Protein Engineering: Past, Present, and Future

Lutz, Stefan; Iamurri, Samantha

doi:10.1007/978-1-4939-7366-8_1

Cited by 49 publications

(31 citation statements)

References 64 publications

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“…Recently, the chemical modification of proteins for improvement of functionality has become widespread with advances in organic synthetic chemistry and protein engineering [1,2]. There are several ways to chemically modify proteins, for instance conjugating polyethylene glycol to protein (PEGylated protein) is of value as this enhances the chemical stability, solubility, and blood retention of the protein during clinical use [3][4][5][6][7][8].…”

Section: Introductionmentioning

confidence: 99%

“…The following are available online.Figure S1:1 H NMR spectra of (a) lysozyme, (b) CHLysozyme, and (c) physical mixture of lysozyme and cholesterol. Lysozyme and CHLysozyme concentration: 21.4 mg/mL; physical mixture of lysozyme and cholesterol (lysozyme [mol]/cholesterol [mol] = 1/12) concentration: 21.4 mg/m, Figure S2: 13 C NMR spectra of lysozyme and CHLysozyme in DMSO-d 6 at 25 • C. (a) Lysozyme, and (b) CHLysozyme.…”

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confidence: 99%

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Synthesis and Characterization of Cholesteryl Conjugated Lysozyme (CHLysozyme)

et al. 2020

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Hydrophobic interaction is important for protein conformation. Conjugation of a hydrophobic group can introduce intermolecular hydrophobic contacts that can be contained within the molecule. It is possible that a strongly folded state can be formed in solution compared with the native state. In this study, we synthesized cholesteryl conjugated lysozyme (CHLysozyme) using lysozyme and cholesterol as the model protein and hydrophobic group, respectively. Cholesteryl conjugation to lysozyme was confirmed by nuclear-magnetic resonance. Differential-scanning calorimetry suggested that CHLysozyme was folded in solution. CHLysozyme secondary structure was similar to lysozyme, although circular dichroism spectra indicated differences to the tertiary structure. Fluorescence measurements revealed a significant increase in the hydrophobic surface of CHLysozyme compared with that of lysozyme; CHLysozyme self-associated by hydrophobic interaction of the conjugated cholesterol but the hydrophobic surface of CHLysozyme decreased with time. The results suggested that hydrophobic interaction changed from intramolecular interaction to an intermolecular interaction. Furthermore, the relative activity of CHLysozyme to lysozyme increased with time. Therefore, CHLysozyme likely forms a folded state with an extended durability of activity. Moreover, lysozyme was denatured in 100% DMSO but the local environment of tryptophan in CHLysozyme was similar to that of a native lysozyme. Thus, this study suggests that protein solution stability and resistance to organic solvents may be improved by conjugation of a hydrophobic group.

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Section: Introductionmentioning

confidence: 99%

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confidence: 99%

Synthesis and Characterization of Cholesteryl Conjugated Lysozyme (CHLysozyme)

et al. 2020

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“…Protein–protein interactions underlie many important biological processes [ 65 – 67 ]. The quantitative estimation of how fast these interactions can be formed has broad implications to protein design [ 68 ] and drug discovery [ 69 ]. The improvement of experimental techniques and the collection of high-throughput experimental data on protein–protein association facilitate the development of computational approaches to model and predict association rates.…”

Section: Discussionmentioning

confidence: 99%

Classification of protein–protein association rates based on biophysical informatics

Dhusia

2021

BMC Bioinformatics

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Background Proteins form various complexes to carry out their versatile functions in cells. The dynamic properties of protein complex formation are mainly characterized by the association rates which measures how fast these complexes can be formed. It was experimentally observed that the association rates span an extremely wide range with over ten orders of magnitudes. Identification of association rates within this spectrum for specific protein complexes is therefore essential for us to understand their functional roles. Results To tackle this problem, we integrate physics-based coarse-grained simulations into a neural-network-based classification model to estimate the range of association rates for protein complexes in a large-scale benchmark set. The cross-validation results show that, when an optimal threshold was selected, we can reach the best performance with specificity, precision, sensitivity and overall accuracy all higher than 70%. The quality of our cross-validation data has also been testified by further statistical analysis. Additionally, given an independent testing set, we can successfully predict the group of association rates for eight protein complexes out of ten. Finally, the analysis of failed cases suggests the future implementation of conformational dynamics into simulation can further improve model. Conclusions In summary, this study demonstrated that a new modeling framework that combines biophysical simulations with bioinformatics approaches is able to identify protein–protein interactions with low association rates from those with higher association rates. This method thereby can serve as a useful addition to a collection of existing experimental approaches that measure biomolecular recognition.

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“…Respective sectors of molecular biology dealing with enzymatic processes and whole-cell bioconversions are Enzyme engineering [6] and Metabolic engineering [7] respectively. Where enzyme engineering provides tools for optimizing protein structure for better performance; and metabolic engineering provides tools for optimizing the microbial genome to redistribute metabolic pathways in favor of the desired product formation.…”

Section: Bioconversion-enzyme or Whole Cell?mentioning

confidence: 99%

Enzymes – Key Elements of the Future Biorefineries

Birikh¹,

Michine²,

Heikkilä³

et al. 2022

Biorefineries - Selected Processes

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The biorefinery concept in its modern meaning has emerged after it has become apparent that biofuel production from non-food biomass is struggling for economic viability. Lignocellulosic biomass is more recalcitrant and more complex than the starch-based feedstocks used for food. The former, therefore, calls for a more complex approach to its utilization. This chapter reflects MetGen’s vision of the future development of biorefineries. We will discuss the zero-waste approach to lignocellulosic biomass utilization and various ways to valorize the resulting streams to boost the economic viability of the biorefinery. We will mostly explore the relevant enzyme-based approaches and will make a special focus on lignin valorization. Enzymatic and cell-based approaches to sugar valorization will be discussed as well.

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Protein Engineering: Past, Present, and Future

Cited by 49 publications

References 64 publications

Synthesis and Characterization of Cholesteryl Conjugated Lysozyme (CHLysozyme)

Synthesis and Characterization of Cholesteryl Conjugated Lysozyme (CHLysozyme)

Classification of protein–protein association rates based on biophysical informatics

Enzymes – Key Elements of the Future Biorefineries

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