736057 DOI: 10.1016/j.jmgm.2021.108046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/14/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022]
Abstract
A misfolded protein compared with its native state lacks its biological function resulting in cell dysregulations and often death. Outdated hypotheses on protein folding must be revised: More realistic molecular models, focusing not only on classical molecular dynamics (MD) but also on ab initio quantum mechanics (QM) at the molecular orbitals (MOs) scale, which is not experimentally achievable, are presented to improve our understanding of the thermodynamics of the protein-protein interactions leading to misfolding and neurodegenerative diseases for future drug design. Protein misfolding is characterized by the formation of highly reactive beta-sheets oligomers leading to fibrillar macroscopic aggregates, which are studied with the models given herein that can be useful for the development of new immunotherapies against the Alzheimer's disease and prion, e.g. The example of the prion - an intrinsically disordered protein - is studied, but the models can be generalized to other misfolding diseases. The binding free energy and interactions in a complex of a misfolded prion with a native prion are first analyzed by MD and compared to a complex of two native conformers. A conversion of residues to toxic beta-sheets is observed in the optimized misfolded complex. Then, QM is used to compute, with a much better accuracy than that of MD, the binding free energy of the hydrophobic binding site, responsible of the aggregation, between the bound misfolded and native conformers in the misfolded complex. The latter quantity is significantly negative, so that aggregation is strong and fast. The frontier MOs from QM are used for docking to determine how the first repetitive beta-sheets building blocks of the nanofibrils can be assembled from initial cleaved complexes of the native and misfolded proteins. Successive aggregation of multiple monomers leads to an amyloid-like nanofibril that grows along a principal elongation direction, as also observed experimentally.
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Extraction of Pigments from Microalgae and Cyanobacteria—A Review on Current Methodologies. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11115187] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Pigments from microalgae and cyanobacteria have attracted great interest for industrial applications due to their bioactive potential and their natural product attributes. These pigments are usually sold as extracts, to overcome purification costs. The extraction of these compounds is based on cell disruption methodologies and chemical solubility of compounds. Different cell disruption methodologies have been used for pigment extraction, such as sonication, homogenization, high-pressure, CO2 supercritical fluid extraction, enzymatic extraction, and some other promising extraction methodologies such as ohmic heating and electric pulse technologies. The biggest constrain on pigment bioprocessing comes from the installation and operation costs; thus, fundamental and applied research are still needed to overcome such constrains and give the microalgae and cyanobacteria industry an opportunity in the world market. In this review, the main extraction methodologies will be discussed, taking into account the advantages and disadvantages for each kind of pigment, type of organism, cost, and final market.
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Gillet JN. Alzheimer’s disease: unraveling APOE4 binding to amyloid-beta peptide and lipids with molecular dynamics and quantum mechanics. J Biomol Struct Dyn 2020; 39:5026-5032. [DOI: 10.1080/07391102.2020.1784287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Jean-Numa Gillet
- Centre for Computational Biology and Bioinformatics, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Farrokh P, Sheikhpour M, Kasaeian A, Asadi H, Bavandi R. Cyanobacteria as an eco-friendly resource for biofuel production: A critical review. Biotechnol Prog 2019; 35:e2835. [PMID: 31063628 DOI: 10.1002/btpr.2835] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/07/2019] [Accepted: 04/24/2019] [Indexed: 12/26/2022]
Abstract
Cyanobacteria are photosynthetic microorganisms which can be found in various environmental habitats. These photosynthetic bacteria are considered as promising feedstock for the production of the third- and the fourth-generation biofuels. The main subject of this review is highlighting the significant aspects of the biofuel production from cyanobacteria. The most recent investigations about the extraction or separation of the bio-oil from cyanobacteria are also adduced in the present review. Moreover, the genetic engineering of cyanobacteria for improving biofuel production and the impact of bioinformatics studies on the designing better-engineered strains are mentioned. The large-scale biofuel production is challenging, so the economic considerations to provide inexpensive biofuels are also cited. It seems that the future of biofuels is strongly dependent to the following items; understanding the metabolic pathways of the cyanobacterial species, progression in the construction of the engineered cyanobacteria, and inexpensive large-scale cultivation of them.
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Affiliation(s)
- Parisa Farrokh
- Department of cell and molecular biology, School of Biology, Damghan University, Damghan, Iran.,Institute of Biological Sciences, Damghan University, Damghan, Iran
| | - Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Alibakhsh Kasaeian
- Faculty of New Science and Technologies, University of Tehran, Tehran, Iran
| | - Hassan Asadi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Roya Bavandi
- Branch-Marine Science and Technology Faculty, Islamic Azad University North Tehran, Tehran, Iran
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Vinayak V, Manoylov KM, Gateau H, Blanckaert V, Hérault J, Pencréac'h G, Marchand J, Gordon R, Schoefs B. Diatom milking: a review and new approaches. Mar Drugs 2015; 13:2629-65. [PMID: 25939034 PMCID: PMC4446598 DOI: 10.3390/md13052629] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 11/16/2022] Open
Abstract
The rise of human populations and the growth of cities contribute to the depletion of natural resources, increase their cost, and create potential climatic changes. To overcome difficulties in supplying populations and reducing the resource cost, a search for alternative pharmaceutical, nanotechnology, and energy sources has begun. Among the alternative sources, microalgae are the most promising because they use carbon dioxide (CO2) to produce biomass and/or valuable compounds. Once produced, the biomass is ordinarily harvested and processed (downstream program). Drying, grinding, and extraction steps are destructive to the microalgal biomass that then needs to be renewed. The extraction and purification processes generate organic wastes and require substantial energy inputs. Altogether, it is urgent to develop alternative downstream processes. Among the possibilities, milking invokes the concept that the extraction should not kill the algal cells. Therefore, it does not require growing the algae anew. In this review, we discuss research on milking of diatoms. The main themes are (a) development of alternative methods to extract and harvest high added value compounds; (b) design of photobioreactors;
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Affiliation(s)
- Vandana Vinayak
- Department of Criminology & Forensic Science, School of Applied Sciences, Dr. H.S. Gour University (Central University), Sagar Madhya Pradesh, India.
| | - Kalina M Manoylov
- Department of Biological & Environmental Sciences, Georgia College and State University, Milledgeville, GA 31061, USA.
| | - Hélène Gateau
- MicroMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, Faculté des Sciences et Techniques, Avenue Olivier Messiaen, 72085 Le Mans cedex 9, France.
| | - Vincent Blanckaert
- MicroMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, IUT de Laval, Rue des Drs Calmette et Guerin, 53020 Laval Cedex 9, France.
| | - Josiane Hérault
- ChimiMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, IUT de Laval, Rue des Drs Calmette et Guerin, 53020 Laval Cedex 9, France.
| | - Gaëlle Pencréac'h
- ChimiMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, IUT de Laval, Rue des Drs Calmette et Guerin, 53020 Laval Cedex 9, France.
| | - Justine Marchand
- MicroMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, Faculté des Sciences et Techniques, Avenue Olivier Messiaen, 72085 Le Mans cedex 9, France.
| | - Richard Gordon
- Gulf Specimen Aquarium & Marine Laboratory, Panacea, FL 32346, USA.
- Mott Center for Human Growth and Development, Department of Obstetrics & Gynecology, Wayne State University, 275 E. Hancock, Detroit, MI 48201, USA.
| | - Benoît Schoefs
- MicroMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, Faculté des Sciences et Techniques, Avenue Olivier Messiaen, 72085 Le Mans cedex 9, France.
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