MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands.

Affinity ranking of structurally diverse small-molecule ligands is a challenging problem with important applications in structure-based drug discovery. Absolute binding free energy methods can model diverse ligands, but the high computational cost of the current methods limits application to data sets with few ligands. We recently developed MELD-Bracket, a Molecular Dynamics method for efficient affinity ranking of ligands [ JCTC 2022, 18 (1), 374-379]. It utilizes a Bayesian framework to guide sampling to relevant regions of phase space, and it couples this with a bracket-like competition on a pool of ligands. Here we find that 6-competitor MELD-Bracket can rank dozens of diverse ligands that have low structural similarity and different net charges. We benchmark it on four protein systems─PTB1B, Tyk2, BACE, and JAK3─having varied modes of interactions. We also validated 8-competitor and 12-competitor protocols. The MELD-Bracket protocols presented here may have the appropriate balance of accuracy and computational efficiency to be suitable for ranking diverse ligands from typical drug discovery campaigns.

Leveraging the potential of nature to meet net zero greenhouse gas emissions in Washington State.

The State of Washington, USA, has set a goal to reach net zero greenhouse gas emissions by 2050, the year around which the Intergovernmental Panel on Climate Change (IPCC) recommended we must limit global warming to 1.5 °C above that of pre-industrial times or face catastrophic changes. We employed existing approaches to calculate the potential for a suite of Natural Climate Solution (NCS) pathways to reduce Washington's net emissions under three implementation scenarios: Limited, Moderate, and Ambitious. We found that NCS could reduce emissions between 4.3 and 8.8 MMT CO2eyr-1 in thirty-one years, accounting for 4% to 9% of the State's net zero goal. These potential reductions largely rely on changing forest management practices on portions of private and public timber lands. We also mapped the distribution of each pathway's Ambitious potential emissions reductions by county, revealing spatial clustering of high potential reductions in three regions closely tied to major business sectors: private industrial forestry in southwestern coastal forests, cropland agriculture in the Columbia Basin, and urban and rural development in the Puget Trough. Overall, potential emissions reductions are provided largely by a single pathway, Extended Timber Harvest Rotations, which mostly clusters in southwestern counties. However, mapping distribution of each of the other pathways reveals wider distribution of each pathway's unique geographic relevance to support fair, just, and efficient deployment. Although the relative potential for a single pathway to contribute to statewide emissions reductions may be small, they could provide co-benefits to people, communities, economies, and nature for adaptation and resiliency across the state.

Impacts of stormwater on coastal ecosystems: the need to match the scales of management objectives and solutions.

Despite their limited area relative to the global ocean, coastal zones-the regions where land meets the sea-play a disproportionately important role in generating ecosystem services. However, coastal ecosystems are under increasing pressure from human populations. In particular, urban stormwater is an increasingly important threat to the integrity of coastal systems. Urban catchments exhibit altered flow regimes that impact ecosystem processes and coastal foodwebs. In addition, urban stormwater contains complex and unpredictable mixtures of chemicals that result in a multitude of lethal and sublethal impacts on species in coastal systems. Along the western coast of the United States, we estimate that hundreds of billions of kilograms of suspended solids flow off land surfaces and enter the Northern California Current each year. However, 70% of this pollution could be addressed by treating only 1.35% of the land area. Determining how to prioritize treatment of stormwater in this region requires a clear articulation of objectives-spatial distribution of appropriate management actions is dependent on the life histories of species, and management schemes optimized for one species may not achieve desired objectives for other species. In particular, we highlight that the scale of stormwater interventions must match the ecological scale relevant to species targeted by management. In many cases, management and policy will require mechanisms in order to ensure that local actions scale-up to efficiently and effectively achieve management objectives. In the face of rapid urbanization of coastal zones, failure to consider the match of management and ecological scales will result in the continued decline of coastal ecosystems and the species they support. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.

NMR-assisted protein structure prediction with MELDxMD.

We describe the performance of MELD-accelerated molecular dynamics (MELDxMD) in determining protein structures in the NMR-data-assisted category in CASP13. Seeded from web server predictions, MELDxMD was found best in the NMR category, over 17 targets, outperforming the next-best groups by a factor of ~4 in z-score. MELDxMD gives ensembles, not single structures; succeeds on a 326-mer, near the current upper limit for NMR structures; and predicts structures that match experimental residual dipolar couplings even though the only NMR-derived data used in the simulations was NOE-based ambiguous atom-atom contacts and backbone dihedrals. MELD can use noisy and ambiguous experimental information to reduce the MD search space. We believe MELDxMD is a promising method for determining protein structures from NMR data.

The unequal vulnerability of communities of color to wildfire.

Globally, environmental disasters impact billions of people and cost trillions of dollars in damage, and their impacts are often felt most acutely by minority and poor communities. Wildfires in the U.S. have similarly outsized impacts on vulnerable communities, though the ethnic and geographic distribution of those communities may be different than for other hazards. Here, we develop a social-ecological approach for characterizing fire vulnerability and apply it to >70,000 census tracts across the United States. Our approach incorporates both the wildfire potential of a landscape and socioeconomic attributes of overlying communities. We find that over 29 million Americans live with significant potential for extreme wildfires, a majority of whom are white and socioeconomically secure. Within this segment, however, are 12 million socially vulnerable Americans for whom a wildfire event could be devastating. Additionally, wildfire vulnerability is spread unequally across race and ethnicity, with census tracts that were majority Black, Hispanic or Native American experiencing ca. 50% greater vulnerability to wildfire compared to other census tracts. Embracing a social-ecological perspective of fire-prone landscapes allows for the identification of areas that are poorly equipped to respond to wildfires.

MELD × MD Folds Nonthreadables, Giving Native Structures and Populations.

A current challenge is to compute the native structures of proteins from their amino acid sequences. A main approach of bioinformatics is threading, in which a protein to be predicted is computationally threaded onto protein fragments of similar sequence having an already known structure. However, ∼15% of proteins cannot be folded in this way; this has been called the glass ceiling, and the proteins are called nonthreadables. For these, physical molecular dynamics (MD) modeling is promising because it does not require templates. We find that MD, when used with an accelerator called MELD, can fold many nonthreadables. For 41 nonthreadable proteins with fewer than 125 residues, MELD-accelerated MD (MELD × MD) folds 20 of them to better than 4 Å error. In 10 cases, MELD × MD succeeds even when the force field does not properly encode the native state. In 11 cases, MELD × MD foretells its own success; seeing large Boltzmann populations in the simulations predicts it has converged to the correct native state. MELD × MD acceleration can be applied to a broad physical protein modeling range.

Assessing the Current State of Amber Force Field Modifications for DNA.

The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years due to the availability of optimized MD software and access to significant computational power, including GPU multicore computing engines and other specialized hardware. This has led researchers to routinely extend conformational sampling times to the microsecond level and beyond. The extended sampling time has allowed the community not only to converge conformational ensembles through complete sampling but also to discover deficiencies and overcome problems with the force fields. Accuracy of the force fields is a key component, along with sampling, toward being able to generate accurate and stable structures of biopolymers. The Amber force field for nucleic acids has been used extensively since the 1990s, and multiple artifacts have been discovered, corrected, and reassessed by different research groups. We present a direct comparison of two of the most recent and state-of-the-art Amber force field modifications, bsc1 and OL15, that focus on accurate modeling of double-stranded DNA. After extensive MD simulations with five test cases and two different water models, we conclude that both modifications are a remarkable improvement over the previous bsc0 force field. Both force field modifications show better agreement when compared to experimental structures. To ensure convergence, the Drew-Dickerson dodecamer (DDD) system was simulated using 100 independent MD simulations, each extended to at least 10 µs, and the independent MD simulations were concatenated into a single 1 ms long trajectory for each combination of force field and water model. This is significantly beyond the time scale needed to converge the conformational ensemble of the internal portions of a DNA helix absent internal base pair opening. Considering all of the simulations discussed in the current work, the MD simulations performed to assess and validate the current force fields and water models aggregate over 14 ms of simulation time. The results suggest that both the bsc1 and OL15 force fields render average structures that deviate significantly less than 1 Å from the average experimental structures. This can be compared to similar but less exhaustive simulations with the CHARMM 36 force field that aggregate to the ∼90 µs time scale and also perform well but do not produce structures as close to the DDD NMR average structures (with root-mean-square deviations of 1.3 Å) as the newer Amber force fields. On the basis of these analyses, any future research involving double-stranded DNA simulations using the Amber force fields should employ the bsc1 or OL15 modification.

DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations.

BI and BII conformational substates in the DNA backbone typify canonical B-form DNA. The BI and BII substates are important for structural variation of DNA and have been implicated in protein-nucleic acid recognition mechanisms. Recent refinements have been made to nucleic acid force fields employed in molecular dynamics simulations that demonstrate a better ability to model the BI and BII states, leading to overall improved modeling of DNA structure and dynamics. These force field improvements have yet to be significantly demonstrated in the context of a protein-DNA system extended to long time scales. Our plan was to run molecular dynamics simulations of a well-studied protein-DNA system (E2-DNA) into the microsecond time scale and determine the ability of the force field to populate BII states in the DNA backbone consistent with dinucleotide steps crystallized in the BII conformation. The results showed that the dinucleotide steps in the E2-DNA complex with the highest BII populations from simulation trajectories corresponded to the dinucleotide steps crystallized in the BII state and that decoy BI and BII states converge to the same results within approximately one microsecond.

Expanding the druggable space of the LSD1/CoREST epigenetic target: new potential binding regions for drug-like molecules, peptides, protein partners, and chromatin.

Lysine specific demethylase-1 (LSD1/KDM1A) in complex with its corepressor protein CoREST is a promising target for epigenetic drugs. No therapeutic that targets LSD1/CoREST, however, has been reported to date. Recently, extended molecular dynamics (MD) simulations indicated that LSD1/CoREST nanoscale clamp dynamics is regulated by substrate binding and highlighted key hinge points of this large-scale motion as well as the relevance of local residue dynamics. Prompted by the urgent need for new molecular probes and inhibitors to understand LSD1/CoREST interactions with small-molecules, peptides, protein partners, and chromatin, we undertake here a configurational ensemble approach to expand LSD1/CoREST druggability. The independent algorithms FTMap and SiteMap and our newly developed Druggable Site Visualizer (DSV) software tool were used to predict and inspect favorable binding sites. We find that the hinge points revealed by MD simulations at the SANT2/Tower interface, at the SWIRM/AOD interface, and at the AOD/Tower interface are new targets for the discovery of molecular probes to block association of LSD1/CoREST with chromatin or protein partners. A fourth region was also predicted from simulated configurational ensembles and was experimentally validated to have strong binding propensity. The observation that this prediction would be prevented when using only the X-ray structures available (including the X-ray structure bound to the same peptide) underscores the relevance of protein dynamics in protein interactions. A fifth region was highlighted corresponding to a small pocket on the AOD domain. This study sets the basis for future virtual screening campaigns targeting the five novel regions reported herein and for the design of LSD1/CoREST mutants to probe LSD1/CoREST binding with chromatin and various protein partners.

Improved coiled-coil design enhances interaction with Bcr-Abl and induces apoptosis.

The oncoprotein Bcr-Abl drives aberrant downstream activity through trans-autophosphorylation of homo-oligomers in chronic myelogenous leukemia (CML).(1, 2) The formation of Bcr-Abl oligomers is achieved through the coiled-coil domain at the N-terminus of Bcr.(3, 4) We have previously reported a modified version of this coiled-coil domain, CCmut2, which exhibits disruption of Bcr-Abl oligomeric complexes and results in decreased proliferation of CML cells and induction of apoptosis.(5) A major contributing factor to these enhanced capabilities is the destabilization of the CCmut2 homodimers, increasing the availability to interact with and inhibit Bcr-Abl. Here, we included an additional mutation (K39E) that could in turn further destabilize the mutant homodimer. Incorporation of this modification into CCmut2 (C38A, S41R, L45D, E48R, Q60E) generated what we termed CCmut3, and resulted in further improvements in the binding properties with the wild-type coiled-coil domain representative of Bcr-Abl [corrected]. A separate construct containing one revert mutation, CCmut4, did not demonstrate improved oligomeric properties and indicated the importance of the L45D mutation. CCmut3 demonstrated improved oligomerization via a two-hybrid assay as well as through colocalization studies, in addition to showing similar biologic activity as CCmut2. The improved binding between CCmut3 and the Bcr-Abl coiled-coil may be used to redirect Bcr-Abl to alternative subcellular locations with interesting therapeutic implications.