Home / Technology / BioScience / Enzyme engineering enables design and construction of entirely new designer enzymes

Enzyme engineering enables design and construction of entirely new designer enzymes

Molecular biology and biochemistry are two closely related fields where the properties of key biological molecules, such as proteins and DNA, and how they interact with each other in living organisms are studied. Research in these areas has become so successful at explaining living processes that it is used in almost all areas of the life sciences from medicine to the study of plants. Researchers play an integral role in the discovery of drugs that help prevent and cure diseases.


Proteins are essential to life. Enzymes (one kind of protein) act as catalysts, conducting chemical reactions that are central to metabolism, detoxification, and the control of cellular function. Catalysts accelerate chemical reactions.


Natural enzymes, which are relatively large protein molecules, are the powerful catalysts that control the reactions that sustain life. They play a central role in the chemical reactions involved in the transformation of food into the essential nutrients that provide energy, among many other critical functions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products.


Enzymes are able to react on a broad range of substrates, and individual enzymes are often highly specific for certain chemical structures. Additionally, some enzymes conduct reactions that produce useful and unusual chemical structures that would be difficult to access using traditional chemistry. These properties have made enzymes a cornerstone of both synthetic biology and biotechnology.


By using individual, or designed cascades of enzymes, desirable chemical reactions can be conducted either within cells or simply in a test tube. Scientists have been able to use enzyme-driven techniques to convert low-value input molecules like farm-waste cellulose into high-value products like flavours, scents, pharmaceuticals, biofuels and oil-replacement plastics. Molecular biology enzymes, find their usage across a numerous range of applications, such as, life science research, research and development and diagnostic testing and drug discovery among others.


Some enzymes are used commercially, for example, in the synthesis of antibiotics. Some household products use enzymes to speed up chemical reactions: enzymes in biological washing powders break down protein, starch or fat stains on clothes, and enzymes in meat tenderizer break down proteins into smaller molecules, making the meat easier to chew.


The most basic tools that enable the core technologies of molecular biology are enzymes and reagents. Molecular Biology Enzymes, Kits, and Reagents are used for the analysis of cell surface markers that act as diagnostic and/or therapeutic targets. Molecular biology enzymes are natural proteins produced by living organisms (animals, plants, and bacteria) and are highly selective biochemical catalysts. Molecular biology reagents are chemicals used in molecular biology reactions to optimize the workflow.


Molecular biology products are used for the analysis of cell surface markers which act as diagnostic and/or therapeutic targets. These products are also used to perform cloning, DNA sequencing, RNA analysis protein analysis, DNA isolation, RNA extraction and polymerase chain reaction (PCR). In Molecular cloning, researchers use two general types of enzymes – restriction enzymes for cutting DNA and modifying enzymes for making nucleic acid modifications, often prior to ligation. For the most sensitive research, the Ultra Pure Modifying Enzymes offer the highest purity available.


Cloning enzymes include DNA ligases, which are typically used for ligation of DNA inserts into vectors, DNA polymerases for initiation of DNA synthesis, and RNA polymerases for initiation of transcription of RNA from a DNA template. DNA modifying enzymes allow manipulation of DNA for specific purposes. For example, nucleases are used to degrade DNA and/or RNA. Each nuclease has its specific purpose. S1 Nuclease and Mung Bean Nuclease both degrade single-stranded DNA and single-stranded RNA, leaving behind blunt-ended double-stranded DNA or RNA. However, Mung Bean Nuclease is more conservative in digestion than S1 Nuclease, as it is less likely to degrade where a nick has occurred in the DNA or RNA.


Choosing the right enzymes for your PCR and molecular biology application can profoundly affect your experimental outcome. The primary requirements for a DNA polymerase for PCR are optimal activity at temperatures around 75 °C and the ability to retain that activity after prolonged incubation at even higher temperatures (95 °C). The first thermostable DNA polymerase to be widely used for PCR was Taq DNA Polymerase.. For PCR applications that require optimization, a routine Taq DNA Polymerase might not be the right choice.


Enzyme Engineering and Designer Enzymes

An enzyme’s activities, namely its substrate specificity and its reaction rate, are dictated by its amino acid sequence. The amino acid sequence also controls the enzyme’s 3D folded structure. However, while the natural repertoire of enzymes is vast (conducting over 10,000 known reactions) natural proteins are, naturally, optimal for their function in nature and not in a laboratory. This can lead to issues with poor enzyme stability, slower-than-expected reaction speeds and weak activity on non-natural chemicals. Such properties often lead to natural enzymes being unsuitable for industrial scale biotechnology. Scientists have therefore conducted significant research on enzyme engineering, in which the amino acid sequence of a protein is modified to optimize its properties.


One highly desirable, but so far elusive application in enzyme engineering is the design and construction of entirely new enzyme sequences from the ground-up. There are no universal rules defining the sequence-structure-function relationship of enzymes, making it almost impossible to design a sequence that can fold into a molecule of desired function. However, the ability to make new enzymes in such a way would allow researchers to do away with everything superfluous in natural enzymes, sticking to just structures required for both catalysis and stability in a given condition. In theory, this will allow for highly efficient bioconversions on any desired molecule, making enzymes far more tractable to the chemical industry.


The speed and selectivity with which enzymes in nature catalyze conversions are enviable. To catalytically boost unnatural reactions, researchers mimic enzymes with the help of protein frameworks realized by computer-aided protein design. Further optimization is achieved through repetition of a Darwinian cycle: 1) diversification through mutation, 2) identification of improved catalysts, and 3) amplification of the more efficient enzyme variants. This allows for the production of designer enzymes with very high activities.


Researchers led by Clemens Mayer and Gerard Roelfes at the University of Groningen (the Netherlands) have now demonstrated that this type of directed evolution is also a method for improving the efficiency of a novel class of designer enzymes: enzymes that contain an amino acid that is not utilized by nature.


Starting with a protein from Lactococcus lactis, a bacterium used in the production of dairy products such as cheese and buttermilk, the researchers synthesized a designer enzyme that contains an amino acid with an abiotic aniline side chain (aminophenylalanine). Like free aniline, this amino acid catalyzes the reaction of aldehydes with hydrazines or hydroxylamines to make hydrazones or oximes, respectively.


To increase the activity of the enzyme, the researchers produced enzyme variants with mutations at amino acids near the aniline side chain. Screening of about 400 mutants yielded two candidates with better activity, one of which was subjected to a second evolutionary round. This led to the discovery of more beneficial mutations. To identify synergetic effects, multiple favorable mutations were combined to produce further variants. In this way, it was possible to increase the conversion rate of the enzyme by a factor of 90.


The researchers emphasize that, akin to natural enzymes, “this drastic increase is based on strengthening the inherent catalytic activity of the aniline side chain. We intend to use this principle to incorporate further organic catalysts as side chains in enzymes, and to use directed evolution to convert these into highly effective designer enzymes that can rapidly and efficiently carry out synthetically important reactions that would otherwise only run very slowly.”


Designer enzymes will have applications for defense against biological warfare, by deactivating pathogenic biological agents, and for creating more effective medications, according to Kendall Houk, professor UCLA chemistry group.


Molecular biology enzymes market

Molecular biology enzymes market is expected to gain market growth in the forecast period of 2021 to 2028. Data Bridge Market Research analyses the market to grow at a CAGR of 8.2% in the above-mentioned forecast period. Increasing funding for genomics research drives the molecular biology enzymes market.


Molecular Biology Enzymes Market Scope and Market Size

Molecular biology enzymes market is segmented on the basis of product, application and end-user. The growth amongst these segments will help you analyse meagre growth segments in the industries, and provide the users with valuable market overview and market insights to help them in making strategic decisions for identification of core market applications.


On the basis of product, the molecular biology enzymes market is segmented into kits and reagents and enzymes.

Application Insights

Based on the Application, it is segmented into polymerase chain reaction (PCR), sequencing, cloning, epigenetics, restriction digestion and synthetic biology. The growth of the segment is mainly attributed to the increasing prevalence of genetic, infectious, and chronic diseases. PCR based tests are increasingly being used to guide patient management, particularly in the fields of infectious disease, cancer, and congenital abnormalities. According to the WHO, cancer is the second leading cause of death globally and is responsible for an estimated 9.6 million deaths in 2018. The PCR techniques are routinely used for tumor profiling and detection of bacterial infections. Pertaining to broad applications of PCR in the field of molecular biology, the market segment is expected to show better growth during the forecast period.


The sequencing segment accounted for the major revenue share of 34.9% in 2019 in the molecular biology enzymes, reagents and kits market. The segment is expected to grow at a lucrative pace. With the introduction of Next-generation Sequencing (NGS), there has been tremendous progress in genetic research and the discovery of human diseases. NGS analysis of tumor epigenomics, genomics, and transcriptomics, drives biomarker discovery for cancer diagnostics and tumor stratification.


The benefits of NGS include detection of the smallest possible mutation, easier combined detection of SNP and larger abnormalities, and most important combination of high-throughput, speed, and resolution. Moreover, a rise in the adoption of personalized medicine through targeted and whole-exome sequencing is expected to drive the demand for sequencing. Thereby, widespread adoption of these technologies accelerates the utilization of molecular biology products under this segment.


In terms of revenue, PCR captured the second-largest revenue share in 2019 in the market for molecular biology enzymes, reagents, and kits. The advent of miniPCR in recent times has made the technique affordable and more portable. On the other hand, the introduction of the droplet digital PCR (ddPCR), which integrates conventional PCR with the fluorescence-activated cell sorting aspects, offers a highly automated and robust technology for the detection of scarce targets in samples. Such advances in PCR technology are expected to drive revenue in this segment.


End-use Insights

The molecular biology enzymes market is also segmented on the basis of end-user into pharmaceutical and biotechnology companies, academic and research institutes, hospitals and diagnostic centres and others. Others have been further segmented into contract research organizations and food and beverage companies.


The pharma and biotech segment dominated the market for molecular biology enzymes and reagents and kits and accounted for the largest revenue share of 36.3% in 2019. This is due to the wide implementation of PCR and NGS for the development of companion diagnostics and diagnostic tests, especially for the assessment of infectious diseases. An increase in the R&D activities and several ongoing clinical trials in the pharma and biotech firms are driving the demand for molecular biology enzymes and reagents. Furthermore, shifting preferences towards personalized medicine and companion diagnostic has propelled collaborations and mergers with respect to sequencing technology, which subsequently surges the demand for sequencing products.


For instance, QIAGEN entered into a 15-year partnership with Illumina, Inc. to broaden the use of NGS-based in vitro diagnostic kits for patient management in October 2019. This collaboration offers QIAGEN with an opportunity to develop companion diagnostic tests for the evaluation of tumors for potential immunotherapies on the TruSight Oncology assays from Illumina. Such initiatives are also expected to fuel the segment growth at a lucrative pace in the market for molecular biology enzymes, reagents, and kits.


Wide applications of NGS and PCR techniques in academic research projects accelerate the uptake of these products by universities and research centers. As reported in March 2020, researchers at the UNC Medical Center Microbiology and Molecular Microbiology Laboratories explored the usage of NGS for accurate COVID-19 diagnosis. Moreover, arise in funding and investment for these entities are expected to augment the academic and research segment at a considerable CAGR.



Drivers: Global Molecular Biology Enzymes Market

Rising use of smartphones and wearable devices into healthcare drives the Molecular Biology Enzymes market.

Cost-effectiveness and patient’s convenience is the vital factor escalating the market growth, also rising aging population, increased involvement of patient population, continuous Increase In lifestyle diseases, rising government expenditure on the healthcare sector to facilitate numerous healthcare services, increased internet penetration in developed and developing countries and rising patient-centric approach are the major factors among others driving the Molecular Biology Enzymes market.

Rising partnerships between the companies and the introduction of connected healthcare in developing economies will further create new opportunities for the Molecular Biology Enzymes market in the forecasted period of 2020-2027.


Global Molecular Biology Enzymes Market

North America dominates the Molecular Biology Enzymes market due to well-developed internet infrastructure, well-developed healthcare sector and presence of major players in this region. Europe is the dominating region in terms of growth in Molecular Biology Enzymes market due to growing number of aged-population suffering from various diseases.


The molecular biology enzymes, kits and reagents market dominates the North America region due to increasing prevalence of genetic and chronic disorders, such as cancer, and favorable government initiatives. According to the American Cancer Society, approximately 1,735,350 new cancer cases were diagnosed in the United States in 2018 and there were around 609,640 deaths during the same year. Furthermore, growing geriatric population, along with rising R&D activities in the region is expected to drive the market over the forecast period.


In the Asia Pacific, the market for molecular biology enzymes, reagents, and kits is projected to register a lucrative growth rate during the forecast period. Continual development and commercialization of point of care PCR equipment and reagents by the regional players are one of the primary factors influencing the growth of the market in the region. For instance, in May 2020, Fujifilm Wako Pure Chemical Corp., a Japan-based firm, initiated the commercialization of PCR reagents for the automated coronavirus test device


In the Asia Pacific, the is projected to witness the fastest growth rate during the forecast period with China as the fastest growing pharmaceutical market globally. Expansion of the pharmaceutical industry along with an increase in the investments from global pharmaceutical firms is expected to boost the market growth in China. In November 2019, AstraZeneca launched an R&D center and AI innovation center in Shanghai. This initiative is expected to drive the usage of molecular biology products in the pharma sector in China


However, lack of awareness about the possible applications of Molecular Biology Enzymes, reluctance to share information regarding the health and rising privacy and cybercrimes are the major factors among others acting as restraints, and will further challenge the growth of Molecular Biology Enzymes market in the forecast period mentioned above.


The major players  are Thermo Fisher Scientific, Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Illumina, Inc., QIAGEN, New England Biolabs., Promega Corporation., Agilent Technologies, Inc, F. Hoffmann-La Roche Ltd, Takara Bio Inc., Bio Basic Inc., Jena Bioscience GmbH, Molecular Biology Resources, Inc., LGC Limited, Promega Corporation., Bio-Rad Laboratories, Inc., BD and Rockland Immunochemicals, Inc., among other domestic and global players..


The companies are continuously expanding their technology portfolios to make these products more widely available, user-friendly, innovative, and affordable. For instance, in January 2020, Agilent Technologies introduced the Agilent SureSelect XT HS2 DNA Kit, which is designed to overcome the challenges faced by researchers during the preparation of DNA sequencing libraries. This new product allows the researchers to select the workflow that better suit their requirements. This product development is expected to accelerate the company’s capture-based enrichment library preparation activities.


Major players, such as Thermo Fisher, Roche, Illumina, QIAGEN, and Bio-Rad, have undertaken several strategic initiatives to reinforce their market share. For instance, in May 2020, Roche acquired Stratos Genomics that allowed Roche to advance the development of its nanopore sequencer using Sequencing by Expansion (SBX), the unique chemistry technology of the Stratos Genomics.




References and Resources also include:



About Rajesh Uppal

Check Also

Revolutionizing Orthopedic Implants: The Crucial Role of Biomaterial Technology

Introduction: In the realm of orthopedic engineering, the focus has historically been on the biomechanical …

error: Content is protected !!