scholarly journals PROTEIN THERMAL STABILITY ENGINEERING USING HOTMUSIC

2019 ◽  
Author(s):  
Fabrizio Pucci ◽  
Jean Marc Kwasigroch ◽  
Marianne Rooman
Keyword(s):  
Thermal Stability ◽  
Rational Design ◽  
Point Mutations ◽  
Rhizomucor Miehei ◽  
Research Field ◽  
Homologous Proteins ◽  
Functional Sites ◽  
Additional Information ◽  
Set Up ◽  
The Impact

AbstractThe rational design of enzymes is a challenging research field, which plays an important role in the optimization of a wide series of biotechnological processes. Computational approaches allow to screen all possible amino acid substitutions in a target protein and to identify a subset likely to have the desired properties. They can thus be used to guide and restrict the huge, time-consuming, search in sequence space to reach protein optimality. Here we present HoTMuSiC, a tool that predicts the impact of point mutations on the protein melting temperature, which uses the experimental or modelled protein structure as sole input, and is available at dezyme.com. Its main advantages include accuracy and speed, which makes it a perfect instrument for thermal stability engineering projects aiming to design new proteins that feature increased heat resistance or remain active and stable in non-physiological conditions. We set up a HoTMuSiC-based pipeline, which uses additional information to avoid mutations of functionally important residues, identified as being too well conserved among homologous proteins or too close to annotated functional sites. The efficiency of this pipeline is successfully demonstrated on Rhizomucor miehei lipase.

scholarly journals High-quality thermodynamic data on the stability changes of proteins upon single-site mutations

2016 ◽  
Author(s):  
Fabrizio Pucci ◽  
Raphaël Bourgeas ◽  
Marianne Rooman
Keyword(s):  
Thermal Stability ◽  
Point Mutations ◽  
Experimental Information ◽  
Thermodynamic Quantities ◽  
High Quality ◽  
Melting Temperatures ◽  
The Difference ◽  
Set Up ◽  
The Stability ◽  
The Impact

We have set up and manually curated a dataset containing experimental information on the impact of amino acid substitutions in a protein on its thermal stability. It consists of a repository of experimentally measured melting temperatures (Tm) and their changes upon point mutations (∆Tm) for proteins having a well-resolved X-ray structure. This high-quality dataset is designed for being used for the training or benchmarking of in silico thermal stability prediction methods. It also reports other experimentally measured thermodynamic quantities when available,i.e.the folding enthalpy (∆H) and heat capacity (∆CP) of the wild type proteins and their changes upon mutations (∆∆H and ∆∆CP), as well as the change in folding free energy (∆∆G) at a reference temperature. These data are analyzed in view of improving our insights into the correlation between thermal and thermodynamic stabilities, the asymmetry between the number of stabilizing and destabilizing mutations, and the difference in stabilization potential of thermostable versus mesostable proteins.

scholarly journals Predicting protein thermal stability changes upon point mutations using statistical potentials: Introducing HoTMuSiC

2016 ◽  
Author(s):  
Fabrizio Pucci ◽  
Raphaël Bourgeas ◽  
Marianne Rooman
Keyword(s):  
Thermal Stability ◽  
Melting Temperature ◽  
Point Mutations ◽  
Model Structure ◽  
Temperature Dependent ◽  
Statistical Potentials ◽  
Validation Procedure ◽  
The Impact ◽  
Fold Cross Validation ◽  
Thermal Stability Of

The accurate prediction of the impact of an amino acid substitution on the thermal stability of a protein is a central issue in protein science, and is of key relevance for the rational optimization of various bioprocesses that use enzymes in unusual conditions. Here we present one of the first computational tools to predict the change in melting temperature ΔTmupon point mutations, given the protein structure and, when available, the melting temperature Tmof the wild-type protein. The key ingredients of our model structure are standard and temperature-dependent statistical potentials, which are combined with the help of an artificial neural network. The model structure was chosen on the basis of a detailed thermodynamic analysis of the system. The parameters of the model were identified on a set of more than 1,600 mutations with experimentally measured ΔTm. The performance of our method was tested using a strict 5-fold cross-validation procedure, and was found to be significantly superior to that of competing methods. We obtained a root mean square deviation between predicted and experimental ΔTmvalues of 4.2°C that reduces to 2.9°C when ten percent outliers are removed. A webserver-based tool is freely available for non-commercial use at soft.dezyme.com.

scholarly journals Enhancing the Thermostability of Rhizomucor miehei Lipase with a Limited Screening Library by Rational-Design Point Mutations and Disulfide Bonds

2017 ◽  
Vol 84 (2) ◽  
Author(s):  
Guanlin Li ◽  
Xingrong Fang ◽  
Feng Su ◽  
Yuan Chen ◽  
Li Xu ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Disulfide Bonds ◽  
Rational Design ◽  
Single Point ◽  
Point Mutations ◽  
Rhizomucor Miehei ◽  
Wild Type ◽  
Content Type ◽  
Eukaryotic Protein ◽  
Screening Library

ABSTRACT Rhizomucor miehei lipase (RML), as a kind of eukaryotic protein catalyst, plays an important role in the food, organic chemical, and biofuel industries. However, RML retains its catalytic activity below 50°C, which limits its industrial applications at higher temperatures. Soluble expression of this eukaryotic protein in Escherichia coli not only helps to screen for thermostable mutants quickly but also provides the opportunity to develop rapid and effective ways to enhance the thermal stability of eukaryotic proteins. Therefore, in this study, RML was engineered using multiple computational design methods, followed by filtration via conservation analysis and functional region assessment. We successfully obtained a limited screening library (only 36 candidates) to validate thermostable single point mutants, among which 24 of the candidates showed higher thermostability and 13 point mutations resulted in an apparent melting temperature ( T m app ) of at least 1°C higher. Furthermore, both of the two disulfide bonds predicted from four rational-design algorithms were further introduced and found to stabilize RML. The most stable mutant, with T18K/T22I/E230I/S56C-N63C/V189C-D238C mutations, exhibited a 14.3°C-higher T m app and a 12.5-fold increase in half-life at 70°C. The catalytic efficiency of the engineered lipase was 39% higher than that of the wild type. The results demonstrate that rationally designed point mutations and disulfide bonds can effectively reduce the number of screened clones to enhance the thermostability of RML. IMPORTANCE R. miehei lipase, whose structure is well established, can be widely applied in diverse chemical processes. Soluble expression of R. miehei lipase in E. coli provides an opportunity to explore efficient methods for enhancing eukaryotic protein thermostability. This study highlights a strategy that combines computational algorithms to predict single point mutations and disulfide bonds in RML without losing catalytic activity. Through this strategy, an RML variant with greatly enhanced thermostability was obtained. This study provides a competitive alternative for wild-type RML in practical applications and further a rapid and effective strategy for thermostability engineering.

The Impact of Bioconjugation on the Interfacial Activity of a Protein Biosurfactant

2018 ◽  
Author(s):  
Hossam H Tayeb ◽  
Marina Stienecker ◽  
Anton Middelberg ◽  
Frank Sainsbury
Keyword(s):  
Polyethylene Glycol ◽  
Colloidal Stability ◽  
Point Mutations ◽  
Pharmaceutical Formulations ◽  
Industrial Processes ◽  
Parent Molecule ◽  
Site Specific ◽  
Interfacial Activity ◽  
Surface Active ◽  
The Impact

Biosurfactants, are surface active molecules that can be produced by renewable, industrially scalable biologic processes. DAMP4, a designer biosurfactant, enables the modification of interfaces via genetic or chemical fusion to functional moieties. However, bioconjugation of addressable amines introduces heterogeneity that limits the precision of functionalization as well as the resolution of interfacial characterization. Here we designed DAMP4 variants with cysteine point mutations to allow for site-specific bioconjugation. The DAMP4 variants were shown to retain the structural stability and interfacial activity characteristic of the parent molecule, while permitting efficient and specific conjugation of polyethylene glycol (PEG). PEGylation results in a considerable reduction on the interfacial activity of both single and double mutants. Comparison of conjugates with one or two conjugation sites shows that both the number of conjugates as well as the mass of conjugated material impacts the interfacial activity of DAMP4. As a result, the ability of DAMP4 variants with multiple PEG conjugates to impart colloidal stability on peptide-stabilized emulsions is reduced. We suggest that this is due to constraints on the structure of amphiphilic helices at the interface. Specific and efficient bioconjugation permits the exploration and investigation of the interfacial properties of designer protein biosurfactants with molecular precision. Our findings should therefore inform the design and modification of biosurfactants for their increasing use in industrial processes, and nutritional and pharmaceutical formulations.

MOTIF DAN DAMPAK PERNIKAHAN DINI DI INDARUNG NGALAU BATU GADANG

2018 ◽  
Vol 1 (1) ◽  
pp. 1
Author(s):  
Murisal Murisal
Keyword(s):  
Young Men ◽  
Early Marriage ◽  
Marriage Law ◽  
Men And Women ◽  
Home Life ◽  
Family Household ◽  
Set Up ◽  
The Impact ◽  
Husband And Wife

Motif and Impact of Early Marriage in Indarung Ngalau Batu Gadang.Penelitian is motivated by teenagers who married early on. Today, young men and women have a tendency to be less prepared to enter the home life, they are only ready to marry (ready here can be interpreted, maturity in terms of financial, understand what the meaning of marriage according to marriage law) is the bond of inner birth between a man and a woman as husband and wife for the purpose of forming a happy and eternal family (household) based on the Supreme Godhead while they are not ready to set up a home, whereas to build a household requires preparation both physically and spiritually . The purpose of this study to determine the motives underlying adolescents to make early marriage and the impact caused in the household as a result of the marriage.

Evaluation of the Impact of Fatty Acid Methyl Ester (FAME) Contamination on the Thermal Stability of Jet A

2013 ◽  
Author(s):  
Jr Morris ◽  
Shardo Robert W. ◽  
Higgins James ◽  
Cook Kim ◽  
Tanner Rhonda ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Fatty Acid ◽  
Methyl Ester ◽  
Fatty Acid Methyl Ester ◽  
Acid Methyl Ester ◽  
Acid Methyl ◽  
The Impact ◽  
Thermal Stability Of

Dissent and Education

2018 ◽  
Author(s):  
Mark Burden
Keyword(s):  
Eighteenth Century ◽  
Seventeenth Century ◽  
Educational Activity ◽  
Educational Institutions ◽  
Higher Educational Institutions ◽  
Legal Restrictions ◽  
Higher Educational ◽  
Set Up ◽  
The Impact ◽  
Dissenting Academies

Much eighteenth-century Dissenting educational activity was built on an older tradition of Puritan endeavour. In the middle of the seventeenth century, the godly had seen education as an important tool in spreading their ideas but, in the aftermath of the Restoration, had found themselves increasingly excluded from universities and schools. Consequently, Dissenters began to develop their own higher educational institutions (in the shape of Dissenting academies) and also began to set up their own schools. While the enforcement of some of the legal restrictions that made it difficult for Dissenting institutions diminished across the eighteenth century, the restrictions did not disappear entirely. While there has been considerable focus on Dissenting academies and their contribution to debates about doctrinal orthodoxy, the impact of Dissenting schools was also considerable.

scholarly journals On Kaufmann's theory of the impact of the pianoforte hammer

1920 ◽  
Vol 97 (682) ◽  
pp. 99-110 ◽  
Keyword(s):  
Initial Conditions ◽  
Practical Importance ◽  
Prima Facie ◽  
Point Of View ◽  
Infinite Length ◽  
Modes Of Vibration ◽  
Rigorous Treatment ◽  
The Subject ◽  
Set Up ◽  
The Impact

The theory of the vibrations of the pianoforte string put forward by Kaufmann in a well-known paper has figured prominently in recent discussions on the acoustics of this instrument. It proceeds on lines radically different from those adopted by Helmholtz in his classical treatment of the subject. While recognising that the elasticity of the pianoforte hammer is not a negligible factor, Kaufmann set out to simplify the mathematical analysis by ignoring its effect altogether, and treating the hammer as a particle possessing only inertia without spring. The motion of the string following the impact of the hammer is found from the initial conditions and from the functional solutions of the equation of wave-propagation on the string. On this basis he gave a rigorous treatment of two cases: (1) a particle impinging on a stretched string of infinite length, and (2) a particle impinging on the centre of a finite string, neither of which cases is of much interest from an acoustical point of view. The case of practical importance treated by him is that in which a particle impinges on the string near one end. For this case, he gave only an approximate theory from which the duration of contact, the motion of the point struck, and the form of the vibration-curves for various points of the string could be found. There can be no doubt of the importance of Kaufmann’s work, and it naturally becomes necessary to extend and revise his theory in various directions. In several respects, the theory awaits fuller development, especially as regards the harmonic analysis of the modes of vibration set up by impact, and the detailed discussion of the influence of the elasticity of the hammer and of varying velocities of impact. Apart from these points, the question arises whether the approximate method used by Kaufmann is sufficiently accurate for practical purposes, and whether it may be regarded as applicable when, as in the pianoforte, the point struck is distant one-eighth or one-ninth of the length of the string from one end. Kaufmann’s treatment is practically based on the assumption that the part of the string between the end and the point struck remains straight as long as the hammer and string remain in contact. Primâ facie , it is clear that this assumption would introduce error when the part of the string under reference is an appreciable fraction of the whole. For the effect of the impact would obviously be to excite the vibrations of this portion of the string, which continue so long as the hammer is in contact, and would also influence the mode of vibration of the string as a whole when the hammer loses contact. A mathematical theory which is not subject to this error, and which is applicable for any position of the striking point, thus seems called for.

News and Idiosyncratic Volatility: The Public Information Processing Hypothesis*

2020 ◽  
Author(s):  
Robert F Engle ◽  
Martin Klint Hansen ◽  
Ahmet K Karagozoglu ◽  
Asger Lunde
Keyword(s):  
Information Processing ◽  
Public Information ◽  
Selection Procedure ◽  
Autoregressive Process ◽  
Return Volatility ◽  
Market Outcomes ◽  
The Public ◽  
Additional Information ◽  
Financial News ◽  
The Impact

Abstract Motivated by the recent availability of extensive electronic news databases and advent of new empirical methods, there has been renewed interest in investigating the impact of financial news on market outcomes for individual stocks. We develop the information processing hypothesis of return volatility to investigate the relation between firm-specific news and volatility. We propose a novel dynamic econometric specification and test it using time series regressions employing a machine learning model selection procedure. Our empirical results are based on a comprehensive dataset comprised of more than 3 million news items for a sample of 28 large U.S. companies. Our proposed econometric specification for firm-specific return volatility is a simple mixture model with two components: public information and private processing of public information. The public information processing component is defined by the contemporaneous relation with public information and volatility, while the private processing of public information component is specified as a general autoregressive process corresponding to the sequential price discovery mechanism of investors as additional information, previously not publicly available, is generated and incorporated into prices. Our results show that changes in return volatility are related to public information arrival and that including indicators of public information arrival explains on average 26% (9–65%) of changes in firm-specific return volatility.

scholarly journals Grading Investment Diversification Options in Presence of Non-Historical Financial Information

Mathematics ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 692
Author(s):  
Clara Calvo ◽  
Carlos Ivorra ◽  
Vicente Liern ◽  
Blanca Pérez-Gladish
Keyword(s):  
Risk Measure ◽  
Statistical Information ◽  
Expected Returns ◽  
Financial Assets ◽  
Expected Return ◽  
Additional Information ◽  
Subjective Risk ◽  
The Impact ◽  
Statistical Risk ◽  
Reduction Index

Modern portfolio theory deals with the problem of selecting a portfolio of financial assets such that the expected return is maximized for a given level of risk. The forecast of the expected individual assets’ returns and risk is usually based on their historical returns. In this work, we consider a situation in which the investor has non-historical additional information that is used for the forecast of the expected returns. This implies that there is no obvious statistical risk measure any more, and it poses the problem of selecting an adequate set of diversification constraints to mitigate the risk of the selected portfolio without losing the value of the non-statistical information owned by the investor. To address this problem, we introduce an indicator, the historical reduction index, measuring the expected reduction of the expected return due to a given set of diversification constraints. We show that it can be used to grade the impact of each possible set of diversification constraints. Hence, the investor can choose from this gradation, the set better fitting his subjective risk-aversion level.

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