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 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.

Characterization of Ni- and Ni(Pt)-Silicide Formation on Narrow Polycrystalline Si Lines by Raman Spectroscopy

1999 ◽  
Vol 591 ◽  
Author(s):  
P. S. Lee ◽  
D. Mangelinck ◽  
K. L. Pey ◽  
J. Ding ◽  
T. Osipowicz ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Raman Spectroscopy ◽  
Raman Mapping ◽  
Silicide Formation ◽  
Nucleation Sites ◽  
The Difference ◽  
The Stability ◽  
Non Destructive ◽  
Thermal Stability Of

ABSTRACTThe formation and thermal stability of Ni- and Ni(Pt) silicide on narrow polycrystalline Si (poly-Si) lines have been investigated using the non-destructive micro-Raman technique. The presence of Ni or Ni(Pt)Si on poly-Si lines with linewidths ranging from 0.5 gtm to 0.25 μm has been monitored by a distinct Raman peak at around 215 cm−1. Ni(Pt)Si was clearly identified to be present up to a RTA temperature of 900°C on narrow poly-Si lines as compared to pure NiSi which was found only up to 750°C. Raman scattering from the 100×100 μm2 poly-Si pads showed the formation of NiSi2 at 750°C for pure Ni-salicidation and 900°C for Ni(Pt)-salicidation respectively. The difference in the stability of NiSi on the poly-Si pads and lines is discussed in terms of agglomeration, inversion and/or nucleation of NiSi2that could be due to difference in nucleation sites and/or stress. In addition, a correlation between the line sheet resistance and the presence of Ni silicide was found using micro-Raman mapping along single poly-Si lines.

scholarly journals Pathology of the Organs of Vision in Metallurgists

2019 ◽  
Vol 15 (4) ◽  
pp. 492-496
Author(s):  
A. L. Onischenko ◽  
A. V. Kolbasko ◽  
M. A. Melnichenko ◽  
S. N. Filimonov
Keyword(s):  
Tear Film ◽  
Control Group ◽  
Length Of Service ◽  
Metallurgical Production ◽  
Outer Corner ◽  
Cataract Development ◽  
The Difference ◽  
The Stability ◽  
The Impact ◽  
Chronic Conjunctivitis

The frequency and structure of ophthalmopathology in workers of the Novokuznetsk Metallurgical Combine (NMC) have been studied. In total 1911 workers of NMC have been examined. The control group comprised 1801 people working in hazardous industrial conditions. The experimental group consisted of employees dealing with management, engineering center, accounting (110 people). Their work was not connected with the impact of unfavorable factors of metallurgical production. In the control group, the hazard classes ranged from 3.2 to 3.4. The difference between the classes of hazard impact consisted in an increase of the intensity of the hazardous factors exposure. In the structure of conjunctival diseases we have diagnosed chronic conjunctivitis (198.3 ‰), chronic blepharoconjunctivitis (109.4 ‰), pinguecula (266.7 ‰) and pterygium (7.2 ‰) in metallurgical workers. Pengucules in the control group of workers was not only more often than in engineers, but also larger, often located in the inner and outer corner of the eye, and was detected in workers under 30–35 years. The workers of the main shops suffered more severely from the function of tear production and the stability of the pre-corneal tear film. The miners suffered from the highest frequency of cataract development — 301 ‰. Thus, a high incidence of inflammatory and dystrophic diseases of the eyelids and conjunctiva, cataracts in metallurgy has been established. An increase in the frequency of ophthalmopathology was noted with an increase in the length of service under harmful conditions of metallurgical production. The authors suggest the term “metallurgy ophthalmopathy”, which includes manifestations of chronic conjunctivitis and / or blepharoconjunctivitis against the background of unstable precorneal film and frequent formation of posterior-subcapsular opacities of the lens.

scholarly journals Design to Data for mutants of β-glucosidase B from Paenibacillus polymyxa: L171M, H178M, M221L, E406W, N160E, F415M

2020 ◽  
Author(s):  
Xiaoqing Huang ◽  
Daniel Kim ◽  
Peishan Huang ◽  
Ashley Vater ◽  
Justin B. Siegel
Keyword(s):  
Thermal Stability ◽  
Protein Design ◽  
Single Point ◽  
Point Mutations ◽  
Paenibacillus Polymyxa ◽  
Biophysical Parameters ◽  
Limited Degree ◽  
Function Relationship ◽  
The Stability ◽  
And Function

ABSTRACTComputational protein design is growing in popularity as a means to engineer enzymes. Currently, protein design algorithms can predict the stability and function of the enzymes to only a limited degree. Thus, further experimental data is required for training software to more accurately characterize the structure-function relationship of enzymes. To date, the Design2Data (D2D) database holds 129 single point mutations of β-glucosidase B (BglB) characterized by kinetic and thermal stability biophysical parameters. In this study, we introduced six mutants into the BglB database and examined their catalytic activity and thermal stability: L171M, H178M, M221L, E406W, N160E, and F415M.

Variance of HRD score from primary to recurrent in high-grade serous ovarian cancer.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e17540-e17540
Author(s):  
Xiaoxiang Chen ◽  
Jing Ni ◽  
Xia Xu ◽  
Wenwen Guo ◽  
Qian Zhao ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Cellular Response ◽  
Copy Number Variants ◽  
Point Mutations ◽  
High Grade ◽  
Serous Ovarian Cancer ◽  
Primary Tumors ◽  
The Difference ◽  
The Stability ◽  
Changes Over Time

e17540 Background: Homologous recombination deficiency (HRD) is an important biomarker of poly (ADP-ribose) polymerase inhibitor (PARPi) in patients with high-grade serous ovarian cancer (HGSOC). The stability of HRD in the recurrent HGSOC and its primary pair from Jiangsu Institute of Cancer Hospital was investigated. Methods: A total of paired 18 samples from 9 HGSOC patients were analyzed. HRD score was evaluated by loss of heterozygosity(LOH) and genetic mutations were also detected from next-generation sequencing.The student t-test evaluated the difference of HRD score between matched tumors. The functional annotation and clustering of affected genes in the recurrent tumor cells were analyzed by the KEGG Orthology (KO) database. Results: The HRD score of recurrent HGSOC tumors was significantly higher than that of the paired primary ones (p = 0.004). A total of 30 new somatic sequence variants at 27 genes presented in the recurrent tumors, were not found in any matched primary tumors. Of which, 19 (63.3%) were copy number variants (CNVs), 3 (10%) variants were rearrangement, and 8 (26.7%) were somatic point mutation. In these17 genes with CNVs, 14 genes had gene amplification variants, among them 50% (7/14) genes associated with the positive regulation of cell proliferation and cellular response to DNA damage stimulus. Four somatic point mutations involved in tumor suppressor pathway. Conclusions: Our data shed first light on the statistically significant changes of HRD score in paired recurrent HGSOC. The HRD score changes over time may imply further instantaneity assay strategy.

scholarly journals The impact of personality on the success of prospecting behavior in changing landscapes

2015 ◽  
Vol 61 (3) ◽  
pp. 557-568 ◽  
Author(s):  
John Curtis Burkhalter ◽  
Nina H. Fefferman ◽  
Julie L. Lockwood
Keyword(s):  
Landscape Composition ◽  
Breeding Habitat ◽  
Relative Fitness ◽  
Costs And Benefits ◽  
Large Role ◽  
High Quality ◽  
New Strategy ◽  
The Difference ◽  
The Impact ◽  
Very High

Abstract Personality can play a large role in dispersal decisions, influencing how each individual estimates and values expected costs versus benefits of venturing out to explore the unknown. We contrast the impact of persistence on fitness using decision theory models to examine the relative success of prospecting movement (which is a widespread behavior used by animals to explore available breeding habitat before determining where to settle) in different landscapes among individuals with different personalities. While evaluating trends in the costs and benefits of movement we provide a quantifiable measure of the impacts of relative tenacity in prospecting behavior on fitness gains/losses. Our model results predict that, regardless of landscape composition, individuals with greater tenacity in prospecting strategy have reduced fitness gains relative to individuals who are more willing to both initiate novel strategies, but then also abandon the new strategy rapidly if initial search does not seem fruitful. We show that fitness gains from choosing an appropriate prospecting strategy (i.e. abandoning poor habitat or staying in rich habitat) can be very high, indicating a potentially large influence from personality on fitness. Importantly, the model predicts that relative fitness gains are highly dependent on the availability of high quality habitat in the landscape, even if the difference under varying fitness outcomes between poor and rich habitat was substantial.

scholarly journals The impact of molecular symmetry and shape on the stability of discotic liquid crystals

2018 ◽  
Vol 96 (2) ◽  
pp. 132-138 ◽  
Author(s):  
Emilie Voisin ◽  
Vance E. Williams
Keyword(s):  
Liquid Crystals ◽  
Chain Structure ◽  
Side Chain ◽  
Discotic Liquid Crystals ◽  
Substitution Pattern ◽  
Melting Temperatures ◽  
Phase Range ◽  
Judicious Choice ◽  
The Stability ◽  
The Impact

Three series of dibenzo[a,c]phenazines were prepared in an order to assess the impact of side chain position on the phase stability of columnar liquid crystals. Each series was composed of four isomeric compounds differing only in the disposition of hexyloxy and decyloxy chains around the central aromatic core, giving rise to electronically similar compounds with varying shapes and symmetries. The substitution pattern was found to have a moderate effect on the clearing transition of the liquid crystal but a larger impact on the melting temperatures. These observations suggest a viable strategy for controlling the phase range of liquid crystals via judicious choice of peripheral chain structure and location.

Comparative theoretical studies of dinitromethyl- or trinitromethyl-modified derivatives of CL-20

2013 ◽  
Vol 91 (12) ◽  
pp. 1243-1251 ◽  
Author(s):  
Yong Pan ◽  
Weihua Zhu ◽  
Heming Xiao
Keyword(s):  
Thermal Stability ◽  
Density Functional ◽  
Parent Compound ◽  
Initial Step ◽  
Impact Sensitivity ◽  
Detonation Properties ◽  
Energetic Properties ◽  
The Stability ◽  
The Impact ◽  
Trinitromethyl Group

The heats of formation (HOFs), energetic properties, strain energies, thermal stability, and impact sensitivity for a series of trinitromethyl- or dinitromethyl-modified CL-20 derivatives were studied by using density functional theory. It is found that the trinitromethyl group is an effective structural unit for improving the gas-phase HOFs and energetic properties of the derivatives. However, incorporating the dinitromethyl group into the parent compound is not favorable for increasing its HOFs and detonation properties. The effects of the dinitromethyl or trinitromethyl groups on the stability of the parent compound are discussed. The studies on strain energies show that the introduction of the trinitromethyl group intensifies the strain of the cage skeleton for the title compounds, whereas for the dinitromethyl groups, the case is quite the contrary. An analysis of the bond dissociation energies for several relatively weak bonds suggests that the substitution of the dinitromethyl or trinitromethyl group decreases the thermal stability of the derivatives. The C−NO2 bond in the dinitromethyl or trinitromethyl group is the weakest one and the homolysis of the C−NO2 bond may be the initial step in thermal decomposition. In addition, according to the calculated free space per molecule, the introduction of the dinitromethyl or trinitromethyl group increases the impact sensitivities of the derivatives. Considering the detonation performance, thermal stability, and impact sensitivity, six compounds can be regarded as the target high-energetic compounds.

Model Reduction of a Parametrically Excited Drivetrain

2012 ◽  
Author(s):  
Thomas Pumhoessel ◽  
Peter Hehenberger ◽  
Klaus Zeman
Keyword(s):  
Stability Margin ◽  
Original System ◽  
Reduced Model ◽  
Parametrically Excited ◽  
System Parameters ◽  
Additional Stability ◽  
System Equations ◽  
The Difference ◽  
Set Up ◽  
The Stability

The complexity of engineering systems is continuously increasing, resulting in mathematical models that become more and more computationally expensive. Furthermore, in model based design, for example, system parameters are subject of change, and therefore, the system equations have to be evaluated repeatedly. Hence, there is a need for providing reduced models which are as compact as possible, but still reflect the properties of the original model in a satisfactory manner. In this contribution, the reduction of differential equations with time-periodic coefficients, termed as parametrically excited systems, is investigated using the method of Proper Orthogonal Decomposition (POD). A reduced model is set up based on the solution of the original system for a certain parametric combination resonance of the difference type, resulting in an additional stability margin of the trivial solution. It is shown that the POD reduced model approximates the stability behavior of the original system much better than a modally reduced model even if system parameters are subject of change.

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