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Relevant bibliographies by topics / Isothermal denaturation

Academic literature on the topic 'Isothermal denaturation'

Author: Grafiati

Published: 6 September 2023

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Journal articles on the topic "Isothermal denaturation"

1

Hinrichs, Jörg, and Britta Rademacher. "High pressure thermal denaturation kinetics of whey proteins." Journal of Dairy Research 71, no. 4 (November 2004): 480–88. http://dx.doi.org/10.1017/s0022029904000238.

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Pressure processing of foodstuff has been applied to produce or modify proteinaceous gel structures. In real pressure processing the treatment is non-isothermal, due to the adiabatic nature of the process and the heat loss from the product to the vessel. In order to estimate the effect of pressurization on milk constituents pressure and temperature dependent kinetics were determined separately from each other. In a detailed kinetic study whey protein isolate was treated under isobaric (200 to 800 MPa) and isothermal conditions (−2 to 70 °C), and the resulting degree of denaturation of β-lactoglobulin A and B and α-lactalbumin was analysed. Kinetic parameters of denaturation were estimated using a one step non-linear regression method which allowed a global fit of the whole data set. The isobaric isothermal denaturation of β-lactoglobulin and α-lactalbumin was found to follow third and second order kinetics, respectively. Isothermal pressure denaturation of both β-lactoglobulin fractions do not differ significantly and were characterized by an activation volume decreasing with increasing temperature from −10 to about −30 ml mol−1, which demonstrates that the denaturation rate is accelerated with increasing temperature. The activation energy of about 70 to 100 kJ mol−1 obtained for β-lactoglobulin A and B is not dependent to a great extent on the pressure which indicates that above 200 MPa denaturation rate is limited by the aggregation rate while pressure forces unfolding of the molecule.

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2

Sarver, Ronald W., Joseph M. Rogers, and Dennis E. Epps. "Determination of Ligand-MurB Interactions by Isothermal Denaturation: Applicatio as a Secondary Assay to Complement High Throughput Screening." Journal of Biomolecular Screening 7, no. 1 (February 2002): 21–28. http://dx.doi.org/10.1177/108705710200700104.

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We used a temperature-jump isothermal denaturation procedure with various methods of detection to evaluate the quality of putative inhibitors of MurB discovered by high-throughput screening. Three optical methods of detection—ultraviolet hyperchromicity of absorbance, fluorescence of bound dyes, and circular dichroism—as well as differential scanning calorimetry were used to dissect the effects of two chemical compounds and a natural substrate on the enzyme. The kinetics of the denaturation process and binding of the compounds detected by quenching of flavin fluorescence were used to quantitate the dose dependencies of the ligand effects. We found that the first step in the denaturation of MurB is the rapid loss of flavin from the active site and that the two chemical inhibitors appeared to destabilize the interaction of the cofactor with the enzyme but stabilize the global unfolding. The kinetics of the denaturation process as well as the loss of flavin fluorescence on binding established that both compounds had nanomolar affinities for the enzyme. We showed that coupling of the various detection methods with isothermal denaturation yields a powerful regimen to provide analytical data for assessing inhibitor specificity for a protein target.

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3

NIELSEN, Anders D., Claus C. FUGLSANG, and Peter WESTH. "Effect of calcium ions on the irreversible denaturation of a recombinant Bacillus halmapalus alpha-amylase: a calorimetric investigation." Biochemical Journal 373, no. 2 (July 15, 2003): 337–43. http://dx.doi.org/10.1042/bj20030220.

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The effect of temperature and calcium ions on the denaturation of a recombinant α-amylase from Bacillus halmapalus α-amylase (BHA) has been studied using calorimetry. It was found that thermal inactivation of BHA is irreversible and that calcium ions have a significant effect on stability. Thus an apparent denaturation temperature (Td) of 83 °C in the presence of excess calcium ions was observed, whereas Td decreased to 48 °C when calcium was removed. The difference in thermal stability with and without calcium ions has been used to develop an isothermal titration calorimetric (ITC) procedure that allows simultaneous determination of kinetic parameters and enthalpy changes of the denaturation of calcium-depleted BHA. An activation energy EA of 101 kJ/mol was found for the denaturation of calcium-depleted BHA. The results support a kinetic denaturation mechanism where the calcium-depleted amylase denatures irreversibly at low temperature and if calcium ions are in excess, the amylase denatures irreversibly at high temperatures. The two denaturation reactions are coupled with the calcium-binding equilibrium between calcium-bound and -depleted amylase. A combination of the kinetic denaturation results and calcium-binding constants, determined by isothermal titration calorimetry, has been used to estimate kinetic stability, expressed in terms of the half-life of BHA as a function of temperature and free-calcium-ion concentration. Thus it is estimated that the apparent EA can be increased to approx. 123 kJ/mol by increasing the free-calcium concentration.

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4

CLAEYS, WENDIE L., ANN M. VAN LOEY, and MARC E. HENDRICKX. "Kinetics of alkaline phosphatase and lactoperoxidase inactivation, and of β-lactoglobulin denaturation in milk with different fat content." Journal of Dairy Research 69, no. 4 (November 2002): 541–53. http://dx.doi.org/10.1017/s0022029902005721.

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In the context of identifying intrinsic time temperature integrators (TTIs) for evaluating heat processing of milk, the extent to which milk fat content has an effect on alkaline phosphatase (ALP) and lactoperoxidase (Lpo) inactivation and on β-lactoglobulin (β-lg) denaturation kinetics was studied. Inactivation and denaturation kinetics were analysed in whole, semi-skimmed and skimmed milk. In previous experiments (isothermal and non-isothermal heating conditions), heat inactivation of ALP and Lpo and heat denaturation of β-lg were found to follow first order kinetics. This allowed experimental design to be simplified. Data analysis was performed by non-linear regression and results were evaluated by construction of joint confidence regions. The possible effect of milk fat was illustrated by temperature time tolerance (TTT-) diagrams. Although initial ALP activity was lower in skimmed milk compared with semi-skimmed or whole milk, kinetics were comparable and fat content did not seem to substantially affect the ALP test result for pasteurized milk. Unlike ALP, Lpo inactivation and β-lg denaturation kinetics differed significantly in milk with different fat content. Differences between Lpo inactivation kinetics were relatively small and acceptable in the context of quantifying the process impact. Denaturation of β-lg, on the other hand, seemed to be enhanced at higher milk fat content (>72 °C).

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5

Istrate, Daniel, Crisan Popescu, and Martin Möller. "Non-Isothermal Kinetics of Hardα-Keratin Thermal Denaturation." Macromolecular Bioscience 9, no. 8 (August 11, 2009): 805–12. http://dx.doi.org/10.1002/mabi.200800344.

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6

Shi, Chao, Fanjin Shang, Meiling Zhou, Pansong Zhang, Yifan Wang, and Cuiping Ma. "Triggered isothermal PCR by denaturation bubble-mediated strand exchange amplification." Chemical Communications 52, no. 77 (2016): 11551–54. http://dx.doi.org/10.1039/c6cc05906f.

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7

Huang, Mengting, Fang Yang, Jiye Fu, Pengfeng Xiao, Jing Tu, and Zuhong Lu. "Reaction parameter comparison and optimization of multiple displacement amplification." Analytical Methods 12, no. 1 (2020): 46–53. http://dx.doi.org/10.1039/c9ay01922g.

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After analysed MDA under different conditions, we found that different DNA denaturation methods before isothermal incubation can influence the amplification speed of MDA, and genome coverage uniformity was correlated with the amplification temperature.

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8

Wafer, Lucas, Marek Kloczewiak, Sharon M. Polleck, and Yin Luo. "Isothermal chemical denaturation of large proteins: Path-dependence and irreversibility." Analytical Biochemistry 539 (December 2017): 60–69. http://dx.doi.org/10.1016/j.ab.2017.10.001.

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9

Epps, Dennis E., Ronald W. Sarver, Joseph M. Rogers, John T. Herberg, and Paul K. Tomich. "The Ligand Affinity of Proteins Measured by Isothermal Denaturation Kinetics." Analytical Biochemistry 292, no. 1 (May 2001): 40–50. http://dx.doi.org/10.1006/abio.2001.5047.

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10

Maltzeva, Yulia I., Daria A. Gorbenko, Ekaterina V. Nikitina, Maria S. Rubel, and Dmitry M. Kolpashchikov. "Visual Detection of Stem-Loop Primer Amplification (SPA) Products without Denaturation Using Peroxidase-like DNA Machines (PxDM)." International Journal of Molecular Sciences 24, no. 9 (April 25, 2023): 7812. http://dx.doi.org/10.3390/ijms24097812.

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Rapid, inexpensive, and accurate determination of nucleic acids is a decisive factor in evaluating population’s health and monitoring treatment at point-of-care (POC) settings. Testing systems with visual outputs can provide instrument-free signal detection. Isothermal amplification technologies can substitute conventional polymerase chain reaction (PCR) testing due to compatibility with the POC diagnostic. Here, we have visually detected DNA fragments obtained by stem-loop-primer-assisted isothermal amplification (SPA), but not those obtained by PCR or LAMP amplification using DNA nanomachines with peroxidase-like activity (PxDM) with sensitivity to a single nucleotide substitution. Compared to the diagnostics with conventional loop-mediated isothermal amplification (LAMP), the PxDM method produces no false positive signals with the non-specific amplification products. The study suggests that PxDM, in conjunction with SPA isothermal amplification, can become a valid platform for POC testing systems.

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Book chapters on the topic "Isothermal denaturation"

1

O’Neil, Pierce T., Alexandra J. Machen, Jackie A. Thompson, Wei Wang, Quyen Q. Hoang, Michael R. Baldwin, Karen R. Khar, John Karanicolas, and Mark T. Fisher. "Constructing Kinetically Controlled Denaturation Isotherms of Folded Proteins Using Denaturant-Pulse Chaperonin Binding." In Methods in Molecular Biology, 293–304. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8820-4_19.

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2

Silva, Jerson L., and Andrea T. Da Poian. "Pressure and Cold Denaturation of Proteins, Protein-DNA Complexes, and Viruses." In High Pressure Effects in Molecular Biophysics and Enzymology. Oxford University Press, 1996. http://dx.doi.org/10.1093/oso/9780195097221.003.0013.

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The application of hydrostatic pressure provides a means of appraising interprotein and intraprotein interactions isothermally and makes it possible to sample partially folded conformations. A number of proteins exhibit cold denaturation and cold dissociation. We have used the combined effects of pressure and low temperature to promote dissociation or denaturation of single-chain proteins, oligomers, protein-DNA complexes, and viruses. In this article, we summarize results that have biological relevance. The dissociation and denaturation of the hexameric protein, allophycocyanin, are accomplished only when the temperature is decreased to —10 °C, indicating the entropic character of the folding and association reaction. The folding and dimerization of Arc repressor in the temperature range of 0—20 °C is also favored by a large positive entropy that counteracts an unfavorable positive enthalpy. On binding operator DNA, Arc repressor becomes extremely stable against denaturation. However, the Arc repressor-operator DNA complex is cold denatured at subzero temperatures under pressure. The entropy increases greatly when Arc repressor binds tightly to its operator sequence but not to a nonspecific sequence. The dissociation and denaturation of icosahedral viruses by pressure and low temperature also have been studied. The procapsid shells of bacteriophage P22 only dissociate by pressure at temperatures below 0 °C. On the other hand, the monomeric coat protein is very unstable toward pressure. Cowpea mosaic virus (CPMV) dissociates only in the presence of 1.0 M urea, at 2.5 kbar when the temperature is decreased to — 15°C. At temperatures close to — 20 °C, partial denaturation is obtained even in the absence of urea. The assembly of CPMV is related to large and positive variations or enthalpy and entropy, making the assembly of ribonucleoprotein components an entropy-driven process. We conclude that protein folding, protein association, and protein-DNA recognition seem to need positive entropy to occur. We are facing a puzzle in which a final, apparently more ordered state is achieved, a state that paradoxically has more entropy. In the last 20 years, several studies have described the cold denaturation of proteins (Brandts, 1964; Sturtevant, 1977; Privalov et al., 1986; Griko et al., 1988; Chen & Schellman, 1989, and as reviewed in Privalov, 1990). However, unlike thermal denaturation, cold denaturation is not well understood.

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Conference papers on the topic "Isothermal denaturation"

1

Persat, Alexandre, Tomoyuki Morita, and Juan G. Santiago. "On-Chip Isothermal Polymerase Chain Reaction." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-43070.

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We present a novel technique for on-chip PCR where temperature is held constant and uniform in the reactor. Specific chemicals, known as denaturants, have the ability to melt DNA. A flow control scheme establishes spatio-temporal fluctuations in the concentration of denaturants along a microchannel, while electromigration drives DNA through this spatially varying denaturant concentration field. Preliminary results show denaturation and extension of a 200 base pairs (bp) DNA template.

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2

Chen, Pin-Chuan, Masahiko Hashimoto, Michael W. Mitchell, Dimitris E. Nikitopoulos, Steven A. Soper, and Michael C. Murphy. "Limiting Performance of High Throughput Continuous Flow Micro-PCR." In ASME 2004 International Mechanical Engineering Congress and Exposition. ASMEDC, 2004. http://dx.doi.org/10.1115/imece2004-62091.

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Continuous flow polymerase chain reaction (CFPCR) devices are compact reactors suitable for microfabrication and the rapid amplification of target DNAs. For a given reactor design, the amplification time can be reduced simply by increasing the flow velocity through the isothermal zones of the device; for flow velocities near the design value, the PCR cocktail reaches thermal equilibrium at each zone quickly, so that near ideal temperature profiles can be obtained. However, at high flow velocities there are penalties of an increased pressure drop and a reduced residence time in each temperature zone for the DNA/reagent mixture, potentially affecting amplification efficiency. This study was carried out to evaluate the thermal and biochemical effects of high flow velocities in a spiral, 20 cycle CFPCR device. Finite element analysis (FEA) was used to determine the steady-state temperature distribution along the micro-channel and the temperature of the DNA/reagent mixture in each temperature zone as a function of linear velocity. The critical transition was between the denaturation (95°C) and renaturation (55°C-68°C) zones; above 6 mm/s the fluid in a passively-cooled channel could not be reduced to the desired temperature and the duration of the temperature transition between zones increased with increased velocity. The amplification performance of the CFPCR as a function of linear velocity was assessed using 500 and 997 base pair (bp) fragments from λ-DNA. Amplifications at velocities ranging from 1 mm/s to 20 mm/s were investigated. Alternative design of PCR was investigated. Shuttle PCR has a single straight channel and a DNA plug, driven by electrokinetic flow, will move forward and backward in the microchannel to achieve the repetitive thermal cycles. Thermal performance, independent insulated temperature blocks, and molecular and thermal diffusion were evaluated.

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