Abstract：
: Microbes utilize enzymes to perform a variety of functions. Enzymes are biocatalysts working as highly efficient machines at the molecular level. In the past, enzymes have been viewed as static entities and their function has been explained on the basis of direct structural interactions between the enzyme and the substrate. A variety of experimental and computational techniques, however, continue to reveal that proteins are dynamically active machines, with various parts exhibiting internal motions at a wide range of time-scales. Increasing evidence also indicates that these internal protein motions play a role in promoting protein function such as enzyme catalysis. Moreover, the thermodynamical fluctuations of the solvent, surrounding the protein, have an impact on internal protein motions and, therefore, on enzyme function. In this review, we describe recent biochemical and theoretical investigations of internal protein dynamics linked to enzyme catalysis. In the enzyme cyclophilin A, investigations have lead to the discovery of a network of protein vibrations promoting catalysis. Cyclophilin A catalyzes peptidyl-prolyl cis/trans isomerization in a variety of peptide and protein substrates. Recent studies of cyclophilin A are discussed in detail and other enzymes (dihydrofolate reductase and liver alcohol dehydrogenase) where similar discoveries have been reported are also briefly discussed. The detailed characterization of the discovered networks indicates that protein dynamics plays a role in rate-enhancement achieved by enzymes. An integrated view of enzyme structure, dynamics and function have wide implications in understanding allosteric and co-operative effects, as well as protein engineering of more efficient enzymes and novel drug design.
journal_name
Microb Cell Factjournal_title
Microbial cell factoriesauthors
Agarwal PKdoi
10.1186/1475-2859-5-2keywords:
subject
Has Abstractpub_date
2006-01-12 00:00:00pages
2issn
1475-2859pii
1475-2859-5-2journal_volume
5pub_type
杂志文章abstract：BACKGROUND:Cephalosporin C (CPC) produced by Acremonium chrysogenum is one of the most important drugs for treatment of bacterial infectious diseases. As the major stimulant, methionine is widely used in the industrial production of CPC. In this study, we found methionine stimulated CPC production through enhancing the...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-018-0936-5
更新日期：2018-06-07 00:00:00
abstract：BACKGROUND:Crocin is a carotenoid-derived natural product found in the stigma of Crocus spp., which has great potential in medicine, food and cosmetics. In recent years, microbial production of crocin has drawn increasing attention, but there were no reports of successful implementation. Escherichia coli has been engin...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-019-1166-1
更新日期：2019-07-05 00:00:00
abstract：BACKGROUND:Emergence of antibiotic resistance and growing consumer trend towards foods containing biopreservatives stimulated the search for alternative antimicrobials. This research is aimed at characterizing, investigating the mechanism of action, scale up optimization and evaluating the biopreservative potential of ...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-018-0972-1
更新日期：2018-08-13 00:00:00
abstract：BACKGROUND:The methylotrophic yeast Pichia pastoris is a well-studied host organism for recombinant protein production, which is usually regulated either by a constitutive promoter (e.g. promoter of glyceraldehyde-3-phosphate dehydrogenase; PGAP) or an inducible promoter (e.g. promoter of alcohol oxidase 1; PAOX1). Bot...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-017-0768-8
更新日期：2017-09-13 00:00:00
abstract：BACKGROUND:The methylotrophic yeast Pichia pastoris is a common host for the production of recombinant proteins. However, hypermannosylation hinders the use of recombinant proteins from yeast in most biopharmaceutical applications. Glyco-engineered yeast strains produce more homogeneously glycosylated proteins, but can...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-018-1032-6
更新日期：2018-11-24 00:00:00
abstract：BACKGROUND:Lactococcus lactis, a lactic acid bacterium traditionally used to ferment milk and manufacture cheeses, is also, in the biotechnology field, an interesting host to produce proteins of medical interest, as it is "Generally Recognized As Safe". Furthermore, as L. lactis naturally secretes only one major endoge...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-015-0271-z
更新日期：2015-07-16 00:00:00
abstract：BACKGROUND:L-tryptophan is an aromatic amino acid widely used in the food, chemical and pharmaceutical industries. In Escherichia coli, L-tryptophan is synthesized from phosphoenolpyruvate and erythrose 4-phosphate by enzymes in the shikimate pathway and L-tryptophan branch pathway, while L-serine and phosphoribosylpyr...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-11-30
更新日期：2012-03-02 00:00:00
abstract：BACKGROUND:Signal peptide peptidases play an important role in the removal of remnant signal peptides in the cell membrane, a critical step for extracellular protein production. Although these proteins are likely a central component for extracellular protein production, there has been a lack of research on whether prot...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-017-0688-7
更新日期：2017-04-24 00:00:00
abstract：BACKGROUND:Although the citric acid fermentation by Aspergillus niger is one of the most important industrial microbial processes and various aspects of the fermentation appear in a very large number of publications since the 1950s, the effect of the spore inoculum level on fungal morphology is a rather neglected area....
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-5-3
更新日期：2006-01-25 00:00:00
abstract：:The biotechnology industry has become a key element in modern societies. Within this industry, the production of recombinant enzymes and biopharmaceutical proteins is of major importance. The global markets for such recombinant proteins are growing rapidly and, accordingly, there is a continuous need for new productio...
journal_title：Microbial cell factories
pub_type： 社论
doi：10.1186/1475-2859-12-3
更新日期：2013-01-14 00:00:00
abstract：BACKGROUND:High-throughput methods are widely-used for strain screening effectively resulting in binary information regarding high or low productivity. Nevertheless achieving quantitative and scalable parameters for fast bioprocess development is much more challenging, especially for heterologous protein production. He...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-11-144
更新日期：2012-10-31 00:00:00
abstract：:The success of recombinant protein expression seems unpredictable and even good yields of soluble proteins do not guarantee the correct folding. The search for soluble constructs can be performed by exploiting libraries and speeded up by automation, but these approaches are money and time consuming and the tags used f...
journal_title：Microbial cell factories
pub_type： 社论
doi：10.1186/1475-2859-3-12
更新日期：2004-10-07 00:00:00
abstract：BACKGROUND:In recent years, it has been gradually realized that bacterial inclusion bodies (IBs) could be biologically active. In particular, several proteins including green fluorescent protein, β-galactosidase, β-lactamase, alkaline phosphatase, D-amino acid oxidase, polyphosphate kinase 3, maltodextrin phosphorylase...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-10-9
更新日期：2011-02-15 00:00:00
abstract：BACKGROUND:Recent interest has been focused on the production of platform chemicals from renewable biomass due to increasing concerns on global warming and depletion of fossil fuel reserves. Microbial production of platform chemicals in biorefineries has been suggested to be a promising solution for these problems. Gam...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-018-0977-9
更新日期：2018-08-21 00:00:00
abstract：BACKGROUND:L-arabinose is an important intermediate for anti-virus drug synthesis and has also been used in food additives for diets-controlling in recent years. Commercial production of L-arabinose is a complex progress consisting of acid hydrolysis of gum arabic, followed by multiple procedures of purification, thus ...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-10-43
更新日期：2011-06-07 00:00:00
abstract：BACKGROUND:Cost-effective production of the highly effective anti-cancer drug, paclitaxel (Taxol®), remains limited despite growing global demands. Low yields of the critical taxadiene precursor remains a key bottleneck in microbial production. In this study, the key challenge of poor taxadiene synthase (TASY) solubili...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-020-01458-2
更新日期：2020-11-02 00:00:00
abstract：BACKGROUND:Increasingly lignocellulosic biomass hydrolysates are used as the feedstock for industrial fermentations. These biomass hydrolysates are complex mixtures of different fermentable sugars, but also inhibitors and salts that affect the performance of the microbial production host. The performance of six industr...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-8-64
更新日期：2009-12-04 00:00:00
abstract：BACKGROUND:For the cultivation of Escherichia coli in bioreactors trace element solutions are generally designed for optimal growth under aerobic conditions. They do normally not contain selenium and nickel. Molybdenum is only contained in few of them. These elements are part of the formate hydrogen lyase (FHL) complex...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-7-26
更新日期：2008-08-07 00:00:00
abstract：BACKGROUND:Extracts and products (roots and/or aerial parts) from Echinacea ssp. represent a profitable market sector for herbal medicines thanks to different functional features. Alkamides and polyacetylenes, phenols like caffeic acid and its derivatives, polysaccharides and glycoproteins are the main bioactive compou...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-12-44
更新日期：2013-05-04 00:00:00
abstract：BACKGROUND:Purine nucleotides exhibit various functions in cellular metabolism. Besides serving as building blocks for nucleic acid synthesis, they participate in signaling pathways and energy metabolism. Further, IMP and GMP represent industrially relevant biotechnological products used as flavor enhancing additives i...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-11-138
更新日期：2012-10-24 00:00:00
abstract：BACKGROUND:The understanding of the molecular basis of yeast tolerance to ethanol may guide the design of rational strategies to increase process performance in industrial alcoholic fermentations. A set of 21 genes encoding multidrug transporters from the ATP-Binding Cassette (ABC) Superfamily and Major Facilitator Sup...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-11-98
更新日期：2012-07-27 00:00:00
abstract：BACKGROUND:The budding yeast Pichia pastoris is widely used for protein production. To determine the best suitable strategy for strain improvement, especially for high secretion, quantitative data of intracellular fluxes of recombinant protein are very important. Especially the balance between intracellular protein for...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-10-47
更新日期：2011-06-26 00:00:00
abstract：BACKGROUND:Nowadays, microbial infections have caused increasing economic losses in aquaculture industry and deteriorated worldwide environments. Many of these infections are caused by opportunistic pathogens through cell-density mediated quorum sensing (QS). The disruption of QS, known as quorum quenching (QQ), is an ...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-020-01448-4
更新日期：2020-10-07 00:00:00
abstract：BACKGROUND:The thermostable serine protease pernisine originates from the hyperthermophilic Archaeaon Aeropyrum pernix and has valuable industrial applications. Due to its properties, A. pernix cannot be cultivated in standard industrial fermentation facilities. Furthermore, pernisine is a demanding target for heterolo...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-019-1245-3
更新日期：2019-11-07 00:00:00
abstract：BACKGROUND:Under aerobic conditions, acetic acid is the major byproduct produced by E. coli during the fermentation. And acetic acid is detrimental to cell growth as it destroys transmembrane pH gradients. Hence, how to reduce the production of acetic acid and how to utilize it as a feedstock are of intriguing interest...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-016-0475-x
更新日期：2016-05-05 00:00:00
abstract：BACKGROUND:The rational design of L-phenylalanine (L-Phe) overproducing microorganisms has been successfully achieved by combining different genetic strategies such as inactivation of the phosphoenolpyruvate: phosphotransferase transport system (PTS) and overexpression of key genes (DAHP synthase, transketolase and cho...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-6-30
更新日期：2007-09-19 00:00:00
abstract：:BACKGROUND: A rapid microtiter plate based sandwich hybridization assay was developed for detection and quantification of single RNA species using magnetic beads. Following solution hybridization target RNA molecules were collected by biotin-streptavidin affinity binding and detected by fluorescence signal generated b...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-2-4
更新日期：2003-04-28 00:00:00
abstract：BACKGROUND:Triacylglycerols are used in various purposes including food applications, cosmetics, oleochemicals and biofuels. Currently the main sources for triacylglycerol are vegetable oils, and microbial triacylglycerol has been suggested as an alternative for these. Due to the low production rates and yields of micr...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/1475-2859-10-36
更新日期：2011-05-18 00:00:00
abstract：:Membrane remodeling and phospholipid biosynthesis are normally tightly regulated to maintain the shape and function of cells. Indeed, different physiological mechanisms ensure a precise coordination between de novo phospholipid biosynthesis and modulation of membrane morphology. Interestingly, the overproduction of ce...
journal_title：Microbial cell factories
pub_type： 杂志文章,评审
doi：10.1186/s12934-020-01433-x
更新日期：2020-09-04 00:00:00
abstract：BACKGROUND:Targeting of cellular proteins to the extracellular environment is directed by a secretory signal sequence located at the N-terminus of a secretory protein. These signal sequences usually contain an N-terminal basic amino acid followed by a stretch containing hydrophobic residues, although no consensus signa...
journal_title：Microbial cell factories
pub_type： 杂志文章
doi：10.1186/s12934-015-0203-y
更新日期：2015-02-14 00:00:00
