Commercial proteases: Present and future

Li, Qing; Li, Yang; Marek, Peter; Iverson, Brent L.

doi:10.1016/j.febslet.2012.12.019

Cited by 212 publications

(134 citation statements)

References 97 publications

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“…Thus, transmutation of only four SDP residues changed the proteolytic function of MMP-16 into that of MMP-17. We believe that this and similar knowledge may contribute to the redesign of MMPs to exhibit unconventional substrate specificity, which could have therapeutic, diagnostic, or other biotechnology applications (56,57). The substrate specificity of several proteases distinct from MMPs has been manipulated (58)(59)(60), but this was thought to be difficult to achieve with MMPs because of their presumed overlapping substrate specificity.…”

Section: Discussionmentioning

confidence: 99%

Basis for substrate recognition and distinction by matrix metalloproteinases

Ratnikov¹,

Cieplak²,

Gramatikoff³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Genomic sequencing and structural genomics produced a vast amount of sequence and structural data, creating an opportunity for structure-function analysis in silico [Radivojac P, et al. (2013) Nat Methods 10(3):221-227]. Unfortunately, only a few large experimental datasets exist to serve as benchmarks for functionrelated predictions. Furthermore, currently there are no reliable means to predict the extent of functional similarity among proteins. Here, we quantify structure-function relationships among three phylogenetic branches of the matrix metalloproteinase (MMP) family by comparing their cleavage efficiencies toward an extended set of phage peptide substrates that were selected from ∼64 million peptide sequences (i.e., a large unbiased representation of substrate space). The observed second-order rate constants [k (obs) ] across the substrate space provide a distance measure of functional similarity among the MMPs. These functional distances directly correlate with MMP phylogenetic distance. There is also a remarkable and near-perfect correlation between the MMP substrate preference and sequence identity of 50-57 discontinuous residues surrounding the catalytic groove. We conclude that these residues represent the specificity-determining positions (SDPs) that allowed for the expansion of MMP proteolytic function during evolution. A transmutation of only a few selected SDPs proximal to the bound substrate peptide, and contributing the most to selectivity among the MMPs, is sufficient to enact a global change in the substrate preference of one MMP to that of another, indicating the potential for the rational and focused redesign of cleavage specificity in MMPs.protease | specificity-determining positions | MMPs A paramount objective of biological research is to understand how sequence encodes function. Previously, functional regions in proteins were identified using large-scale mutagenesis (e.g., alanine scanning) (1). More recently, our insights are largely gained by computational approaches aimed at comparing sequences and structures of large protein sets across multiple genomes. The vast increase in the number of available sequences makes it possible to compare homology between sequences from genome projects to proteins of known structure and function and, as a result, identify functional similarities in silico (2-4). Because the global fold of most ordered proteins can be reliably predicted (5, 6) and because the catalytic residues of most classes of enzymes are either known or can be inferred (7,8), protein sequences can now be directly used to elucidate and classify major protein functions (9-12), and are even being extended to predict enzyme substrates (13).However, such classifications fail to explain the specialization and expansion of function that is required for organismal plasticity, complexity, and adaptability, all of which are normally driven by gene duplications and subsequent divergence. Computational approaches aimed at identifying functional distinctions across protein families have pri...

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Section: Discussionmentioning

confidence: 99%

Basis for substrate recognition and distinction by matrix metalloproteinases

Ratnikov¹,

Cieplak²,

Gramatikoff³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…The exopeptidases act on the ends of polypeptide chains and endopeptidases act randomly in the inner regions of polypeptide chains. The endopeptidases are further classified into six groups, based on the catalytic residue present in the active site: serine, aspartic, cysteine, metallo, glutamic acid and threonine protease (43). Plant proteases such as bromelain, ficin and papain are widely used in food industry for various applications such as brewing, tenderization of meat, coagulation of milk and as a digestive aid (44).…”

Section: Proteasesmentioning

confidence: 99%

Applications of Microbial Enzymes in Food Industry

Sindhu

Binod

Ummalyma

et al. 2018

Food Technol. Biotechnol.

525

230

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SUMMARYThe use of enzymes or microorganisms in food preparations is an age-old process. With the advancement of technology, novel enzymes with wide range of applications and specificity have been developed and new application areas are still being explored. Microorganisms such as bacteria, yeast and fungi and their enzymes are widely used in several food preparations for improving the taste and texture and they offer huge economic benefits to industries. Microbial enzymes are the preferred source to plants or animals due to several advantages such as easy, cost-effective and consistent production. The present review discusses the recent advancement in enzyme technology for food industries. A comprehensive list of enzymes used in food processing, the microbial source of these enzymes and the wide range of their application are discussed.

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“…Broths subjected to fermentation process are comprised of target protein in higher concentration together with other components present in media, specifically salts and carbohydrates [1][2][3][4][5][6][7][8][9][10][11][12][13]. Fermentation method involving downstream processing is useful to carry out extraction, filtration and separation process to remove impurities from the medium [14,15]. However there is no method involved in removing specific component from the medium.…”

Section: Introductionmentioning

confidence: 99%

Fermentative Production of Microbial Enzymes and their Applications: Present status and future prospects

2017

J App Biol Biotech

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Microbial enzymes are widely used in different industries mainly because of vast availability of sources. Microbial enzymes could be genetically modified and are considered as economical in comparison to plant and animal enzymes. Production of microbial enzymes by application of fermentation procedures involves microbial propagation to get desired product. The process of fermentation is classified based on specific parameters. Microbial enzymes exhibit wide variety of applications in different industries like food, wine, dairy, baking, milling, beverages, and cereals. There are different techniques employed to produce microbial enzymes using downstream processing methods that are aimed at enzyme purification and recovery. The improvement in concentration, purity and percentage of recovery of enzymes can be achieved based on standard principles which are microbial sources, improvement of strain and application of membrane augmented downstream processing method to improve specific activity of enzyme. The article reviews on principles include microbial sources, methods of strain improvement and modern techniques associated with improvement of enzyme activity and recovery process. The application of microbial enzymes in various industries and their importance in biotechnology is highlighted.

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Commercial proteases: Present and future

Cited by 212 publications

References 97 publications

Basis for substrate recognition and distinction by matrix metalloproteinases

Basis for substrate recognition and distinction by matrix metalloproteinases

Applications of Microbial Enzymes in Food Industry

Fermentative Production of Microbial Enzymes and their Applications: Present status and future prospects

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