Ion partitioning effect on the electrophoresis of a soft particle with hydrophobic core

2018 ◽  
Vol 98 (2) ◽  
Author(s):  
Saurabh K. Maurya ◽  
Partha P. Gopmandal ◽  
S. Bhattacharyya ◽  
H. Ohshima
Keyword(s):  
Soft Particle ◽  
Hydrophobic Core ◽  
Ion Partitioning

A Numerical Study on Hydrodynamics of a Soft Particle with Hydrophobic Core

2018 ◽  
Vol 10 (4) ◽  
Author(s):  
Ujjwal K. Ghoshal ◽  
Somnath Bhattacharyya ◽  
Partha P. Gopmandal
Keyword(s):  
Numerical Study ◽  
Soft Particle ◽  
Hydrophobic Core

scholarly journals Effect of hydrophobic core on the electrophoresis of a diffuse soft particle

2017 ◽  
Vol 473 (2199) ◽  
pp. 20160942 ◽  
Author(s):  
Partha P. Gopmandal ◽  
S. Bhattacharyya ◽  
H. Ohshima
Keyword(s):  
Hydrophobic Surface ◽  
Weak Field ◽  
Gradual Transition ◽  
Soft Particle ◽  
Hydrophobic Core ◽  
Particle Mobility ◽  
The Core ◽  
Segment Distribution ◽  
Low Charge ◽  
The Impact

Electrophoresis of a diffuse soft particle with a charged hydrophobic core is considered under the weak field and low charge density assumptions. The hydrophobic surface of the core is coated with a diffuse polyelectrolyte layer (PEL) in which a gradual transition of the polymer segment distribution from the impenetrable core to the surrounding electrolyte medium is considered. A mathematical model is adopted to analyse the impact of the core hydrophobicity on the diffuse soft particle electrophoresis. The mobility based on the present model for the limiting cases such as bare colloids with hydrophobic core and soft particles with no-slip rigid cores are in good agreement with the existing results. The presence of PEL charges produces the impact of the core hydrophobicity on the soft particle mobility different from the corresponding bare colloid with hydrophobic surface in an electrolyte medium. The impact of the core hydrophobicity is subtle when the hydrodynamic screening length of the PEL is low. Reversal in mobility can be achieved by tuning the core hydrophobicity for an oppositely charged core and PEL.

scholarly journals Mutations in the hydrophobic core and in the protein-RNA interface affect the packing and stability of icosahedral viruses

2003 ◽  
Vol 271 (1) ◽  
pp. 135-145 ◽  
Author(s):  
Sheila M. B. Lima ◽  
David S. Peabody ◽  
Jerson L. Silva ◽  
Andr��a C. De Oliveira
Keyword(s):  
Hydrophobic Core ◽  
Icosahedral Viruses

scholarly journals Molecular Dynamics of Chloroplast Membranes Isolated from Wild-Type Barley and a Brassinosteroid-Deficient Mutant Acclimated to Low and High Temperatures

Biomolecules ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Iwona Sadura ◽  
Dariusz Latowski ◽  
Jana Oklestkova ◽  
Damian Gruszka ◽  
Marek Chyc ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Temperature Stress ◽  
High Temperatures ◽  
Biological Membrane ◽  
Hydrophobic Core ◽  
Wild Type ◽  
Chloroplast Membranes ◽  
Paramagnetic Resonance ◽  
Photosynthetic Membranes

Plants have developed various acclimation strategies in order to counteract the negative effects of abiotic stresses (including temperature stress), and biological membranes are important elements in these strategies. Brassinosteroids (BR) are plant steroid hormones that regulate plant growth and development and modulate their reaction against many environmental stresses including temperature stress, but their role in modifying the properties of the biological membrane is poorly known. In this paper, we characterise the molecular dynamics of chloroplast membranes that had been isolated from wild-type and a BR-deficient barley mutant that had been acclimated to low and high temperatures in order to enrich the knowledge about the role of BR as regulators of the dynamics of the photosynthetic membranes. The molecular dynamics of the membranes was investigated using electron paramagnetic resonance (EPR) spectroscopy in both a hydrophilic and hydrophobic area of the membranes. The content of BR was determined, and other important membrane components that affect their molecular dynamics such as chlorophylls, carotenoids and fatty acids in these membranes were also determined. The chloroplast membranes of the BR-mutant had a higher degree of rigidification than the membranes of the wild type. In the hydrophilic area, the most visible differences were observed in plants that had been grown at 20 °C, whereas in the hydrophobic core, they were visible at both 20 and 5 °C. There were no differences in the molecular dynamics of the studied membranes in the chloroplast membranes that had been isolated from plants that had been grown at 27 °C. The role of BR in regulating the molecular dynamics of the photosynthetic membranes will be discussed against the background of an analysis of the photosynthetic pigments and fatty acid composition in the chloroplasts.

scholarly journals Structural Basis for the C-Terminal Domain of Mycobacterium tuberculosis Ribosome Maturation Factor RimM to Bind Ribosomal Protein S19

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 597
Author(s):  
Haoran Zhang ◽  
Qiuxiang Zhou ◽  
Chenyun Guo ◽  
Liubin Feng ◽  
Huilin Wang ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Ribosomal Protein ◽  
Solution Structure ◽  
Molecular Mechanisms ◽  
Structural Model ◽  
Ribosomal Subunit ◽  
Structural Basis ◽  
Hydrophobic Core ◽  
Terminal Domain ◽  
Ribosomal Protein S19

Multidrug-resistant tuberculosis (TB) is a serious threat to public health, calling for the development of new anti-TB drugs. Chaperon protein RimM, involved in the assembly of ribosomal protein S19 into 30S ribosomal subunit during ribosome maturation, is a potential drug target for TB treatment. The C-terminal domain (CTD) of RimM is primarily responsible for binding S19. However, both the CTD structure of RimM from Mycobacterium tuberculosis (MtbRimMCTD) and the molecular mechanisms underlying MtbRimMCTD binding S19 remain elusive. Here, we report the solution structure, dynamics features of MtbRimMCTD, and its interaction with S19. MtbRimMCTD has a rigid hydrophobic core comprised of a relatively conservative six-strand β-barrel, tailed with a short α-helix and interspersed with flexible loops. Using several biophysical techniques including surface plasmon resonance (SPR) affinity assays, nuclear magnetic resonance (NMR) assays, and molecular docking, we established a structural model of the MtbRimMCTD–S19 complex and indicated that the β4-β5 loop and two nonconserved key residues (D105 and H129) significantly contributed to the unique pattern of MtbRimMCTD binding S19, which might be implicated in a form of orthogonality for species-dependent RimM–S19 interaction. Our study provides the structural basis for MtbRimMCTD binding S19 and is beneficial to the further exploration of MtbRimM as a potential target for the development of new anti-TB drugs.

Sound damping in soft particle packings: the interplay between configurational disorder and inelasticity

Soft Matter ◽  
2021 ◽  
Vol 17 (15) ◽  
pp. 4204-4212
Author(s):  
Kuniyasu Saitoh ◽  
Hideyuki Mizuno
Keyword(s):  
Soft Particle ◽  
Two Dimensional ◽  
Particle Packings

We numerically investigate sound damping in disordered two-dimensional soft particle packings. Our findings suggest that sound damping in soft particle packings is determined by the interplay between elastic heterogeneities and inelasticity.

scholarly journals Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing

Crystals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 273
Author(s):  
Yoshita Srivastava ◽  
Rachel Bonn-Breach ◽  
Sai Shashank Chavali ◽  
Geoffrey M. Lippa ◽  
Jermaine L. Jenkins ◽  
...  
Keyword(s):  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Molecular Replacement ◽  
Hydrophobic Core ◽  
Anomalous Diffraction ◽  
Recognition Motif ◽  
Determination Process ◽  
Experimental Phasing ◽  
Crystal Contacts ◽  
Apical Loop

RNA plays a central role in all organisms and can fold into complex structures to orchestrate function. Visualization of such structures often requires crystallization, which can be a bottleneck in the structure-determination process. To promote crystallization, an RNA-recognition motif (RRM) of the U1A spliceosomal protein has been co-opted as a crystallization module. Specifically, the U1-snRNA hairpin II (hpII) single-stranded loop recognized by U1A can be transplanted into an RNA target to promote crystal contacts and to attain phase information via molecular replacement or anomalous diffraction methods using selenomethionine. Herein, we produced the F37M/F77M mutant of U1A to augment the phasing capability of this powerful crystallization module. Selenomethionine-substituted U1A(F37M/F77M) retains high affinity for hpII (KD of 59.7 ± 11.4 nM). The 2.20 Å resolution crystal structure reveals that the mutated sidechains make new S-π interactions in the hydrophobic core and are useful for single-wavelength anomalous diffraction. Crystals were also attained of U1A(F37M/F77M) in complex with a bacterial preQ1-II riboswitch. The F34M/F37M/F77M mutant was introduced similarly into a lab-evolved U1A variant (TBP6.9) that recognizes the internal bulged loop of HIV-1 TAR RNA. We envision that this short RNA sequence can be placed into non-essential duplex regions to promote crystallization and phasing of target RNAs. We show that selenomethionine-substituted TBP6.9(F34M/F37M/F77M) binds a TAR variant wherein the apical loop was replaced with a GNRA tetraloop (KD of 69.8 ± 2.9 nM), laying the groundwork for use of TBP6.9(F34M/F37M/F77M) as a crystallization module. These new tools are available to the research community.

Sign in / Sign up

Export Citation Format

Share Document