Comparison of Accuracy and Efficiency of Milestoning Variants: Introducing Buffer Milestoning.

The Milestoning algorithm is a method for long-time molecular dynamics simulations. It enables the sampling of rare events. The precise calculations of observables depend on accurately determining the first hitting point distribution (FHPD) for each milestone.

Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations.

Biological processes require DNA and RNA helices to pack together in specific interhelical orientations. While electrostatic repulsion between backbone charges is expected to be maximized when helices are in parallel alignment, such orientations are commonplace in nature. To better understand how the repulsion is overcome, we used experimental and computational approaches to investigate how the orientational preferences of DNA helices depend on the concentration and valence of mobile cations.

Approximating First Hitting Point Distribution in Milestoning for Rare Event Kinetics.

Milestoning is an efficient method for rare event kinetics calculation using short trajectory parallelization. Mean first passage time (MFPT) is the key kinetic output of Milestoning, whose accuracy crucially depends on the initial distribution of the short trajectory ensemble. The true initial distribution, i.

Defect Formation and Peptide Permeation across Phospholipid Membranes.

Cell penetrating peptides (CPPs) are natural agents that efficiently permeate biological membranes. They are frequently positively charged, which is surprising since membranes pose hydrophobic barriers. In this Perspective, I discuss computations and experiments of a permeation model that couples permeant displacement with a membrane defect.

A combination of a cell penetrating peptide and a protein translation inhibitor kills metastatic breast cancer cells.

Cell Penetrating Peptides (CPPs) are promising anticancer and antimicrobial drugs. We recently reported that a peptide derived from the human mitochondrial/ER membrane-anchored NEET protein, Nutrient Autophagy Factor 1 (NAF-1; NAF-1), selectively permeates and kills human metastatic epithelial breast cancer cells (MDA-MB-231), but not control epithelial cells. As cancer cells alter their phenotype during growth and metastasis, we tested whether NAF-1 would also be efficient in killing other human epithelial breast cancer cells that may have a different phenotype.

Visualization of Molecular Permeation into a Multi-compartment Phospholipid Vesicle.

Passive permeation of small molecules into vesicles with multiple compartments is a critical event in many chemical and biological processes. We consider the translocation of the peptide NAF-1 labeled with a fluorescent fluorescein dye across membranes of rhodamine-labeled 1,2-dioleoyl--glycero-3-phosphocholine (DOPC) into liposomes with internal vesicles. Time-resolved microscopy revealed a sequential absorbance of the peptide in both the outer and inner micrometer vesicles that developed over a time period of minutes to hours, illustrating the spatial and temporal progress of the permeation.

The Structures of Heterogeneous Membranes and Their Interactions with an Anticancer Peptide: A Molecular Dynamics Study.

We conduct molecular dynamics simulations of model heterogeneous membranes and their interactions with a 24-amino acid peptide-NAF-1. NAF-1 is an anticancer peptide that selectively permeates and kills malignant cells; it does not permeate normal cells. We examine three membranes with different binary mixtures of lipids, DOPC-DOPA, DOPC-DOPS, and DOPC-DOPE, with a single peptide embedded in each as models for the diversity of biological membranes.

ScMiles2: A Script to Conduct and Analyze Milestoning Trajectories for Long Time Dynamics.

Milestoning is a theory and an algorithm that computes kinetics and thermodynamics at long time scales. It is based on partitioning the (phase) space into cells and running a large number of short trajectories between the boundaries of the cells. The termination points of the trajectories are analyzed with the Milestoning theory to obtain kinetic and thermodynamic information.

Milestoning simulation of ligand dissociation from the glycogen synthase kinase 3β.

As drug-binding kinetics has become an important factor to be considered in modern drug discovery, this work evaluated the ability of the Milestoning method in computing the absolute dissociation rate of a ligand from the serine-threonine kinase, glycogen synthase kinase 3β, which is a target for designing drugs to treat diseases such as neurodegenerative disorders and diabetes. We found that the Milestoning method gave good agreement with experiment with modest computational costs. Although the time scale for dissociation lasted tens of seconds, the collective molecular dynamics simulations total less than 1μs.

Design of Peptides for Membrane Insertion: The Critical Role of Charge Separation.

A physical understanding of membrane permeation and translocation by small, positively charged molecules can illuminate cell penetrating peptide mechanisms of entry and inform drug design. We have previously investigated the permeation of the doubly charged peptide WKW and proposed a defect-assisted permeation mechanism where a small molecule with +2 charge can achieve a metastable state spanning the bilayer by forming a membrane defect with charges stabilized by phospholipid phosphate groups. Here, we investigate the membrane permeation of two doubly charged peptides, WWK and WWWK, with charges separated by different lengths.

A peptide-derived strategy for specifically targeting the mitochondria and ER of cancer cells: a new approach in fighting cancer.

An effective anti-cancer therapy should exclusively target cancer cells and trigger in them a broad spectrum of cell death pathways that will prevent avoidance. Here, we present a new approach in cancer therapy that specifically targets the mitochondria and ER of cancer cells. We developed a peptide derived from the flexible and transmembrane domains of the human protein NAF-1/CISD2.

Peptide Permeation across a Phosphocholine Membrane: An Atomically Detailed Mechanism Determined through Simulations and Supported by Experimentation.

Cell-penetrating peptides (CPPs) facilitate translocation across biological membranes and are of significant biological and medical interest. Several CPPs can permeate into specific cells and organelles. We examine the incorporation and translocation of a novel anticancer CPP in a dioleoylphosphatidylcholine (DOPC) lipid bilayer membrane.

Impact of the Protonation State of Phosphatidylinositol 4,5-Bisphosphate (PIP2) on the Binding Kinetics and Thermodynamics to Transient Receptor Potential Vanilloid (TRPV5): A Milestoning Study.

The binding of phosphatidylinositol 4,5-bisphosphate (PIP2) to the ion channel transient receptor potential vanilloid 5 (TRPV5) is critical for its function. We use atomically detailed simulations and the milestoning theory to compute the free energy profile and the kinetics of PIP2 binding to TRPV5. We estimate the rate of binding and the impact of the protonation state on the process.

Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning.

Gleevec (a.k.a.

Catalytic Magnesium as a Door Stop for DNA Sliding.

The protein HIV Reverse Transcriptase (HIV RT) synthesizes a DNA strand according to a template. During the synthesis, the polymerase slides on the double stranded DNA to allow the entry of a new nucleotide to the active site. We use Molecular Dynamics simulations to estimate the free energy profile and the time scale of the DNA-protein's relative displacement in the complex's closed state.

Interfacial Dynamics in Lipid Membranes: The Effects of Headgroup Structures.

Phospholipid membranes support essential biochemical processes, yet remain difficult to characterize due to their compositional and structural heterogeneity. The two most common phospholipid headgroup structures in biological membranes are phosphatidylcholine (PC) and phosphatidylethanolamine (PE), but interactions between PC and PE lipids remain underexplored. In this study, we apply ultrafast two-dimensional infrared (2D IR) spectroscopy to quantify the headgroup effects on interfacial dynamics in PC/PE lipid mixtures.

Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2.

Severe acute respiratory syndrome (SARS) and novel coronavirus disease (COVID-19) are caused by two closely related beta-coronaviruses, SARS-CoV and SARS-CoV-2, respectively. The envelopes surrounding these viruses are decorated with spike proteins, whose receptor binding domains (RBDs) initiate invasion by binding to the human angiotensin-converting enzyme 2 (ACE2). Subtle changes at the interface with ACE2 seem to be responsible for the enhanced affinity for the receptor of the SARS-CoV-2 RBD compared to SARS-CoV RBD.

Computer simulations of a heterogeneous membrane with enhanced sampling techniques.

Computational determination of the equilibrium state of heterogeneous phospholipid membranes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in membranes are long compared to typical time scales of computer simulations.

Value of Temporal Information When Analyzing Reaction Coordinates.

Reaction coordinates chart pathways from reactants to products of chemical reactions. Determination of reaction coordinates from ensembles of molecular trajectories has thus been the focus of many studies. A widely used and insightful choice of a reaction coordinate is the committor function, defined as the probability that a trajectory will reach the product before the reactant.

Dramatic Shape Changes Occur as Cytochrome Folds.

Extensive experimental studies on the folding of cytochrome (Cyt ) make this small protein an ideal target for atomic detailed simulations for the purposes of quantitatively characterizing the structural transitions and the associated time scales for folding to the native state from an ensemble of unfolded states. We use previously generated atomically detailed folding trajectories by the stochastic difference equation in length to calculate the time-dependent changes in the small-angle X-ray scattering (SAXS) profiles. Excellent agreement is obtained between experiments and simulations for the time-dependent SAXS spectra, allowing us to identify the structures of the folding intermediates, which shows that Cyt reaches the native state by a sequential folding mechanism.

Milestoning with wind: Exploring the impact of a biasing potential in exact calculation of kinetics.

We consider the algorithm wind-assisted reweighted Milestoning of Grazioli and Andricioaei [J. Chem. Phys 149(8), 084103 (2018)], expand it, and assess its performance.

Phase Transition in a Heterogeneous Membrane: Atomically Detailed Picture.

Membranes serve diverse functions in biological systems. Variations in their molecular compositions impact their physical properties and lead to rich phase behavior such as switching from the gel to fluid phase and/or separation to micro- and macrodomains with different molecular compositions. We present a combined computational and experimental study of the phase behavior of a mixed membrane of 1,2-dipalmitoyl--glycero-3-phosphocholine (DPPC) and 1,2-dilauroyl--glycero-3-phosphocholine (DLPC) molecules.

Simple and Analytical Model of RNA Collapse.

An analytical model for the free energy change during collapse of an RNA molecule from an extended to a compact conformation is proposed. It considers explicit binding of water and ion molecules to the RNA and the exchange of these molecules with the aqueous solution. Microscopic states of the system are captured on a two-dimensional square lattice and evaluated using contact energies.

Milestoning: An Efficient Approach for Atomically Detailed Simulations of Kinetics in Biophysics.

Recent advances in theory and algorithms for atomically detailed simulations open the way to the study of the kinetics of a wide range of molecular processes in biophysics. The theories propose a shift from the traditionally very long molecular dynamic trajectories, which are exact but may not be efficient in the study of kinetics, to the use of a large number of short trajectories. The short trajectories exploit a mapping to a mesh in coarse space and allow for efficient calculations of kinetics and thermodynamics.