Nonlinear Amplification in Electrokinetic Pumping in Nanochannels in the Presence of Hydrophobic Interactions

2013 ◽  
Vol 110 (18) ◽  
Author(s):  
Suman Chakraborty ◽  
Dipankar Chatterjee ◽  
Chirodeep Bakli
Keyword(s):  
Hydrophobic Interactions ◽  
Nonlinear Amplification ◽  
Electrokinetic Pumping

Effect of Consonant-Vowel Ratio Modification on Amplitude Envelope Cues for Consonant Recognition

1991 ◽  
Vol 34 (2) ◽  
pp. 415-426 ◽  
Author(s):  
Richard L. Freyman ◽  
G. Patrick Nerbonne ◽  
Heather A. Cote
Keyword(s):  
White Noise ◽  
Intensity Ratio ◽  
Recognition Performance ◽  
Amplitude Envelope ◽  
Signal To Noise ◽  
Noise Masking ◽  
Spectral Cues ◽  
Consonant Recognition ◽  
Nonlinear Amplification ◽  
Speech Envelope

This investigation examined the degree to which modification of the consonant-vowel (C-V) intensity ratio affected consonant recognition under conditions in which listeners were forced to rely more heavily on waveform envelope cues than on spectral cues. The stimuli were 22 vowel-consonant-vowel utterances, which had been mixed at six different signal-to-noise ratios with white noise that had been modulated by the speech waveform envelope. The resulting waveforms preserved the gross speech envelope shape, but spectral cues were limited by the white-noise masking. In a second stimulus set, the consonant portion of each utterance was amplified by 10 dB. Sixteen subjects with normal hearing listened to the unmodified stimuli, and 16 listened to the amplified-consonant stimuli. Recognition performance was reduced in the amplified-consonant condition for some consonants, presumably because waveform envelope cues had been distorted. However, for other consonants, especially the voiced stops, consonant amplification improved recognition. Patterns of errors were altered for several consonant groups, including some that showed only small changes in recognition scores. The results indicate that when spectral cues are compromised, nonlinear amplification can alter waveform envelope cues for consonant recognition.

Molecular Basis of Iterative C–H Oxidation by TamI, a Multifunctional P450 Monooxygenase from the Tirandamycin Biosynthetic Pathway

2020 ◽  
Author(s):  
Sean A. Newmister ◽  
Kinshuk Raj Srivastava ◽  
Rosa V. Espinoza ◽  
Kersti Caddell Haatveit ◽  
Yogan Khatri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Basis ◽  
Hydrophobic Interactions ◽  
Cytochromes P450 ◽  
Targeted Mutagenesis ◽  
P450 Monooxygenase ◽  
Bond Functionalization ◽  
Dynamics Simulations

Biocatalysis offers an expanding and powerful strategy to construct and diversify complex molecules by C-H bond functionalization. Due to their high selectivity, enzymes have become an essential tool for C-H bond functionalization and offer complementary reactivity to small-molecule catalysts. Hemoproteins, particularly cytochromes P450, have proven effective for selective oxidation of unactivated C-H bonds. Previously, we reported the in vitro characterization of an oxidative tailoring cascade in which TamI, a multifunctional P450 functions co-dependently with the TamL flavoprotein to catalyze regio- and stereoselective hydroxylations and epoxidation to yield tirandamycin A and tirandamycin B. TamI follows a defined order including 1) C10 hydroxylation, 2) C11/C12 epoxidation, and 3) C18 hydroxylation. Here we present a structural, biochemical, and computational investigation of TamI to understand the molecular basis of its substrate binding, diverse reactivity, and specific reaction sequence. The crystal structure of TamI in complex with tirandamycin C together with molecular dynamics simulations and targeted mutagenesis suggest that hydrophobic interactions with the polyene chain of its natural substrate are critical for molecular recognition. QM/MM calculations and molecular dynamics simulations of TamI with variant substrates provided detailed information on the molecular basis of sequential reactivity, and pattern of regio- and stereo-selectivity in catalyzing the three-step oxidative cascade.<br>

Coaction of Electrostatic and Hydrophobic Interactions: Dynamic Constraints on Disordered TrkA Juxtamembrane Domain

2019 ◽  
Author(s):  
Zichen Wang ◽  
Huaxun Fan ◽  
Xiao Hu ◽  
John Khamo ◽  
Jiajie Diao ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Function ◽  
Hydrophobic Interactions ◽  
Transmembrane Helix ◽  
Point Mutations ◽  
Salt Bridge ◽  
Receptor Activation ◽  
Membrane Dynamics ◽  
Juxtamembrane Domain ◽  
Joint Work

<p>The receptor tyrosine kinase family transmits signals into cell via a single transmembrane helix and a flexible juxtamembrane domain (JMD). Membrane dynamics makes it challenging to study the structural mechanism of receptor activation experimentally. In this study, we employ all-atom molecular dynamics with Highly Mobile Membrane-Mimetic to capture membrane interactions with the JMD of tropomyosin receptor kinase A (TrkA). We find that PIP<sub>2 </sub>lipids engage in lasting binding to multiple basic residues and compete with salt bridge within the peptide. We discover three residues insertion into the membrane, and perturb it through computationally designed point mutations. Single-molecule experiments indicate the contribution from hydrophobic insertion is comparable to electrostatic binding, and in-cell experiments show that enhanced TrkA-JMD insertion promotes receptor ubiquitination. Our joint work points to a scenario where basic and hydrophobic residues on disordered domains interact with lipid headgroups and tails, respectively, to restrain flexibility and potentially modulate protein function.</p>

Micellization Behaviour of Cationic Surfactants in the Presence of Food Additives: Conductance and Spectroscopic Investigations

2020 ◽  
Vol 10 ◽  
Author(s):  
Sonika Arti ◽  
Neha Aggarwal
Keyword(s):  
Glutamic Acid ◽  
Cationic Surfactants ◽  
Hydrophobic Interactions ◽  
Food Additives ◽  
Specific Conductance ◽  
Food Additive ◽  
Nmr Studies ◽  
Degree Of Ionization ◽  
Increase With Increase ◽  
Micellization Process

Aim: The micellization behavior of cationic surfactants have been studied in the presence of food additives. Objectives: Micellization behaviour of cationic surfactants, cetyltrimethylammonium bromide (CTAB) and tetradecyltrimethylammonium bromide (TTAB) has been studied in water and in various concentrations of salts (food additives) L-glutamic acid, sodium propionate, sodium citrate tribasic dihydrate and disodium tartrate dihydrate at (298.15, 308.15 and 318.15) K. Methods: Two methods used in the present study are specific conductance measurements and spectroscopy (NMR) studies. Results: From the specific conductance(κ), various parameters such as critical micelle concentration (CMC), degree of ionization of micelle (α), standard Gibbs free energy (ΔGom), enthalpy (ΔHom), and entropy (ΔSom) of micellization have also been calculated. Thermodynamic parameters related to the micellization process were also analyzed through NMR studies. Conclusion: The CMC values are influenced by the presence of food additive. The magnitude of CMC values increase with increase in concentration of food additive. In all the cases, enthalpy of micellization, ∆Hom values are found to be negative whereas entropy of micellization, ∆S om values are positive which indicate that hydrophobic interactions play a major role in the micellization process. Also, NMR studies reveal that tartrate and citrate are more hydrated than glutamic acid and propionate, resulting in more downfield shift.

scholarly journals Acoustic Modeling and Vibration Characteristics of Supersonic Inlet Buzz

Energies ◽  
2020 ◽  
Vol 13 (8) ◽  
pp. 2048
Author(s):  
Jianfeng Zhu ◽  
Wenguo Luo ◽  
Yuqing Wei ◽  
Cheng Yan ◽  
Yancheng You
Keyword(s):  
Numerical Simulations ◽  
Pressure Oscillation ◽  
Resonant Mode ◽  
Acoustic Model ◽  
Oscillation System ◽  
Nonlinear Simulation ◽  
Supersonic Inlet ◽  
Nonlinear Amplification ◽  
Oscillation Damping ◽  
The Ideal

The buzz phenomenon of a typical supersonic inlet is analyzed on the basis of numerical simulations and duct acoustic theory. Considering that the choked inlet could be treated as a duct with one end closed, a one-dimensional (1D) mathematical model based on the duct acoustic theory is proposed to describe the periodic pressure oscillation of the little buzz and the big buzz. The results of the acoustic model agree well with that of the numerical simulations and the experimental data. It could verify that the dominated oscillation patterns of the little buzz and the big buzz are closely related to the first and second resonant mode of the standing wave, respectively. The discrepancies between the numerical simulation and the ideal acoustic model might be attributed to the viscous damping in the fluid oscillation system. In order to explore the damping, a small perturbation jet is introduced to trigger the resonance of the buzz system and the nonlinear amplification effect of resonance might be helpful to estimate the damping. Through the comparison between the linear acoustic model and the nonlinear simulation, the calculated pressure oscillation damping of the little buzz and the big buzz are 0.33 and 0.16, which could be regarded as an estimation of real damping.

scholarly journals Insight into the HIV-1 Vif SOCS-box–ElonginBC interaction

Open Biology ◽  
2013 ◽  
Vol 3 (11) ◽  
pp. 130100 ◽  
Author(s):  
Zhisheng Lu ◽  
Julien R. C. Bergeron ◽  
R. Andrew Atkinson ◽  
Torsten Schaller ◽  
Dennis A. Veselkov ◽  
...  
Keyword(s):  
Solution Structure ◽  
Hydrophobic Interactions ◽  
Dynamic Information ◽  
Ubiquitin Ligase Complex ◽  
Biophysical Studies ◽  
Viral Infectivity Factor ◽  
Β Sheet ◽  
Socs Box ◽  
Insight Into ◽  
Hiv 1

The HIV-1 viral infectivity factor (Vif) neutralizes cell-encoded antiviral APOBEC3 proteins by recruiting a cellular ElonginB (EloB)/ElonginC (EloC)/Cullin5-containing ubiquitin ligase complex, resulting in APOBEC3 ubiquitination and proteolysis. The suppressors-of-cytokine-signalling-like domain (SOCS-box) of HIV-1 Vif is essential for E3 ligase engagement, and contains a BC box as well as an unusual proline-rich motif. Here, we report the NMR solution structure of the Vif SOCS–ElonginBC (EloBC) complex. In contrast to SOCS-boxes described in other proteins, the HIV-1 Vif SOCS-box contains only one α-helical domain followed by a β-sheet fold. The SOCS-box of Vif binds primarily to EloC by hydrophobic interactions. The functionally essential proline-rich motif mediates a direct but weak interaction with residues 101–104 of EloB, inducing a conformational change from an unstructured state to a structured state. The structure of the complex and biophysical studies provide detailed insight into the function of Vif's proline-rich motif and reveal novel dynamic information on the Vif–EloBC interaction.

scholarly journals Activation of the DNA-binding ability of human heat shock transcription factor 1 may involve the transition from an intramolecular to an intermolecular triple-stranded coiled-coil structure.

1994 ◽  
Vol 14 (11) ◽  
pp. 7557-7568 ◽  
Author(s):  
J Zuo ◽  
R Baler ◽  
G Dahl ◽  
R Voellmy
Keyword(s):  
Transcription Factor ◽  
Heat Stress ◽  
Heat Shock ◽  
Dna Binding ◽  
Hydrophobic Interactions ◽  
Coiled Coil ◽  
Heat Shock Transcription Factor ◽  
Single Amino Acid ◽  
Binding Ability ◽  
Heat Shock Element

Heat stress regulation of human heat shock genes is mediated by human heat shock transcription factor hHSF1, which contains three 4-3 hydrophobic repeats (LZ1 to LZ3). In unstressed human cells (37 degrees C), hHSF1 appears to be in an inactive, monomeric state that may be maintained through intramolecular interactions stabilized by transient interaction with hsp70. Heat stress (39 to 42 degrees C) disrupts these interactions, and hHSF1 homotrimerizes and acquires heat shock element DNA-binding ability. hHSF1 expressed in Xenopus oocytes also assumes a monomeric, non-DNA-binding state and is converted to a trimeric, DNA-binding form upon exposure of the oocytes to heat shock (35 to 37 degrees C in this organism). Because endogenous HSF DNA-binding activity is low and anti-hHSF1 antibody does not recognize Xenopus HSF, we employed this system for mapping regions in hHSF1 that are required for the maintenance of the monomeric state. The results of mutagenesis analyses strongly suggest that the inactive hHSF1 monomer is stabilized by hydrophobic interactions involving all three leucine zippers which may form a triple-stranded coiled coil. Trimerization may enable the DNA-binding function of hHSF1 by facilitating cooperative binding of monomeric DNA-binding domains to the heat shock element motif. This view is supported by observations that several different LexA DNA-binding domain-hHSF1 chimeras bind to a LexA-binding site in a heat-regulated fashion, that single amino acid replacements disrupting the integrity of hydrophobic repeats render these chimeras constitutively trimeric and DNA binding, and that LexA itself binds stably to DNA only as a dimer but not as a monomer in our assays.

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