TBA loop mapping with 3′-inverted-deoxythymidine for fine-tuning of the binding affinity for α-thrombin

2019 ◽  
Vol 17 (9) ◽  
pp. 2403-2412 ◽  
Author(s):  
Zhilong Chai ◽  
Lei Guo ◽  
Hongwei Jin ◽  
Yang Li ◽  
Shanshan Du ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Binding Affinity ◽  
Fine Tuning ◽  
New Locations ◽  
Position Dependence ◽  
Loop Residue

Inverted thymine was used for replacing each loop residue, respectively, and the new locations of thymine induced increased thermal stability and anti-coagulant ability, with position dependence.

Metal-binding hydrazone photoswitches for visible light reactivity and variable relaxation kinetics

2017 ◽  
Vol 16 (11) ◽  
pp. 1604-1612 ◽  
Author(s):  
Kacey C. Hall ◽  
Andrew T. Franks ◽  
Rory C. McAtee ◽  
Michael S. Wang ◽  
Vivian I. Lu ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Visible Light ◽  
Binding Affinity ◽  
Blue Light ◽  
Metal Binding ◽  
Relaxation Kinetics ◽  
Photostationary State ◽  
State Composition

Photoactive aroylhydrazones demonstrate variability in UVA, UVC and blue light photoreactivity, photostationary state composition, photoisomer thermal stability, and relative iron(iii) binding affinity in ways that may inform metal-gated photoswitching applications.

Synthesis and fine-tuning of thermal stability of the negative nitrile-rich photochromes of hydroxytricyanopyrrole (HTCP) series

2020 ◽  
Vol 46 (7) ◽  
pp. 3477-3490
Author(s):  
Mikhail Yu. Belikov ◽  
Mikhail Yu. Ievlev ◽  
Sergey V. Fedoseev ◽  
Oleg V. Ershov
Keyword(s):  
Thermal Stability ◽  
Fine Tuning ◽  
Thermal Stability Of

scholarly journals Antigen-binding affinity and thermostability of chimeric mouse-chicken IgY and mouse-human IgG antibodies with identical variable domains

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Juho Choi ◽  
Minjae Kim ◽  
Joungmin Lee ◽  
Youngsil Seo ◽  
Yeonkyoung Ham ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Binding Affinity ◽  
Antigen Binding ◽  
Chimeric Mouse ◽  
Binding Parameters ◽  
Igg Antibodies ◽  
Human Igg ◽  
Variable Domains ◽  
Thermal Stability Of ◽  
Parental Mouse

AbstractConstant (C)-region switching of heavy (H) and/or light (L) chains in antibodies (Abs) can affect their affinity and specificity, as demonstrated using mouse, human, and chimeric mouse-human (MH) Abs. However, the consequences of C-region switching between evolutionarily distinct mammalian and avian Abs remain unknown. To explore C-region switching in mouse-chicken (MC) Abs, we investigated antigen-binding parameters and thermal stability of chimeric MC-6C407 and MC-3D8 IgY Abs compared with parental mouse IgGs and chimeric MH Abs (MH-6C407 IgG and MH-3D8 IgG) bearing identical corresponding variable (V) regions. The two MC-IgYs exhibited differences in antigen-binding parameters and thermal stability from their parental mouse Abs. However, changes were similar to or less than those between chimeric MH Abs and their parental mouse Abs. The results demonstrate that mammalian and avian Abs share compatible V-C region interfaces, which may be conducive for the design and utilization of mammalian-avian chimeric Abs.

scholarly journals Proteins Feel More Than They See: Fine-Tuning of Binding Affinity by Properties of the Non-Interacting Surface

2014 ◽  
Vol 426 (14) ◽  
pp. 2632-2652 ◽  
Author(s):  
Panagiotis L. Kastritis ◽  
João P.G.L.M. Rodrigues ◽  
Gert E. Folkers ◽  
Rolf Boelens ◽  
Alexandre M.J.J. Bonvin
Keyword(s):  
Binding Affinity ◽  
Fine Tuning

Effects of estradiol and 4-hydroxytamoxifen on the conformation, thermal stability, and DNA recognition of estrogen receptor β

2007 ◽  
Vol 85 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Veena Vijayanathan ◽  
Norma J. Greenfield ◽  
T. J. Thomas ◽  
Margarita M. Ivanova ◽  
Valentyn V. Tyulmenkov ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Binding Affinity ◽  
Dna Recognition ◽  
Thermal Unfolding ◽  
Estrogen Response Element ◽  
Cd Spectrum ◽  
Estrogen Response ◽  
Helical Content ◽  
Partial Unfolding ◽  
Thermal Stability Of

Estrogen receptors (ERα and ERβ) are ligand-activated transcription factors. We examined the effects of estradiol (E2), 4-hydroxytamoxifen (HT), and the estrogen response element (ERE) on the helical content and thermal unfolding of ERβ. A circular dichroism (CD) spectrum of ERβ showed changes at 210 and 222 nm that were due to the presence of E2, which is indicative of partial unfolding. In contrast, HT did not alter the CD spectrum of ERβ. The addition of E2 + ERE caused an increase in the α-helical content and an increase in the temperature midpoint of folding transition (TM) from 39 ± 0.7 °C to 57.2 ± 1 °C. The addition of E2 + mutant ERE, or E2 + control oligonucleotide, increased the TM of ERβ to 45 ± 2 °C only. In the presence of HT, ERβ yielded similar TM values (55–58 °C) with ERE, mutant ERE, or control oligodeoxynucleotide. The binding affinity of ERβ for ERE increased 125.7-fold as a result of the presence of E2, but only 4-fold as a result of HT. These results demonstrate coupled effects of E2 and ERE on ERβ stability and binding affinity. The increased thermal stability of HT–ERβ–ERE was associated with reduced specificity of ERβ–ERE recognition, illustrating profound differences in conformational states of ERβ induced by E2 and HT.

scholarly journals Folding in Place: Design of β-Strap Motifs to Stabilize the Folding of Hairpins with Long Loops

2020 ◽  
Author(s):  
Alexis Richaud ◽  
Guangkuan zhao ◽  
Stephane Roche ◽  
Samir Hobloss
Keyword(s):  
Thermal Stability ◽  
Binding Affinity ◽  
Protein Function ◽  
Antibody Binding ◽  
Attractive Alternative ◽  
Stability Behavior ◽  
Cooperative Interactions ◽  
Spectroscopic Probes ◽  
Macrocyclic Peptides ◽  
Present Design

Despite their pivotal role in protein function and antibody binding affinity, <i>β</i>-hairpins bearing long non-canonical loops are a challenge to modern synthesis because of the large entropic penalty associated with their folding. Little is known about the contribution and impact of stabilizing motifs on the folding of <i>β</i>-hairpins of variable length and plasticity. Here we report a direct comparison between these <i>b</i>-straps thermodynamics and their thermal stability behavior using several local spectroscopic probes of the folding/unfolding landscape. The judicious cooperative interactions crafted in <i>β</i>-Strap <u>R</u>W(<u>V</u>W)•••(W<u>V</u>/<u>H</u>)W<u>E</u> (<i>strap</i> = <i>str</i>and + c<i>ap</i>) greatly stabilized hairpins with up to 10-residue loops lacking an innate nucleating-turn locus (<i>T<sub>m</sub> </i>up to 52 <sup>o</sup>C; 88 ± 1% folded at 291 K). The present design of novel <i>β</i>-straps aims to provide the foundation to study new classes of long hairpins and ultimately offer an attractive alternative to macrocyclic peptides for the mimicry of functional loops from proteins and antibodies.

scholarly journals Folding in Place: Design of β-Strap Motifs to Stabilize the Folding of Hairpins with Long Loops

2021 ◽  
Author(s):  
Alexis Richaud ◽  
Guangkuan zhao ◽  
Stephane Roche ◽  
Samir Hobloss
Keyword(s):  
Thermal Stability ◽  
Binding Affinity ◽  
Protein Function ◽  
Antibody Binding ◽  
Attractive Alternative ◽  
Stability Behavior ◽  
Cooperative Interactions ◽  
Spectroscopic Probes ◽  
Macrocyclic Peptides ◽  
Present Design

Despite their pivotal role in protein function and antibody binding affinity, <i>β</i>-hairpins bearing long non-canonical loops are a challenge to modern synthesis because of the large entropic penalty associated with their folding. Little is known about the contribution and impact of stabilizing motifs on the folding of <i>β</i>-hairpins of variable length and plasticity. Here we report a direct comparison between these <i>b</i>-straps thermodynamics and their thermal stability behavior using several local spectroscopic probes of the folding/unfolding landscape. The judicious cooperative interactions crafted in <i>β</i>-Strap <u>R</u>W(<u>V</u>W)•••(W<u>V</u>/<u>H</u>)W<u>E</u> (<i>strap</i> = <i>str</i>and + c<i>ap</i>) greatly stabilized hairpins with up to 10-residue loops lacking an innate nucleating-turn locus (<i>T<sub>m</sub> </i>up to 52 <sup>o</sup>C; 88 ± 1% folded at 291 K). The present design of novel <i>β</i>-straps aims to provide the foundation to study new classes of long hairpins and ultimately offer an attractive alternative to macrocyclic peptides for the mimicry of functional loops from proteins and antibodies.

scholarly journals Impact of A134 and E218 Amino Acid Residues of Tropomyosin on Its Flexibility and Function

2020 ◽  
Vol 21 (22) ◽  
pp. 8720
Author(s):  
Marina A. Marchenko ◽  
Victoria V. Nefedova ◽  
Daria S. Yampolskaya ◽  
Galina V. Kopylova ◽  
Daniil V. Shchepkin ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Fine Tuning ◽  
Actin Binding ◽  
Sliding Velocity ◽  
Scanning Calorimetry ◽  
In Vitro Motility Assay ◽  
In Vitro Motility ◽  
High Flexibility ◽  
Thermal Stability Of

Tropomyosin (Tpm) is one of the major actin-binding proteins that play a crucial role in the regulation of muscle contraction. The flexibility of the Tpm molecule is believed to be vital for its functioning, although its role and significance are under discussion. We choose two sites of the Tpm molecule that presumably have high flexibility and stabilized them with the A134L or E218L substitutions. Applying differential scanning calorimetry (DSC), molecular dynamics (MD), co-sedimentation, trypsin digestion, and in vitro motility assay, we characterized the properties of Tpm molecules with these substitutions. The A134L mutation prevented proteolysis of Tpm molecule by trypsin, and both substitutions increased the thermal stability of Tpm and its bending stiffness estimated from MD simulation. None of these mutations affected the primary binding of Tpm to F-actin; still, both of them increased the thermal stability of the actin-Tpm complex and maximal sliding velocity of regulated thin filaments in vitro at a saturating Ca2+ concentration. However, the mutations differently affected the Ca2+ sensitivity of the sliding velocity and pulling force produced by myosin heads. The data suggest that both regions of instability are essential for correct regulation and fine-tuning of Ca2+-dependent interaction of myosin heads with F-actin.

Sign in / Sign up

Export Citation Format

Share Document