Learning From Biological Systems: Novel Routes to Biomimetic Synthesis of Ordered Silica Structures

1999 ◽  
Vol 599 ◽  
Author(s):  
Jennifer N. Chal ◽  
Katsuhiko Shimizu ◽  
Yan Zhou ◽  
Sean C. Christiansen ◽  
Bradley F. Chmelka ◽  
...  
Keyword(s):  
Structural Control ◽  
Catalytic Mechanism ◽  
Ambient Pressure ◽  
Biological Systems ◽  
Dry Weight ◽  
Biomimetic Synthesis ◽  
Skeletal System ◽  
Structural Determinants ◽  
Axial Filament ◽  
Block Copolypeptides

AbstractBiological systems have evolved mechanisms that precisely control inorganic structures on both the micro- and nanoscale, operating at ambient pressures and temperatures. In both the calcium carbonate, calcium phosphate and silicon dioxide utilizing organisms, proteins and polysaccharides have been found to play integral roles in the organization of these biominerals[1–3]. The organic constituents generally have been thought to act as direct templates or modulators for the deposition of the particular mineral. We have explored the synthesis and structural control of silica by the marine sponge, Tethya aurantia. Needles of amorphous silica comprise the skeletal system of this organism, representing 75% of the dry weight of the organism. These glassy needles, called spicules, are 2 mm in length and 30 μn in width[4,5]. We have characterized the structure, genetics and functions of the proteins that form an occluded axial filament within each silica spicule. Based on our discovery, a unique structure-directing catalytic mechanism exhibited by these protein filaments, and the structural determinants responsible for the catalytic activity, we have designed novel block copolypeptides that catalyze and spatially direct he condensation of silicon alkoxides to form organized silica structures ranging from transparent spheres to lath-like structures at ambient pressure, low temperature and neutral pH.

scholarly journals Structural determinants of the catalytic mechanism of Plasmodium CCT, a key enzyme of malaria lipid biosynthesis

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Ewelina Guca ◽  
Gergely N. Nagy ◽  
Fanni Hajdú ◽  
Lívia Marton ◽  
Richard Izrael ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Lipid Biosynthesis ◽  
Structural Determinants ◽  
Key Enzyme

Biomimetic synthesis of ordered silica structures mediated by block copolypeptides

Nature ◽  
2000 ◽  
Vol 403 (6767) ◽  
pp. 289-292 ◽  
Author(s):  
Jennifer N. Cha ◽  
Galen D. Stucky ◽  
Daniel E. Morse ◽  
Timothy J. Deming
Keyword(s):  
Biomimetic Synthesis ◽  
Block Copolypeptides

scholarly journals Structural and Functional Characterization of NadR from Lactococcus lactis

Molecules ◽  
2020 ◽  
Vol 25 (8) ◽  
pp. 1940
Author(s):  
Artem Stetsenko ◽  
Rajkumar Singh ◽  
Michael Jaehme ◽  
Albert Guskov ◽  
Dirk Jan Slotboom
Keyword(s):  
Crystal Structure ◽  
Lactococcus Lactis ◽  
Catalytic Mechanism ◽  
Adenine Nucleotides ◽  
Functional Characterization ◽  
Bifunctional Enzyme ◽  
Structural Determinants ◽  
Nicotinamide Riboside ◽  
Atp Concentration ◽  
Nicotinamide Mononucleotide

NadR is a bifunctional enzyme that converts nicotinamide riboside (NR) into nicotinamide mononucleotide (NMN), which is then converted into nicotinamide adenine dinucleotide (NAD). Although a crystal structure of the enzyme from the Gram-negative bacterium Haemophilus influenzae is known, structural understanding of its catalytic mechanism remains unclear. Here, we purified the NadR enzyme from Lactococcus lactis and established an assay to determine the combined activity of this bifunctional enzyme. The conversion of NR into NAD showed hyperbolic dependence on the NR concentration, but sigmoidal dependence on the ATP concentration. The apparent cooperativity for ATP may be explained because both reactions catalyzed by the bifunctional enzyme (phosphorylation of NR and adenylation of NMN) require ATP. The conversion of NMN into NAD followed simple Michaelis-Menten kinetics for NMN, but again with the sigmoidal dependence on the ATP concentration. In this case, the apparent cooperativity is unexpected since only a single ATP is used in the NMN adenylyltransferase catalyzed reaction. To determine the possible structural determinants of such cooperativity, we solved the crystal structure of NadR from L. lactis (NadRLl). Co-crystallization with NAD, NR, NMN, ATP, and AMP-PNP revealed a ‘sink’ for adenine nucleotides in a location between two domains. This sink could be a regulatory site, or it may facilitate the channeling of substrates between the two domains.

scholarly journals Plant asparaginyl endopeptidases and their structural determinants of function

2021 ◽  
Author(s):  
Samuel G. Nonis ◽  
Joel Haywood ◽  
Joshua S. Mylne
Keyword(s):  
Protein Sequence ◽  
Biological Systems ◽  
Catalytic Efficiency ◽  
Circular Permutation ◽  
Structural Determinants ◽  
Pharmaceutical Applications

Asparaginyl endopeptidases (AEPs) are versatile enzymes that in biological systems are involved in producing three different catalytic outcomes for proteins, namely (i) routine cleavage by bond hydrolysis, (ii) peptide maturation, including macrocyclisation by a cleavage-coupled intramolecular transpeptidation and (iii) circular permutation involving separate cleavage and transpeptidation reactions resulting in a major reshuffling of protein sequence. AEPs differ in their preference for cleavage or transpeptidation reactions, catalytic efficiency, and preference for asparagine or aspartate target residues. We look at structural analyses of various AEPs that have laid the groundwork for identifying important determinants of AEP function in recent years, with much of the research impetus arising from the potential biotechnological and pharmaceutical applications.

scholarly journals Multidisciplinary approaches to solar hydrogen

2015 ◽  
Vol 5 (3) ◽  
pp. 20140091 ◽  
Author(s):  
Kara L. Bren
Keyword(s):  
Catalytic Mechanism ◽  
Biological Systems ◽  
Engineering Systems ◽  
Hydrogen Fuel ◽  
Electron Hole ◽  
Biomolecular Systems ◽  
Solar Hydrogen ◽  
Molecular Systems ◽  
Great Insight

This review summarizes three different approaches to engineering systems for the solar-driven evolution of hydrogen fuel from water: molecular, nanomaterials and biomolecular. Molecular systems have the advantage of being highly amenable to modification and detailed study and have provided great insight into photophysics, electron transfer and catalytic mechanism. However, they tend to display poor stability. Systems based on nanomaterials are more robust but also are more difficult to synthesize in a controlled manner and to modify and study in detail. Biomolecular systems share many properties with molecular systems and have the advantage of displaying inherently high efficiencies for light absorption, electron–hole separation and catalysis. However, biological systems must be engineered to couple modules that capture and convert solar photons to modules that produce hydrogen fuel. Furthermore, biological systems are prone to degradation when employed in vitro . Advances that use combinations of these three tactics also are described. Multidisciplinary approaches to this problem allow scientists to take advantage of the best features of biological, molecular and nanomaterials systems provided that the components can be coupled for efficient function.

Structural determinants of specificity and catalytic mechanism in mammalian 25-kDa thiamine triphosphatase

2013 ◽  
Vol 1830 (10) ◽  
pp. 4513-4523 ◽  
Author(s):  
David Delvaux ◽  
Frédéric Kerff ◽  
Mamidanna R.V.S. Murty ◽  
Bernard Lakaye ◽  
Jan Czerniecki ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Structural Determinants

Note. Sugar, Moisture Contents, and Color of Chestnuts during Different Storage Regimes

2009 ◽  
Vol 15 (2) ◽  
pp. 169-178 ◽  
Author(s):  
F. Chenlo ◽  
R. Moreira ◽  
L. Chaguri ◽  
M.D. Torres
Keyword(s):  
Moisture Content ◽  
Room Temperature ◽  
Ambient Pressure ◽  
Sugar Content ◽  
Castanea Sativa ◽  
Dry Weight ◽  
Sucrose Content ◽  
Color Changes ◽  
Moisture Contents ◽  
Castanea Sativa Mill

Color, moisture and sucrose, glucose and fructose contents of chestnuts (Castanea sativa Mill.) at several initial states (whole and undried; whole, peeled, and partially air-dried, with or without prior sucrose treatment; peeled, broken, and undried or partially air-dried) were monitored for 11 months during storage under various conditions (unpacked, packed in plastic bags at ambient pressure, or vacuum packed) and temperature (at room temperature, 3°C or -18°C). Moisture content decreased considerably in all cases except in those of packed whole peeled chestnuts without sucrose treatment and stored at room temperature or 3°C. Chestnuts stored for 2 months in contact with the atmosphere had moisture contents of only ∼4% of their dry weight. After 4 months storage, sucrose content had fallen (in some cases to zero) in all samples except in broken chestnuts dried to a 2% moisture content and conventionally stored whole unpeeled chestnuts (in which sucrose content rose slightly). Glucose and fructose contents generally peaked after 1-2 months of storage, and by month 4 returned to initial or lower levels. Sugar content was hardly affected by initial moisture or sugar contents except when moisture content had been reduced to 2%. Color changes were least during storage in air or at 3°C.

scholarly journals Terminal Olefin (1-Alkene) Biosynthesis by a Novel P450 Fatty Acid Decarboxylase fromJeotgalicoccusSpecies

2011 ◽  
Vol 77 (5) ◽  
pp. 1718-1727 ◽  
Author(s):  
Mathew A. Rude ◽  
Tarah S. Baron ◽  
Shane Brubaker ◽  
Murtaza Alibhai ◽  
Stephen B. Del Cardayre ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Catalytic Mechanism ◽  
Fatty Acid Biosynthesis ◽  
Draft Genome ◽  
Industrial Applications ◽  
Acid Decarboxylase ◽  
Cytochrome P450 Enzyme ◽  
Structural Determinants ◽  
Terminal Olefin ◽  
Terminal Olefins

ABSTRACTTerminal olefins (1-alkenes) are natural products that have important industrial applications as both fuels and chemicals. However, their biosynthesis has been largely unexplored. We describe a group of bacteria,Jeotgalicoccusspp., which synthesize terminal olefins, in particular 18-methyl-1-nonadecene and 17-methyl-1-nonadecene. These olefins are derived from intermediates of fatty acid biosynthesis, and the key enzyme inJeotgalicoccussp. ATCC 8456 is a terminal olefin-forming fatty acid decarboxylase. This enzyme,Jeotgalicoccussp. OleT (OleTJE), was identified by purification from cell lysates, and its encoding gene was identified from a draft genome sequence ofJeotgalicoccussp. ATCC 8456 using reverse genetics. Heterologous expression of the identified gene conferred olefin biosynthesis toEscherichia coli.OleTJEis a P450 from the cyp152 family, which includes bacterial fatty acid hydroxylases. Some cyp152 P450 enzymes have the ability to decarboxylate and to hydroxylate fatty acids (in α- and/or β-position), suggesting a common reaction intermediate in their catalytic mechanism and specific structural determinants that favor one reaction over the other. The discovery of these terminal olefin-forming P450 enzymes represents a third biosynthetic pathway (in addition to alkane and long-chain olefin biosynthesis) to convert fatty acid intermediates into hydrocarbons. Olefin-forming fatty acid decarboxylation is a novel reaction that can now be added to the catalytic repertoire of the versatile cytochrome P450 enzyme family.

Metabolic signalling and the partitioning of resources in plant storage organs

1999 ◽  
Vol 133 (3) ◽  
pp. 243-249 ◽  
Author(s):  
NIGEL G. HALFORD
Keyword(s):  
Dry Weight ◽  
Wild Relatives ◽  
Crop Plants ◽  
Wild Plants ◽  
Young Plant ◽  
Carbon And Nitrogen ◽  
Cultivated Potato ◽  
Metabolic Signalling ◽  
Storage Organs ◽  
Plant Storage

The most important harvested organs of crop plants, such as seeds, tubers and fruits, are often described as assimilate sinks. They play little or no part in the fixation of carbon through the production of sugars through photosynthesis, or in the uptake of nitrogen and sulphur, but import these assimilated resources to support metabolism and to store them in the form of starch, oils and proteins. Wild plants store resources in seeds and tubers to later support an emergent young plant. Cultivated crops are effectively storing resources to provide us with food and many have been bred to accumulate much more than would be required otherwise. For example, approximately 80% of a cultivated potato plant's dry weight is contained in its tubers, ten times the proportion in the tubers of its wild relatives (Inoue & Tanaka 1978). Cultivation and breeding has brought about a shift in the partitioning of carbon and nitrogen assimilate between the organs of the plant.

Transmission Electron Microscopy of Protein Macromolecules

1971 ◽  
Vol 29 ◽  
pp. 424-425
Author(s):  
Henry S. Slayter
Keyword(s):  
Biological Systems ◽  
Metal Vapor ◽  
Resolving Power ◽  
Electron Microscopic ◽  
Chemical Methods ◽  
Molecular Weights ◽  
The Past ◽  
Physical Chemical ◽  
Transmission Electron

Electron microscopic methods have been applied increasingly during the past fifteen years, to problems in structural molecular biology. Used in conjunction with physical chemical methods and/or Fourier methods of analysis, they constitute powerful tools for determining sizes, shapes and modes of aggregation of biopolymers with molecular weights greater than 50, 000. However, the application of the e.m. to the determination of very fine structure approaching the limit of instrumental resolving power in biological systems has not been productive, due to various difficulties such as the destructive effects of dehydration, damage to the specimen by the electron beam, and lack of adequate and specific contrast. One of the most satisfactory methods for contrasting individual macromolecules involves the deposition of heavy metal vapor upon the specimen. We have investigated this process, and present here what we believe to be the more important considerations for optimizing it. Results of the application of these methods to several biological systems including muscle proteins, fibrinogen, ribosomes and chromatin will be discussed.

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