RH Logo
Hubs
About
Live
Leaderboard

My Hubs
All
ResearchHub Feeds
My Hubs
All

Trending Users

Author Profile Avatar
kusuma .
Author Profile Avatar
Brian Novak
Author Profile Avatar
xue pan
Author Profile Avatar
ayotune adebayo
Author Profile Avatar
Arye Lipman
Author Profile Avatar
Jordan Nelson
Author Profile Avatar
Luc Moser
Author Profile Avatar
Emeka A. Ezewudo
Author Profile Avatar
Titus Osikhiana Ogahbrai
Author Profile Avatar
Boomer

Trending Papers in Biomolecules

Trending
Today
Trending
Today

Sign in to discover all of the research papers you care about, live as they're published.

15
Published: Jul 2020
Published: Jul 2020
In this work, we deliver a proof of concept for a fast method that introduces pH effects into classical coarse-grained (CG) molecular dynamics simulations. Our approach is based upon the latest version of the popular Martini CG model to which explicit proton mimicking particles are added. We verify our approach against experimental data involving several different molecules and different environmental conditions. In particular, we compute titration curves, pH dependent free energies of transfer, and lipid bilayer membrane affinities as a function of pH. Using oleic acid as an example compound, we further illustrate that our method can be used to study passive translocation in lipid bilayers via protonation. Finally, our model reproduces qualitatively the expansion of the macromolecule dendrimer poly(propylene imine) as well as the associated pKa shift of its different generations. This example demonstrates that our model is able to pick up collective interactions between titratable sites in large molecules comprising many titratable functional groups.
15
From Paper: Constant pH simulations with the coarse-grained MARTINI model — Application to oleic acid aggregates
Published: Sep 2013
From Paper: Constant pH simulations with the coarse-grained MARTINI model — Application to oleic acid aggregates
Published: Sep 2013
Long chain fatty acids are biologically important molecules with complex and pH sensitive aggregation behavior. The carboxylic head group of oleic acid is ionizable, with the pK shifting to larger values, even above a value of 7, in certain aggregate states. While experiments have determined the macroscopic phase behavior, we have yet to understand the molecular level details for this complex behavior. This level of detail is likely required to fully appreciate the role of fatty acids in biology and for nanoscale biotechnological and industrial applications. Here, we introduce the use of constant pH molecular dynamics (MD) simulations with the coarse-grained MARTINI model and apply the method to oleic acid aggregates and a model lipid bilayer. By running simulations at different constant pH values, we determined titration curves and the resulting pK for oleic acid in different environments. The coarse-grained model predicts positive pK shifts, with a shift from 4.8 in water to 6.5 in a small micelle, and 6.6 in a dioleoylphosphatidylcholine (DOPC) bilayer, similar to experimental estimates. The size of the micelles increased as the pH increased, and correlated with the fraction of deprotonated oleic acid. We show this combination of constant pH MD and the coarse-grained MARTINI model can be used to model pH-dependent surfactant phase behavior. This suggests a large number of potential new applications of large-scale MARTINI simulations in other biological systems with ionizable molecules.
12
Published: Jan 2021
Published: Jan 2021
An implementation of the replica exchange with dynamical scaling (REDS) method in the commonly used molecular dynamics program GROMACS is presented. REDS is a replica exchange method that requires fewer replicas than conventional replica exchange while still providing data over a range of temperatures and can be used in either constant volume or constant pressure ensembles. Details for running REDS simulations are given, and an application to the human islet amyloid polypeptide (hIAPP) 11-25 fragment shows that the model efficiently samples conformational space.
24
From Paper: Interaction of Migrating Twin Boundaries with Obstacles in Magnesium
Published: Jan 2021
From Paper: Interaction of Migrating Twin Boundaries with Obstacles in Magnesium
Published: Jan 2021
The asymmetry in the shapes of folded and unfolded states are probed using two parameters, one being a measure of the sphericity and the other that describes the shape. For the folded states, whose interiors are densely packed,the radii of gyration (Rg) and these two parameters are calculated using the coordinates of the experimentally determined structures. Although Rg scales as expected for maximally compact structures, the distributions of the shape parameters show that there is considerable asymmetry in the shapes of folded structures. The degree of asymmetry is greater for proteins that form oligomers. Analysis of the two- and three-body contacts in the native structures shows that the presence of near equal number of contacts between backbone and side-chains and between side-chains gives rise to dense packing.We suggest that proteins with relatively large values of shape parameters can tolerate volume mutations without greatly affecting the network of contacts or their stability. To probe shape characteristics of denatured states we have developed a model of a WW-like domain. The shape parameters, which are calculated using Langevin simulations, change dramatically in the course of coil to globule transition. Comparison of the values of shape parameters between the globular state and the folded state of WW domain shows that both energetic (especially dispersion in the hydrophobic interactions) and steric effects are important in determining packing in proteins.
Slide 1 of 1
  • Paper Preview Page 1
306
From Paper: Nb-based MXenes for efficient electrochemical sensing of small biomolecules in the anodic potential
Published: Aug 2020
From Paper: Nb-based MXenes for efficient electrochemical sensing of small biomolecules in the anodic potential
Published: Aug 2020
The electrochemical performance of Nb2CTx and Nb4C3Tx MXenes in aqueous media was evaluated. • Both Nb2CTx and Nb4C3Tx are electrochemically stable up to an anodic potential of 0.5 V. • It was found that Nb4C3Tx is more electrochemically active than Nb2CTx. • Nb4C3Tx can be used as an immobilization platform for the sensitive detection of dopamine with a detection limit of 23 nM.
613
From Paper: Synergistic integration of metal nanoclusters and biomolecules as hybrid systems for therapeutic applications
Published: Dec 2020
From Paper: Synergistic integration of metal nanoclusters and biomolecules as hybrid systems for therapeutic applications
Published: Dec 2020
Abnormalities in biological systems, such as gene mutations, protein deficiency, pathogen infections (e.g., Coronavirus disease 2019), immunity disorders, and tumoral metastasis have considerably threatened human health and economic development due to intrinsic complexity and variability.
15
Authors: Alexey V. Onufriev, David A. Case
Published: May 2019
Authors: Alexey V. Onufriev, David A. Case
Published: May 2019
It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation and can be very efficient compared to the explicit treatment of the solvent. Here, we review a particular class of so-called fast implicit solvent models, generalized Born (GB) models, which are widely used for molecular dynamics (MD) simulations of proteins and nucleic acids. These approaches model hydration effects and provide solvent-dependent forces with efficiencies comparable to molecular-mechanics calculations on the solute alone; as such, they can be incorporated into MD or other conformational searching strategies in a straightforward manner. The foundations of the GB model are reviewed, followed by examples of newer, emerging models and examples of important applications. We discuss their strengths and weaknesses, both for fidelity to the underlying continuum model and for the ability to replace explicit consideration of solvent molecules in macromolecular simulations.
14
From Paper: Lignin-Graft-Poly(lactic- <i>co</i> -glycolic) Acid Biopolymers for Polymeric Nanoparticle Synthesis
Published: Apr 2020
From Paper: Lignin-Graft-Poly(lactic- <i>co</i> -glycolic) Acid Biopolymers for Polymeric Nanoparticle Synthesis
Published: Apr 2020
A lignin-graft-poly(lactic-co-glycolic) acid (PLGA) biopolymer was synthesized with two types of lignin (LGN), alkaline lignin (ALGN) and sodium lignosulfonate (SLGN), at different (A/S)LGN/PLGA ratios (1:2, 1:4, and 1:6 w/w). 1H NMR and Fourier-transform infrared spectroscopy (FT-IR) confirmed the conjugation of PLGA to LGN. The (A/S)LGN-graft-PLGA biopolymers were used to form nanodelivery systems suitable for entrapment and delivery of drugs for disease treatment. The LGN-graft-PLGA NPs were generally small (100–200 nm), increased in size with the amount of PLGA added, monodisperse, and negatively charged (−48 to −60 mV). Small-angle scattering data showed that particles feature a relatively smooth surface and a compact spherical structure with a distinct core and a shell. The core size and shell thickness varied with the LGN/PLGA ratio, and at a 1:6 ratio, the particles deviated from the core–shell structure to a complex internal structure. The newly developed (A/S)LGN-graft-PLGA NPs are proposed as a potential delivery system for applications in biopharmaceutical, food, and agricultural sectors.
185
From Paper: Integrative/Hybrid Modeling Approaches for Studying Biomolecules
Published: Feb 2020
From Paper: Integrative/Hybrid Modeling Approaches for Studying Biomolecules
Published: Feb 2020
Integrative/hybrid modeling combines input from multiple biophysical experiments. • Computation plays a crucial role in implementation of hybrid methods. • Advancements in cryo-EM and XL-MS have led to growth in hybrid modeling. • New methods such as XFEL hold promise for further development of hybrid methods.
Slide 1 of 1
  • Paper Preview Page 1
105
From Paper: Two-field transverse relaxation-optimized spectroscopy for the study of large biomolecules – An in silico investigation
Published: Dec 2020
From Paper: Two-field transverse relaxation-optimized spectroscopy for the study of large biomolecules – An in silico investigation
Published: Dec 2020
Optimal relaxation properties can be found at vastly different magnetic fields for two nuclear spins in the same spin system. • Two-field transverse relaxation optimized experiments can benefit from excellent relaxation properties for both nuclei within a single experiment. • Numerical simulations of 13C-19F pairs in aromatic side-chains of large proteins show an increase of sensitivity >x10 and better resolution with two-field methods.
Slide 1 of 1
  • Paper Preview Page 1
Load More Papers