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Journal articles on the topic 'Isothermal denaturation'

Author: Grafiati

Published: 6 September 2023

Last updated: 31 July 2025

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1

Hinrichs, Jörg, and Britta Rademacher. "High pressure thermal denaturation kinetics of whey proteins." Journal of Dairy Research 71, no. 4 (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-lactog

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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 (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 quantitat

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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 (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

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4

CLAEYS, WENDIE L., ANN M. VAN LOEY та 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, № 4 (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 experiment

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5

Istrate, Daniel, Crisan Popescu та Martin Möller. "Non-Isothermal Kinetics of Hardα-Keratin Thermal Denaturation". Macromolecular Bioscience 9, № 8 (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 (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 (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 nanomachine

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11

Augustijn, Dillen, Alina Kulakova, Sujata Mahapatra, Pernille Harris, and Åsmund Rinnan. "Isothermal Chemical Denaturation: Data Analysis, Error Detection, and Correction by PARAFAC2." Analytical Chemistry 92, no. 10 (2020): 6958–67. http://dx.doi.org/10.1021/acs.analchem.9b05748.

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12

OWUSU-APENTEN, RICHARD K. "REVISED CONFORMATIONAL STABILITY PARAMETERS FOR BETA-LACTOGLOBULIN ISOTHERMAL DENATURATION BY UREA." Journal of Food Biochemistry 26, no. 3 (2002): 181–90. http://dx.doi.org/10.1111/j.1745-4514.2002.tb00851.x.

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13

Schön, Arne, Benjamin R. Clarkson, Maria Jaime, and Ernesto Freire. "Temperature stability of proteins: Analysis of irreversible denaturation using isothermal calorimetry." Proteins: Structure, Function, and Bioinformatics 85, no. 11 (2017): 2009–16. http://dx.doi.org/10.1002/prot.25354.

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14

CHEN, FUR-CHI, Y. H. PEGGY HSIEH, ROGER C. BRIDGMAN, and AGNES KILONZO-NTHENGE. "Kinetics of Tropomyosin Denaturation as a Predictive Model for Verifying Thermal Processing of Beef Products." Journal of Food Protection 69, no. 10 (2006): 2447–53. http://dx.doi.org/10.4315/0362-028x-69.10.2447.

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An enzyme-linked immunosorbent assay (ELISA) was developed to study thermal denaturation of tropomyosin (Tm) using the time-temperature requirements for cooked beef. The ELISA employed a monoclonal antibody (MAb 2C9) raised against bovine Tm for quantifying residual Tm in muscle extracts. The specificity of MAb 2C9 to bovine Tm was demonstrated by Western blot and the analytical validity of ELISA was confirmed by dot blot. Thermal denaturation of Tm, in the temperature range between 54.4 and 70.0°C, showed first-order dependency. Kinetic parameters of Tm denaturation were derived from isotherm

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15

Chen, S. S., N. T. Wright, and J. D. Humphrey. "Heat-Induced Changes in the Mechanics of a Collagenous Tissue: Isothermal, Isotonic Shrinkage." Journal of Biomechanical Engineering 120, no. 3 (1998): 382–88. http://dx.doi.org/10.1115/1.2798005.

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We present data from isothermal, isotonic-shrinkage tests wherein bovine chordae tendineae were subjected to well-defined constant temperatures (from 65 to 90°C), durations of heating (from 180 to 3600 s), and isotonic uniaxial stresses during heating (from 100 to 650 kPa). Tissue response during heating and “recovery” at 37°C following heating was evaluated in terms of the axial shrinkage, a gross indicator of underlying heat-induced denaturation. There were three key findings. First, scaling the heating time via temperature and load-dependent characteristic times for the denaturation process

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16

Mahran, R., N. Vello, A. Komulainen, H. Härmä, and K. Kopra. "64P Isothermal chemical KRAS denaturation assay for monitoring stability and inhibitors interactions." ESMO Open 8, no. 1 (2023): 100922. http://dx.doi.org/10.1016/j.esmoop.2023.100922.

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17

Chandran, Harish, Nikhil Gopalkrishnan, Bernard Yurke, and John Reif. "Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions." Journal of The Royal Society Interface 9, no. 72 (2012): 1637–53. http://dx.doi.org/10.1098/rsif.2011.0819.

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Can a wide range of complex biochemical behaviour arise from repeated applications of a highly reduced class of interactions? In particular, can the range of DNA manipulations achieved by protein enzymes be simulated via simple DNA hybridization chemistry? In this work, we develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based on strands of DNA as the only component molecules. Various enzymatic manipulations of these mDNA molecules are simulated via toehold-mediated DNA strand displacement reactions. We provide a formal model to describe the required properties and op

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18

FRANCO, Ricardo, Guangyue BAI, Vesna PROSINECKI, Filipa ABRUNHOSA, Gloria C. FERREIRA, and Margarida BASTOS. "Porphyrin-substrate binding to murine ferrochelatase: effect on the thermal stability of the enzyme." Biochemical Journal 386, no. 3 (2005): 599–605. http://dx.doi.org/10.1042/bj20040921.

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Ferrochelatase (EC 4.99.1.1), the terminal enzyme of the haem biosynthetic pathway, catalyses the chelation of Fe(II) into the protoporphyrin IX ring. The energetics of the binding between murine ferrochelatase and mesoporphyrin were determined using isothermal titration calorimetry, which revealed a stoichiometry of one molecule of mesoporphyrin bound per protein monomer. The binding is strongly exothermic, with a large intrinsic enthalpy (ΔH=−97.1 kJ · mol−1), and is associated with the uptake of two protons from the buffer. This proton transfer suggests that hydrogen bonding between ferroch

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19

BEHBAHANI, G. REZAEI, M. SHALBAFAN, N. GHEIBI, et al. "DENATURATION OF HUMAN SERUM ALBUMIN BY CERIUM (III) CHLORIDE." Biophysical Reviews and Letters 08, no. 01n02 (2013): 59–71. http://dx.doi.org/10.1142/s1793048013500033.

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Cerium (III) Chloride-induced conformational changes of human serum albumin, HSA, in phosphate buffer, 10 mM at pH 7.4 was investigated, using isothermal titration calorimetry (ITC), UV and fluorescence emission spectroscopic methods. The results indicate that CeCl3, Ce3+, induces irreversible denaturation of the HSA structure. The UV absorption intensity of HSA + Ce3+ shows a slight blueshift in the absorbance wavelength with increasing Ce3+ concentration. The fluorescence intensity was increased regularly and a slight redshift was observed in the emission wavelength. The HSA + Ce3+ complex q

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20

Hartdégen, Márton, András József Laki, Kolos Farkasvölgyi, Kristóf Iván, and Judit Plutzer. "Evaluation of Touchdown Loop-Mediated Isothermal Amplification for the Detection of Giardia duodenalis." Parasitologia 5, no. 2 (2025): 25. https://doi.org/10.3390/parasitologia5020025.

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Giardia duodenalis is a flagellated protozoan pathogen causing parasitic enteric disease outbreaks worldwide. Among detection methods, loop-mediated isothermal amplification (LAMP) has high selectivity and sensitivity, and the detection time is lower than that of conventional molecular methods. In this study, three published Giardia LAMP primer sets were tested and adapted to touchdown LAMP conditions. The measurement time, the volume of reagents, the effect of the denaturation step, different kinds of polymerases, and the presence or absence of betaine on the reaction were tested and evaluate

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21

Nasreen, Khalida, Zahoor Ahmad Parray, Shahzaib Ahamad, et al. "Interactions Under Crowding Milieu: Chemical-Induced Denaturation of Myoglobin is Determined by the Extent of Heme Dissociation on Interaction with Crowders." Biomolecules 10, no. 3 (2020): 490. http://dx.doi.org/10.3390/biom10030490.

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Generally, in vivo function and structural changes are studied by probing proteins in a dilute solution under in vitro conditions, which is believed to be mimicking proteins in intracellular milieu. Earlier, thermal-induced denaturation of myoglobin, in the milieu of crowder molecule showed destabilization of the metal protein. Destabilization of protein by thermal-induced denaturation involves a large extrapolation, so, the reliability is questionable. This led us to measure the effects of macromolecular crowding on its stability by chemical-induced denaturation of the protein using probes li

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22

Suzuki, Ryota, Masaru Ihira, Yoshihiko Enomoto, et al. "Heat denaturation increases the sensitivity of the cytomegalovirus loop-mediated isothermal amplification method." Microbiology and Immunology 54, no. 8 (2010): 466–70. http://dx.doi.org/10.1111/j.1348-0421.2010.00236.x.

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23

Senisterra, Guillermo A., Bum Soo Hong, Hee-Won Park, and Masoud Vedadi. "Application of High-Throughput Isothermal Denaturation to Assess Protein Stability and Screen for Ligands." Journal of Biomolecular Screening 13, no. 5 (2008): 337–42. http://dx.doi.org/10.1177/1087057108317825.

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Many diseases in humans are caused by mutations that decrease the stability of specific proteins or increase their susceptibility to aggregation. Consequently, the availability of high-throughput methods for assessing protein stability and aggregation properties under physiological conditions (e.g., 37 °C) is necessary to analyze physicochemical properties under conditions that are closer to in vivo models. Therefore, the authors have explored the use of isothermal denaturation (ITD) in a 384-well format to evaluate the reproducibility of the method in assessing the stability of proteins at te

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24

Shahrajabian, Mohamad H., Wenli Sun, and Qi Cheng. "Different Methods for Molecular and Rapid Detection of Human Novel Coronavirus." Current Pharmaceutical Design 27, no. 25 (2021): 2893–903. http://dx.doi.org/10.2174/1381612827666210604114411.

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Introduction: While PCR has been recognized as one of the appropriate ways to diagnose infectious diseases, Loop-mediated isothermal amplification (LAMP) which is a nucleic acid amplification method, can be considered as an alternative to PCR, and it is faster, cost-effective, and easier to perform than nested PCR. Patients and Methods: Keywords were searched in PubMed/MEDLINE, Scopus and Institute for Scientific Information Web of Science, as well as the search engine of Google Scholar. Keywords included PCR, LAMP, RAA, RPA, Virus and COVID-19. Results: LAMP technology has been extensively ap

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25

BAJAJ, Kanika, Ghadiyaram CHAKSHUSMATHI, Kiran BACHHAWAT-SIKDER, Avadhesha SUROLIA, and Raghavan VARADARAJAN. "Thermodynamic characterization of monomeric and dimeric forms of CcdB (controller of cell division or death B protein)." Biochemical Journal 380, no. 2 (2004): 409–17. http://dx.doi.org/10.1042/bj20031528.

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The protein CcdB (controller of cell division or death B) is an F-plasmid-encoded toxin that acts as an inhibitor of Escherichia coli DNA gyrase. The stability and aggregation state of CcdB have been characterized as a function of pH and temperature. Size-exclusion chromatography revealed that the protein is a dimer at pH 7.0, but a monomer at pH 4.0. CD analysis and fluorescence spectroscopy showed that the monomer is well folded, and has similar tertiary structure to the dimer. Hence intersubunit interactions are not required for folding of individual subunits. The stability of both forms wa

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26

Taneja, S., and F. Ahmad. "Increased thermal stability of proteins in the presence of amino acids." Biochemical Journal 303, no. 1 (1994): 147–53. http://dx.doi.org/10.1042/bj3030147.

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This study is a systematic attempt to understand the roles of osmolytes in protecting proteins against denaturing stress. Thermal denaturation of cytochrome c has been studied in the presence of various concentrations of all L-amino acids that are more hydrophobic than glycine and have a solubility of 0.1 M or higher in water at 25 degrees C. The basic observations are as follows. (1) Arginine and histidine destabilize the native protein; both Tm (the midpoint of thermal transition) and delta GDH2O (25 degrees C) (the Gibbs energy of stabilization) decrease with increasing amino acid concentra

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27

Chen, S. S., N. T. Wright, and J. D. Humphrey. "Heat-Induced Changes in the Mechanics of a Collagenous Tissue: Isothermal Free Shrinkage." Journal of Biomechanical Engineering 119, no. 4 (1997): 372–78. http://dx.doi.org/10.1115/1.2798281.

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We present data from isothermal free-shrinkage tests (i.e., performed in the absence of mechanical loads) wherein bovine chordae tendineae were subjected to temperatures from 65 to 85°C for 120 to 1200 s. These data reveal four new insights into heat-induced denaturation of a collagenous tissue. First, a characteristic time for the free shrinkage appears to exhibit an Arrhenius-type relationship with temperature. Second, scaling the actual heating time via the characteristic time results in a single correlation between free shrinkage and the duration of heating; this correlation suggests a tim

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28

Ross, Patrick, Wilhelm Weihofen, Fai Siu, et al. "Isothermal chemical denaturation to determine binding affinity of small molecules to G-protein coupled receptors." Analytical Biochemistry 473 (March 2015): 41–45. http://dx.doi.org/10.1016/j.ab.2014.11.019.

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29

Soroka, Marianna, Barbara Wasowicz, and Anna Rymaszewska. "Loop-Mediated Isothermal Amplification (LAMP): The Better Sibling of PCR?" Cells 10, no. 8 (2021): 1931. http://dx.doi.org/10.3390/cells10081931.

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In 1998, when the PCR technique was already popular, a Japanese company called Eiken Chemical Co., Ltd. designed a method known as the loop-mediated isothermal amplification of DNA (LAMP). The method can produce up to 109 copies of the amplified DNA within less than an hour. It is also highly specific due to the use of two to three pairs of primers (internal, external, and loop), which recognise up to eight specific locations on the DNA or RNA targets. Furthermore, the Bst DNA polymerase most used in LAMP shows a high strand displacement activity, which eliminates the DNA denaturation stage. O

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30

CLAEYS, WENDIE L., LINDA R. LUDIKHUYZE, ANN M. VAN LOEY та MARC E. HENDRICKX. "Inactivation kinetics of alkaline phosphatase and lactoperoxidase, and denaturation kinetics of β-lactoglobulin in raw milk under isothermal and dynamic temperature conditions". Journal of Dairy Research 68, № 1 (2001): 95–107. http://dx.doi.org/10.1017/s002202990000460x.

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A detailed kinetic study of alkaline phosphatase, lactoperoxidase and β-lactoglobulin was carried out in the context of identifying intrinsic time–temperature indicators for controlling the heat processing of milk. The heat inactivation or denaturation of alkaline phosphatase, lactoperoxidase and β-lactoglobulin under isothermal conditions was found to follow first order kinetics. Experimental results were analysed using both a two step linear regression and a one step non-linear regression method. Results obtained using the two statistical techniques were comparable, but the 95% confidence in

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31

Datta, Nivedita, Maurice G. Hayes, Hilton C. Deeth, and Alan L. Kelly. "Significance of frictional heating for effects of high pressure homogenisation on milk." Journal of Dairy Research 72, no. 4 (2005): 393–99. http://dx.doi.org/10.1017/s0022029905001056.

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High pressure homogenisation (HPH) is a novel dairy processing tool, which has many effects on enzymes, microbes, fat globules and proteins in milk. The effects of HPH on milk are due to a combination of shear forces and frictional heating of the milk during processing; the relative importance of these different factors is unclear, and was the focus of this study. The effect of milk inlet temperature (in the range 10–50 °C) on residual plasmin, alkaline phosphatase, lactoperoxidase and lipase activities in raw whole bovine milk homogenised at 200 MPa was investigated. HPH caused significant he

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32

Tang, Chuanning, Scott Lew, and Dacheng He. "Using a second-order differential model to fit data without baselines in protein isothermal chemical denaturation." Protein Science 25, no. 4 (2016): 898–904. http://dx.doi.org/10.1002/pro.2878.

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Harris, J. L., P. B. Wells, and J. D. Humphrey. "Altered Mechanical Behavior of Epicardium Due to Isothermal Heating Under Biaxial Isotonic Loads." Journal of Biomechanical Engineering 125, no. 3 (2003): 381–88. http://dx.doi.org/10.1115/1.1567754.

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Recent isothermal biaxial isotonic tests suggest that increasing the temperature hastens the rate of denaturation of epicardium whereas increasing the mechanical load during heating delays this process, findings that are consistent with prior uniaxial tests on tendons. Yet, contrary to uniaxial reports, a clear time-temperature-load equivalency was not found in this multiaxial setting. There is, therefore, a need to delineate multiaxial thermomechanical behavior in greater detail, and ultimately, to correlate changes therein with the underlying microstructure. Toward this end, we describe a ne

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34

Saboury, A. A., M. Miroliae, M. Nemat-Gorgani, and A. A. Moosavi-Movahedi. "Kinetics denaturation of yeast alcohol dehydrogenase and the effect of temperature and trehalose. An isothermal microcalorimetry study." Thermochimica Acta 326, no. 1-2 (1999): 127–31. http://dx.doi.org/10.1016/s0040-6031(98)00588-7.

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35

Sarver, Ronald W., Joseph M. Rogers, and Dennis E. Epps. "Determination of Ligand-MurB Interactions by Isothermal Denaturation: Application as a Secondary Assay to Complement High Throughput Screening." Journal of Biomolecular Screening 7, no. 1 (2002): 21–28. http://dx.doi.org/10.1089/108705702753520305.

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Rubio, Ana R., Natalia Busto, José M. Leal, and Begoña García. "Doxorubicin binds to duplex RNA with higher affinity than ctDNA and favours the isothermal denaturation of triplex RNA." RSC Advances 6, no. 103 (2016): 101142–52. http://dx.doi.org/10.1039/c6ra21387a.

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The higher affinity of DOX with AU to give the intercalated complex AU/DOX is responsible for the disproportionation of the groove binding complex, UAU/DOX, to give rise to the AU/DOX and the U/DOX complexes at 25 °C

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Haque, M. Amdadul, Peter Aldred, Jie Chen, Colin J. Barrow, and Benu Adhikari. "Comparative study of denaturation of whey protein isolate (WPI) in convective air drying and isothermal heat treatment processes." Food Chemistry 141, no. 2 (2013): 702–11. http://dx.doi.org/10.1016/j.foodchem.2013.03.035.

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38

Gooran, Negin, and Kari Kopra. "Fluorescence-Based Protein Stability Monitoring—A Review." International Journal of Molecular Sciences 25, no. 3 (2024): 1764. http://dx.doi.org/10.3390/ijms25031764.

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Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluoresce

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Liu, Mengmeng, Mengzhe Li, Cuiping Ma, and Chao Shi. "Detection of canine parvovirus and feline panleukopenia virus in fecal samples by strand exchange amplification." Journal of Veterinary Diagnostic Investigation 32, no. 6 (2020): 880–86. http://dx.doi.org/10.1177/1040638720962067.

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Canine parvovirus 2 (CPV-2) and feline panleukopenia virus (FPLV) often cause acute enteric disease in their hosts. A simple, rapid, and effective method for the on-site detection of these viruses would be useful. We used a denaturation bubble-mediated strand exchange amplification (SEA) method to successfully detect CPV-2 and FPLV in fecal samples. SEA could detect as little as 3.6 pg/μL of CPV-2 and 6.6 pg/μL of FPLV genomic DNA following a 40-min incubation at an isothermal temperature of 61°C. Unlike PCR, SEA does not require complicated equipment, and positive samples produce a color chan

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40

Fleischman, Marianna L., Rajoshi Chaudhuri, Ria T. Caringal, Lisa Kueltzo, K. C. Cheng, and Frank Arnold. "Optimization of Formulation Conditions for Broadly Neutralizing Antibodies (bnAb): Utilizing Isothermal Chemical Denaturation as a High-throughput Screening Method." Biophysical Journal 116, no. 3 (2019): 334a. http://dx.doi.org/10.1016/j.bpj.2018.11.1817.

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41

Kushwah, Vinita Chauhan, Ritika Chauhan, and Ram Kumar Dhaked. "Fluorescence Thermal Shift Assay based High Through-put Screening in Small Molecule Drug Discovery: A Brief Overview." Journal of Modern Biology and Drug Discovery 3 (May 28, 2024): 3. http://dx.doi.org/10.53964/jmbdd.2024003.

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Background: The Early drug discovery process was majorly phenotypic, lacking target specificity, and mechanism of action causing short and/or long-term toxicological impacts on the patients leading to several drug withdrawals from the market. Biochemical procedures and methods used in drug discovery and development make it lengthy in terms of time requiring approx. 15 years with the investment of billions of dollars for a new drug molecule. Technological advancement leading to the identification of protein structures through crystallography paved a new path toward targeted drug discovery. Obje

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Nye, Dillon B., and Nathan A. Tanner. "Chimeric DNA byproducts in strand displacement amplification using the T7 replisome." PLOS ONE 17, no. 9 (2022): e0273979. http://dx.doi.org/10.1371/journal.pone.0273979.

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Recent advances in next generation sequencing technologies enable reading DNA molecules hundreds of kilobases in length and motivate development of DNA amplification methods capable of producing long amplicons. In vivo, DNA replication is performed not by a single polymerase enzyme, but multiprotein complexes called replisomes. Here, we investigate strand-displacement amplification reactions using the T7 replisome, a macromolecular complex of a helicase, a single-stranded DNA binding protein, and a DNA polymerase. The T7 replisome may initiate processive DNA synthesis from DNA nicks, and the r

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Licheri, Matthias, Manon Flore Licheri, Kemal Mehinagic, Nicolas Ruggli, and Ronald Dijkman. "A Novel and Rapid Selective Viral Genome Amplification and Sequencing Method for African Swine Fever Virus." Viruses 16, no. 11 (2024): 1664. http://dx.doi.org/10.3390/v16111664.

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African swine fever virus (ASFV) is the etiological agent of African swine fever, a highly contagious hemorrhagic disease affecting both wild boars and domestic pigs with lethality rates up to 100%. Until now, the most effective measure to prevent an outbreak of ASFV was early detection. In this situation, whole genome sequencing (WGS) allows the gathering of detailed information about the identity and epidemiology of the virus. However, due to the large genome size and complex genome ends, WGS is challenging. Current WGS workflows require either elaborate enrichment methods or are based on ti

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Nai, Yi Heng, Egan H. Doeven, and Rosanne M. Guijt. "An improved nucleic acid sequence-based amplification method mediated by T4 gene 32 protein." PLOS ONE 17, no. 3 (2022): e0265391. http://dx.doi.org/10.1371/journal.pone.0265391.

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The uptake of Nucleic Acid Sequence-Based Amplification (NASBA) for point of care testing may be hindered by a complexity in the workflow due the requirement of a thermal denaturation step to initiate the cyclic isothermal amplification before the addition of the amplification enzymes. Despite reports of successful enhancement of other DNA and RNA amplification methods using DNA and RNA binding proteins, this has not been reported for NASBA. Here, three single-stranded binding proteins, RecA, Extreme Thermostable Single-stranded binding protein (ET SSB) and T4 gene gp32 protein (gp32), were in

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Liu, Wentao, and Guoying Li. "Non-isothermal kinetic analysis of the thermal denaturation of type I collagen in solution using isoconversional and multivariate non-linear regression methods." Polymer Degradation and Stability 95, no. 12 (2010): 2233–40. http://dx.doi.org/10.1016/j.polymdegradstab.2010.09.012.

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Svilenov, Hristo, Uroš Markoja, and Gerhard Winter. "Isothermal chemical denaturation as a complementary tool to overcome limitations of thermal differential scanning fluorimetry in predicting physical stability of protein formulations." European Journal of Pharmaceutics and Biopharmaceutics 125 (April 2018): 106–13. http://dx.doi.org/10.1016/j.ejpb.2018.01.004.

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Cotrina, Ellen Y., Ângela Oliveira, José Pedro Leite, et al. "Repurposing Benzbromarone for Familial Amyloid Polyneuropathy: A New Transthyretin Tetramer Stabilizer." International Journal of Molecular Sciences 21, no. 19 (2020): 7166. http://dx.doi.org/10.3390/ijms21197166.

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Transthyretin (TTR) is a homotetrameric protein involved in human amyloidosis, including familial amyloid polyneuropathy (FAP). Discovering small-molecule stabilizers of the TTR tetramer is a therapeutic strategy for these diseases. Tafamidis, the only approved drug for FAP treatment, is not effective for all patients. Herein, we discovered that benzbromarone (BBM), a uricosuric drug, is an effective TTR stabilizer and inhibitor against TTR amyloid fibril formation. BBM rendered TTR more resistant to urea denaturation, similarly to iododiflunisal (IDIF), a very potent TTR stabilizer. BBM compe

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Jensen, Jaime L., Beau D. Jernberg, Sangita C. Sinha, and Christopher L. Colbert. "Structural basis of cell-surface signaling by a conserved sigma regulator in Gram-negative bacteria." Journal of Biological Chemistry 295, no. 17 (2020): 5795–806. http://dx.doi.org/10.1074/jbc.ra119.010697.

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Cell-surface signaling (CSS) in Gram-negative bacteria involves highly conserved regulatory pathways that optimize gene expression by transducing extracellular environmental signals to the cytoplasm via inner-membrane sigma regulators. The molecular details of ferric siderophore-mediated activation of the iron import machinery through a sigma regulator are unclear. Here, we present the 1.56 Å resolution structure of the periplasmic complex of the C-terminal CSS domain (CCSSD) of PupR, the sigma regulator in the Pseudomonas capeferrum pseudobactin BN7/8 transport system, and the N-terminal sign

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Sultana, Tajnin, David M. Morgan, Beau D. Jernberg, Peyton Zak, Sangita C. Sinha, and Christopher L. Colbert. "Biophysical and Solution Structure Analysis of Critical Residues Involved in the Interaction between the PupB N-Terminal Signaling Domain and PupR C-Terminal Cell Surface Signaling Domain from Pseudomonas capeferrum." Biomolecules 14, no. 9 (2024): 1108. http://dx.doi.org/10.3390/biom14091108.

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Abstract: Cell surface signaling (CSS) is a means of rapidly adjusting transcription in response to extracellular stimuli in Gram-negative bacteria. The pseudobactin BN7/8 uptake (Pup) system not only imports iron but also upregulates its own transcription through CSS in Pseudomonas capeferrum. In the absence of ferric pseudobactin BN7/8, the signaling components are maintained in a resting state via the formation of a periplasmic complex between the N-terminal signaling domain (NTSD) of the outer membrane iron-transporter, PupB, and the C-terminal CSS domain (CCSSD) of the sigma regulator, Pu

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Trollope, K. M., J. F. Görgens та H. Volschenk. "Semirational Directed Evolution of Loop Regions in Aspergillus japonicus β-Fructofuranosidase for Improved Fructooligosaccharide Production". Applied and Environmental Microbiology 81, № 20 (2015): 7319–29. http://dx.doi.org/10.1128/aem.02134-15.

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ABSTRACTTheAspergillus japonicusβ-fructofuranosidase catalyzes the industrially important biotransformation of sucrose to fructooligosaccharides. Operating at high substrate loading and temperatures between 50 and 60°C, the enzyme activity is negatively influenced by glucose product inhibition and thermal instability. To address these limitations, the solvent-exposed loop regions of the β-fructofuranosidase were engineered using a combined crystal structure- and evolutionary-guided approach. This semirational approach yielded a functionally enriched first-round library of 36 single-amino-acid-

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