Exploring Free Energy Landscapes for Protein Partitioning into Membrane Domains in All-Atom and Coarse-Grained Simulations.

It is known that membrane environment can impact the structure and function of integral membrane proteins. As such, elucidation of the thermodynamic driving forces governing protein partitioning between membrane domains of varying lipid composition is a fundamental topic in membrane biophysics. Molecular dynamics simulations provide valuable tools for quantitatively characterizing the free energy landscapes governing protein partitioning at the molecular level.

Probing the Origins of the Disorder-to-Order Transition of a Modified Cholesterol in Ternary Lipid Bilayers.

In a recent study, spectroscopic observations of modified cholesterol in both lipid-coated nanoparticles and liposomes provided evidence for a disorder-to-order orientational transition with increasing temperature. Below a critical temperature, in a membrane composed of modified cholesterol, saturated (DPPC) lipid, and anionic (DOPS) lipid, a roughly equal population of head-out and head-in conformations was observed. Surprisingly, as temperature was increased the modified cholesterol presented an abrupt transition to a population of all head-in orientations.

A nanoscale photonic thermal transistor for sub-second heat flow switching.

Control of heat flow is critical for thermal logic devices and thermal management and has been explored theoretically. However, experimental progress on active control of heat flow has been limited. Here, we describe a nanoscale radiative thermal transistor that comprises of a hot source and a cold drain (both are ~250 nm-thick silicon nitride membranes), which are analogous to the source and drain electrodes of a transistor.

Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane.

The accurate calculation of equilibrium constants for protein-protein association is of fundamental importance to quantitative biology and remains an outstanding challenge for computational biophysics. Traditionally, equilibrium constants have been computed from one-dimensional free energy surfaces derived from sampling along a single collective variable. Importantly, recent advances in enhanced sampling methodology have facilitated the characterization of multidimensional free energy landscapes, often exposing multiple thermodynamically important minima missed by more restrictive sampling methods.

The Metal-Insulator Transition in Vanadium Oxide Nanofilms Enables Microkelvin-Resolution Thermometry.

High-resolution thermometry is critical for probing nanoscale energy transport. Here, we demonstrate how high-resolution thermometry can be accomplished using vanadium oxide (VO), which features a sizable temperature-dependence of its resistance at room temperature and an even stronger dependence at its metal-insulator-transition (MIT) temperature. We microfabricate VO nanofilm-based electrical resistance thermometers that undergo a metal-insulator-transition at ∼337 K and systematically quantify their temperature-dependent resistance, noise characteristics, and temperature resolution.

The role of structural heterogeneity in the homodimerization of transmembrane proteins.

The equilibrium association of transmembrane proteins plays a fundamental role in membrane protein function and cellular signaling. While the study of the equilibrium binding of single pass transmembrane proteins has received significant attention in experiment and simulation, the accurate assessment of equilibrium association constants remains a challenge to experiment and simulation. In experiment, there remain wide variations in association constants derived from experimental studies of the most widely studied transmembrane proteins.

Synergistic computational and experimental studies of a phosphoglycosyl transferase membrane/ligand ensemble.

Complex glycans serve essential functions in all living systems. Many of these intricate and byzantine biomolecules are assembled employing biosynthetic pathways wherein the constituent enzymes are membrane-associated. A signature feature of the stepwise assembly processes is the essentiality of unusual linear long-chain polyprenol phosphate-linked substrates of specific isoprene unit geometry, such as undecaprenol phosphate (UndP) in bacteria.

Opto-thermoelectric trapping of fluorescent nanodiamonds on plasmonic nanostructures.

Deterministic optical manipulation of fluorescent nanodiamonds (FNDs) in fluids has emerged as an experimental challenge in multimodal biological imaging. Designing and developing nano-optical trapping strategies to serve this purpose is an important task. In this Letter, we show how chemically prepared gold nanoparticles and silver nanowires can facilitate an opto-thermoelectric force to trap individual entities of FNDs using a long working distance lens, low power-density illumination (532-nm laser, 12 µW/µm).

Molecular typing of dengue virus in Mizoram, Northeast India.

Introduction: Dengue is an emerging vector-borne public health threat and characterization at the molecular level is important for proper management of the disease. The aim of the study is to examine the diversity of the dengue viral serotypes from a hilly mountainous region of Northeast India.

Methodology: Thirty-six blood samples that were positive for dengue virus IgM antibodies identified by the enzyme-linked immunosorbent assay (ELISA) method were collected and quantified for the IL6 gene expression by using reverse transcriptase polymerase chain reaction (RT-PCR).

On Computing Equilibrium Binding Constants for Protein-Protein Association in Membranes.

Protein association in lipid membranes is fundamental to membrane protein function and of great biomedical relevance. All-atom and coarse-grained models have been extensively used to understand the protein-protein interactions in the membrane and to compute equilibrium association constants. However, slow translational and rotational diffusion of protein in membrane presents challenges to the effective sampling of conformations defining the ensembles of free and bound states contributing to the association equilibrium and the free energy of dimerization.

Interfacial hydration determines orientational and functional dimorphism of sterol-derived Raman tags in lipid-coated nanoparticles.

Lipid-coated noble metal nanoparticles (L-NPs) combine the biomimetic surface properties of a self-assembled lipid membrane with the plasmonic properties of a nanoparticle (NP) core. In this work, we investigate derivatives of cholesterol, which can be found in high concentrations in biological membranes, and other terpenoids, as tunable, synthetic platforms to functionalize L-NPs. Side chains of different length and polarity, with a terminal alkyne group as Raman label, are introduced into cholesterol and betulin frameworks.

Addressing the Excessive Aggregation of Membrane Proteins in the MARTINI Model.

The MARTINI model is a widely used coarse-grained force field popular for its capacity to represent a diverse array of complex biomolecules. However, efforts to simulate increasingly realistic models of membranes, involving complex lipid mixtures and multiple proteins, suggest that membrane protein aggregates are overstabilized by the MARTINI v2.2 force field.

Computational screening of antimicrobial peptides for Acinetobacter baumannii.

Acinetobacter baumannii, has been developing resistance to even the last line of drugs. Antimicrobial peptides (AMPs) to which bacteria do not develop resistance easily may be the last hope. A few independent experimental studies have designed and studied the activity of AMPs on A.