The structural influence of the oncogenic driver mutation N642H in the STAT5B SH2 domain.

The point mutation N642H of the signal transducer and activator of transcription 5B (STAT5B) protein is associated with aggressive and drug-resistant forms of leukemia. This mutation is thought to promote cancer due to hyperactivation of STAT5B caused by increased stability of the active, parallel dimer state. However, the molecular mechanism leading to this stabilization is not well understood as there is currently no structure of the parallel dimer.

The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops Is Determined by Ligand Binding and Interprotomer Allostery.

The main protease (M) of SARS-CoV-2 is essential for viral replication and is, therefore, an important drug target. Here, we investigate two flexible loops in M that play a role in catalysis. Using all-atom molecular dynamics simulations, we analyze the structural ensemble of M in an apo state and substrate-bound state.

Functional protein dynamics in a crystal.

Proteins are molecular machines and to understand how they work, we need to understand how they move. New pump-probe time-resolved X-ray diffraction methods open up ways to initiate and observe protein motions with atomistic detail in crystals on biologically relevant timescales. However, practical limitations of these experiments demands parallel development of effective molecular dynamics approaches to accelerate progress and extract meaning.

Introduction to the themed collection on .

Megan O'Mara, Sarah Rauscher and Stacey Wetmore introduce the themed collection on .

Fluorescent protein lifetimes report densities and phases of nuclear condensates during embryonic stem-cell differentiation.

Fluorescent proteins (FP) are frequently used for studying proteins inside cells. In advanced fluorescence microscopy, FPs can report on additional intracellular variables. One variable is the local density near FPs, which can be useful in studying densities within cellular bio-condensates.

Functional Protein Dynamics in a Crystal.

Proteins are molecular machines and to understand how they work, we need to understand how they move. New pump-probe time-resolved X-ray diffraction methods open up ways to initiate and observe protein motions with atomistic detail in crystals on biologically relevant timescales. However, practical limitations of these experiments demands parallel development of effective molecular dynamics approaches to accelerate progress and extract meaning.

Unfermented β-fructan Fibers Fuel Inflammation in Select Inflammatory Bowel Disease Patients.

Background & Aims: Inflammatory bowel diseases (IBD) are affected by dietary factors, including nondigestible carbohydrates (fibers), which are fermented by colonic microbes. Fibers are overall beneficial, but not all fibers are alike, and some patients with IBD report intolerance to fiber consumption. Given reproducible evidence of reduced fiber-fermenting microbes in patients with IBD, we hypothesized that fibers remain intact in select patients with reduced fiber-fermenting microbes and can then bind host cell receptors, subsequently promoting gut inflammation.

LAWS: Local alignment for water sites-Tracking ordered water in simulations.

Accurate modeling of protein-water interactions in molecular dynamics (MD) simulations is important for understanding the molecular basis of protein function. Data from x-ray crystallography can be useful in assessing the accuracy of MD simulations, in particular, the locations of crystallographic water sites (CWS) coordinated by the protein. Such a comparison requires special methodological considerations that take into account the dynamic nature of proteins.

Point (S-to-G) Mutations in the W(S/G)GE Motif in Red/Green Cyanobacteriochrome GAF Domains Enhance Thermal Reversion Rates.

Cyanobacteriochromes (CBCRs) are photoreceptors consisting of single or tandem GAF (cGMP-phosphodiesterase/adenylate cyclase/FhlA) domains that bind bilin chromophores. Canonical red/green CBCR GAF domains are a well-characterized subgroup of the expanded red/green CBCR GAF domain family that binds phycocyanobilin (PCB) and converts between a thermally stable red-absorbing Pr state and a green-absorbing Pg state. The rate of thermal reversion from Pg to Pr varies widely among canonical red/green CBCR GAF domains, with half-lives ranging from days to seconds.

Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins.

Intrinsically disordered proteins are proteins whose native functional states represent ensembles of highly diverse conformations. Such ensembles are a challenge for quantitative structure comparisons because their conformational diversity precludes optimal superimposition of the atomic coordinates necessary for deriving common similarity measures such as the root mean-square deviation of these coordinates. Here, we introduce superimposition-free metrics that are based on computing matrices of the Cα-Cα distance distributions within ensembles and comparing these matrices between ensembles.

Atomistic Simulation Tools to Study Protein Self-Aggregation.

Aberrant aggregation of proteins into poorly soluble, toxic structures that accumulate intracellularly or extracellularly leads to a range of disease states including Alzheimer's, Parkinson's, Huntington's, prion diseases, and type II diabetes. Many of the disease-associated amyloidogenic proteins are intrinsically disordered, which makes their experimental investigation challenging due to a limited number of experimental observables to effectively characterize their ensemble of conformations. Molecular dynamics simulations provide dynamic information with atomistic detail, and are increasingly employed to study aggregation processes, offering valuable structural and mechanistic insights.

Structural and functional consequences of the STAT5B driver mutation.

Hyper-activated STAT5B variants are high value oncology targets for pharmacologic intervention. STAT5B, a frequently-occurring oncogenic driver mutation, promotes aggressive T-cell leukemia/lymphoma in patient carriers, although the molecular origins remain unclear. Herein, we emphasize the aggressive nature of STAT5B in driving T-cell neoplasia upon hematopoietic expression in transgenic mice, revealing evidence of multiple T-cell subset organ infiltration.

A Novel Polar Core and Weakly Fixed C-Tail in Squid Arrestin Provide New Insight into Interaction with Rhodopsin.

Photoreceptors of the squid Loligo pealei contain a G-protein-coupled receptor (GPCR) signaling system that activates phospholipase C in response to light. Analogous to the mammalian visual system, signaling of the photoactivated GPCR rhodopsin is terminated by binding of squid arrestin (sArr). sArr forms a light-dependent, high-affinity complex with squid rhodopsin, which does not require prior receptor phosphorylation for interaction.

The liquid structure of elastin.

The protein elastin imparts extensibility, elastic recoil, and resilience to tissues including arterial walls, skin, lung alveoli, and the uterus. Elastin and elastin-like peptides are hydrophobic, disordered, and undergo liquid-liquid phase separation upon self-assembly. Despite extensive study, the structure of elastin remains controversial.

CHARMM36m: an improved force field for folded and intrinsically disordered proteins.

The all-atom additive CHARMM36 protein force field is widely used in molecular modeling and simulations. We present its refinement, CHARMM36m (http://mackerell.umaryland.

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment.

Intrinsically disordered proteins (IDPs) are notoriously challenging to study both experimentally and computationally. The structure of IDPs cannot be described by a single conformation but must instead be described as an ensemble of interconverting conformations. Atomistic simulations are increasingly used to obtain such IDP conformational ensembles.

The conformational ensemble of the β-casein phosphopeptide reveals two independent intrinsically disordered segments.

The β-casein phosphopeptide 1-25 (βCPP) is involved in calcium binding, cellular transduction, and dental remineralization. Though the net charge of 13e suggests an intrinsically disordered peptide, it has been shown to possibly maintain partial structure. To investigate the nature and extent of its conformational disorder, 100 independent molecular dynamics simulations (cumulative time of 30 μs) were conducted in explicit water with 0.

Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal.

All molecular dynamics simulations are susceptible to sampling errors, which degrade the accuracy and precision of observed values. The statistical convergence of simulations containing atomistic lipid bilayers is limited by the slow relaxation of the lipid phase, which can exceed hundreds of nanoseconds. These long conformational autocorrelation times are exacerbated in the presence of charged solutes, which can induce significant distortions of the bilayer structure.

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides.

We present an extension of the coarse-grained MARTINI model for proteins and apply this extension to amyloid- and elastin-like peptides. Atomistic simulations of tetrapeptides, octapeptides, and longer peptides in solution are used as a reference to parametrize a set of pseudodihedral potentials that describe the internal flexibility of MARTINI peptides. We assess the performance of the resulting model in reproducing various structural properties computed from atomistic trajectories of peptides in water.

Structural disorder and protein elasticity.

An emerging class of disordered proteins underlies the elasticity of many biological tissues. Elastomeric proteins are essential to the function of biological machinery as diverse as the human arterial wall, the capture spiral of spider webs and the jumping mechanism of fleas. In this chapter, we review what is known about the molecular basis and the functional role of structural disorder in protein elasticity.

Binding of inositol stereoisomers to model amyloidogenic peptides.

The self-aggregation of proteins into amyloid fibrils is a pathological hallmark of numerous incurable diseases such as Alzheimer's disease. scyllo-Inositol is a stereochemistry-dependent in vitro inhibitor of amyloid formation. As the first step to elucidate its mechanism of action, we present molecular dynamics simulations of scyllo-inositol and its inactive stereoisomer, chiro-inositol, with simple peptide models, alanine dipeptide (ADP) and (Gly-Ala)(4).

Molecular mechanism of β-sheet self-organization at water-hydrophobic interfaces.

The capacity to form β-sheet structure and to self-organize into amyloid aggregates is a property shared by many proteins. Severe neurodegenerative pathologies such as Alzheimer's disease are thought to involve the interaction of amyloidogenic protein oligomers with neuronal membranes. To understand the experimentally observed catalysis of amyloid formation by lipid membranes and other water-hydrophobic interfaces, we examine the physico-chemical basis of peptide adsorption and aggregation in a model membrane using atomistic molecular simulations.

Molecular simulations of protein disorder.

Protein disorder is abundant in proteomes throughout all kingdoms of life and serves many biologically important roles. Disordered states of proteins are challenging to study experimentally due to their structural heterogeneity and tendency to aggregate. Computer simulations, which are not impeded by these properties, have recently emerged as a useful tool to characterize the conformational ensembles of intrinsically disordered proteins.

Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling.

Generalized-ensemble algorithms in temperature space have become popular tools to enhance conformational sampling in biomolecular simulations. A random walk in temperature leads to a corresponding random walk in potential energy, which can be used to cross over energetic barriers and overcome the problem of quasi-nonergodicity. In this paper, we introduce two novel methods: simulated tempering distributed replica sampling (STDR) and virtual replica exchange (VREX).

Proline and glycine control protein self-organization into elastomeric or amyloid fibrils.

Elastin provides extensible tissues, including arteries and skin, with the propensity for elastic recoil, whereas amyloid fibrils are associated with tissue-degenerative diseases, such as Alzheimer's. Although both elastin-like and amyloid-like materials result from the self-organization of proteins into fibrils, the molecular basis of their differing physical properties is poorly understood. Using molecular simulations of monomeric and aggregated states, we demonstrate that elastin-like and amyloid-like peptides are separable on the basis of backbone hydration and peptide-peptide hydrogen bonding.