scholarly journals Molecular Model for Wall Slip:  Role of Convective Constraint Release

2001 ◽  
Vol 34 (10) ◽  
pp. 3412-3420 ◽  
Author(s):  
Yogesh M. Joshi ◽  
Ashish K. Lele ◽  
R. A. Mashelkar
Keyword(s):  
Molecular Model ◽  
Wall Slip ◽  
Constraint Release ◽  
Convective Constraint Release

scholarly journals Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER

2021 ◽  
Vol 7 (21) ◽  
pp. eabg0942
Author(s):  
Jae Ho Lee ◽  
Ahmad Jomaa ◽  
SangYoon Chung ◽  
Yu-Hsien Hwang Fu ◽  
Ruilin Qian ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Translocation ◽  
Molecular Model ◽  
Genetic Diseases ◽  
Signal Recognition Particle ◽  
Biological Regulation ◽  
Single Molecule Studies ◽  
Guanosine Triphosphatase ◽  
Gtpase Cycle

The conserved signal recognition particle (SRP) cotranslationally delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum (ER). The molecular mechanism by which eukaryotic SRP transitions from cargo recognition in the cytosol to protein translocation at the ER is not understood. Here, structural, biochemical, and single-molecule studies show that this transition requires multiple sequential conformational rearrangements in the targeting complex initiated by guanosine triphosphatase (GTPase)–driven compaction of the SRP receptor (SR). Disruption of these rearrangements, particularly in mutant SRP54G226E linked to severe congenital neutropenia, uncouples the SRP/SR GTPase cycle from protein translocation. Structures of targeting intermediates reveal the molecular basis of early SRP-SR recognition and emphasize the role of eukaryote-specific elements in regulating targeting. Our results provide a molecular model for the structural and functional transitions of SRP throughout the targeting cycle and show that these transitions provide important points for biological regulation that can be perturbed in genetic diseases.

What Evolutionary Evidence Implies About the Identity of the Mechanoelectrical Couplers in Vascular Smooth Muscle Cells

Physiology ◽  
2021 ◽  
Vol 36 (5) ◽  
pp. 292-306
Author(s):  
Heather A. Drummond
Keyword(s):  
Transient Receptor Potential ◽  
Molecular Model ◽  
Receptor Potential ◽  
Transient Receptor Potential Channels ◽  
Potential Channels ◽  
Transient Receptor ◽  
Paradigm Shifting ◽  
G Protein Coupled ◽  
Evolutionary Role

Loss of pressure-induced vasoconstriction increases susceptibility to renal and cerebral vascular injury. Favored paradigms underlying initiation of the response include transient receptor potential channels coupled to G protein-coupled receptors or integrins as transducers. Degenerin channels may also mediate the response. This review addresses the 1) evolutionary role of these molecules in mechanosensing, 2) limitations to identifying mechanosensitive molecules, and 3) paradigm shifting molecular model for a VSMC mechanosensor.

Microscopic theory of convective constraint release

2001 ◽  
Vol 45 (2) ◽  
pp. 539-563 ◽  
Author(s):  
S. T. Milner ◽  
T. C. B. McLeish ◽  
A. E. Likhtman
Keyword(s):  
Microscopic Theory ◽  
Constraint Release ◽  
Convective Constraint Release

scholarly journals The role of amino acid α38 in the control of oxygen binding to human adult and embryonic haemoglobin Portland

1999 ◽  
Vol 343 (3) ◽  
pp. 681-685 ◽  
Author(s):  
Tao ZHENG ◽  
Thomas BRITTAIN ◽  
Nicholas J. WATMOUGH ◽  
Roy E. WEBER
Keyword(s):  
Amino Acid ◽  
Ligand Binding ◽  
Significant Contribution ◽  
Molecular Model ◽  
Site Directed Mutagenesis ◽  
Oxygen Binding ◽  
Naturally Occurring ◽  
Two State Model ◽  
T State

The role of the amino acid at position α38 in haemoglobin has been probed using site-directed mutagenesis. When the Thr residue at position α38 (which is totally conserved in all mammals) is changed to a Gln, the equilibrium properties of the protein are significantly altered. Equilibrium and kinetic data show that the R-state properties of the protein are essentially unaffected by the mutation whilst the allosteric equilibrium and T-state properties are changed. Mutation of the naturally occurring Gln38 of the human embryonic haemoglobin ζ-chain (the only known non-Thr containing globin) to a Thr residue shows the converse change in properties produced by the adult mutation, although in this case the situation is complicated by significant chain heterogeneity in the T state. An extension of the two-state model of co-operativity is presented to describe quantitatively the equilibrium ligand binding in the presence of T-state chain heterogeneity. A molecular model is described in which the putative interaction of αGln38 and βTyr145 is identified which make a significant contribution to the previously reported unusual ligand-binding properties of the ζ-chain containing human embryonic haemoglobins.

scholarly journals Contraction of Entangled Polymers After Large Step Shear Deformations in Slip-Link Simulations

Polymers ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 370 ◽  
Author(s):  
Yuichi Masubuchi
Keyword(s):  
Dynamics Simulation ◽  
Uniaxial Deformation ◽  
Single Chain ◽  
Orientational Relaxation ◽  
Entangled Polymers ◽  
Constraint Release ◽  
Large Step ◽  
Entangled Polymer ◽  
Convective Constraint Release ◽  
Chain Contraction

Although the tube framework has achieved remarkable success to describe entangled polymer dynamics, the chain motion assumed in tube theories is still a matter of discussion. Recently, Xu et al. [ACS Macro Lett. 2018, 7, 190–195] performed a molecular dynamics simulation for entangled bead-spring chains under a step uniaxial deformation and reported that the relaxation of gyration radii cannot be reproduced by the elaborated single-chain tube model called GLaMM. On the basis of this result, they criticized the tube framework, in which it is assumed that the chain contraction occurs after the deformation before the orientational relaxation. In the present study, as a test of their argument, two different slip-link simulations developed by Doi and Takimoto and by Masubuchi et al. were performed and compared to the results of Xu et al. In spite of the modeling being based on the tube framework, the slip-link simulations excellently reproduced the bead-spring simulation result. Besides, the chain contraction was observed in the simulations as with the tube picture. The obtained results imply that the bead-spring results are within the scope of the tube framework whereas the failure of the GLaMM model is possibly due to the homogeneous assumption along the chain for the fluctuations induced by convective constraint release.

scholarly journals A molecular model for the role of SYCP3 in meiotic chromosome organisation

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Johanna Liinamaria Syrjänen ◽  
Luca Pellegrini ◽  
Owen Richard Davies
Keyword(s):  
Molecular Model ◽  
Meiotic Chromosome ◽  
Lateral Element ◽  
Homologous Chromosomes ◽  
Meiotic Chromosomes ◽  
Double Stranded Dna ◽  
Evolutionarily Conserved ◽  
20 Nm ◽  
Chromosome Organisation

The synaptonemal complex (SC) is an evolutionarily-conserved protein assembly that holds together homologous chromosomes during prophase of the first meiotic division. Whilst essential for meiosis and fertility, the molecular structure of the SC has proved resistant to elucidation. The SC protein SYCP3 has a crucial but poorly understood role in establishing the architecture of the meiotic chromosome. Here we show that human SYCP3 forms a highly-elongated helical tetramer of 20 nm length. N-terminal sequences extending from each end of the rod-like structure bind double-stranded DNA, enabling SYCP3 to link distant sites along the sister chromatid. We further find that SYCP3 self-assembles into regular filamentous structures that resemble the known morphology of the SC lateral element. Together, our data form the basis for a model in which SYCP3 binding and assembly on meiotic chromosomes leads to their organisation into compact structures compatible with recombination and crossover formation.

3D Simulations and Experimental Validation Using the Molecular Strain Function Model With Convective Constraint Release

2008 ◽  
Author(s):  
P. Olley ◽  
T. Gough ◽  
P. D. Coates
Keyword(s):  
Constitutive Model ◽  
Release Mechanism ◽  
Finite Width ◽  
Function Model ◽  
Cross Sectional ◽  
Constraint Release ◽  
Contraction Ratio ◽  
Vortex Size ◽  
Convective Constraint Release ◽  
Strain Function

The Molecular Strain Function model with Convective Constraint Release has been demonstrated by Wagner to fit elongational and shear viscosities, and First and Second Normal stress differences for a variety of polymer melts, when used with a Convective Constraint Release mechanism [J. Rheol. 45 (2001), 1387]. A modification to the CCR mechanism was shown to give more accurate representation of corner vortices in an abrupt contraction flow [JNNFM 135 (2006), 68] for both planar and axisymmetric contraction flows. It is highly desirable to assess the model against 3D flows. A primary advantage of 3D simulation in assessing a constitutive model is that, experimentally, it is very difficult to produce truly 2D data; the side walls of a finite die affect stress birefringence measurements (since this is a ‘line of sight’ cumulative measurement), and also induce significant 3D motion into the flow. The existing 2-dimensional code has been extended to fully 3-dimensional flows using 27-node ‘brick’ elements, and using a number of developments to deal with tracking and storage problems inherent in 3D time-integral solution. The 3D code is assessed against known 2-dimensional solutions to verify its accuracy; the constitutive model is then assessed against experimental data for a 4:1 contraction ratio die, which has finite width (5:3 depth to inlet height), inducing 3D effects. Stress birefringence, vortex size, and cross-sectional flow rate data at a number of flow rates are compared. The model is shown to give good accuracy against this flow.

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