The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1, and χ2 potential energy ...surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields.
Muscarinic acetylcholine receptors are G protein-coupled receptors that respond to acetylcholine and play important signaling roles in the nervous system. There are five muscarinic receptor subtypes ...(M1R to M5R), which, despite sharing a high degree of sequence identity in the transmembrane region, couple to different heterotrimeric GTP-binding proteins (G proteins) to transmit signals. M1R, M3R, and M5R couple to the G
family, whereas M2R and M4R couple to the G
family. Here, we present and compare the cryo-electron microscopy structures of M1R in complex with G
and M2R in complex with G
The M1R-G
complex exhibits distinct features, including an extended transmembrane helix 5 and carboxyl-terminal receptor tail that interacts with G protein. Detailed analysis of these structures provides a framework for understanding the molecular determinants of G-protein coupling selectivity.
The COVID-19 pandemic, and resultant "Stay-at-Home" orders, may have impacted adults' positive health behaviors (sleep, physical activity) and negative health behaviors (alcohol consumption, drug ...use, and tobacco use). The purpose of this study was to investigate how these health behaviors changed (increased/improved or decreased/worsened) at the early stages of the pandemic, what participant characteristics were associated with health behavior changes, and why these behavioral changes may have occurred. A convenience sample of 1809 adults residing in the United States completed a 15-min self-report questionnaire in April and May 2020. Multinomial logistic regressions and descriptive statistics were used to evaluate how, for whom, and why these health behaviors changed. Participants were primarily female (67.4%), aged 35-49 years (39.8%), college graduates (83.3%), non-tobacco users (74.7%), and had previously used marijuana (48.6%). Overall, participants primarily reported a decrease in physical activity, while sleep and all of the negative health behaviors remained the same. Changes in negative health behaviors were related (
< 0.05) to sex, age, parental status, educational status, job status, BMI, and depression scores. Changes in positive health behaviors were related (
< 0.05) to sex, parental status, job status, and depression scores. Having more time available during the pandemic was the most commonly cited reason for changing health behaviors (negative and positive). Public health efforts should address the potential for long-term health consequences due to behavior change during COVID-19.
Drug discovery in the era of cryo-electron microscopy Robertson, Michael J.; Meyerowitz, Justin G.; Skiniotis, Georgios
Trends in biochemical sciences,
February 2022, 2022-02-00, 20220201, Letnik:
47, Številka:
2
Journal Article
Recenzirano
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Structure-based drug discovery (SBDD) is an indispensable approach for the design and optimization of new therapeutic agents. Here, we highlight the rapid progress that has turned cryo‐electron ...microscopy (cryoEM) into an exceptional SBDD tool, and the wealth of new structural information it is providing for high-value pharmacological targets. We review key advantages of a technique that directly images vitrified biomolecules without the need for crystallization; both in terms of a broader array of systems that can be studied and the different forms of information it can provide, including heterogeneity and dynamics. We discuss near- and far-future developments, working in concert towards achieving the resolution and throughput necessary for cryoEM to make a widespread impact on the SBDD pipeline.
CryoEM has recently obtained resolutions sufficient for informing SBDD.The use of cryoEM allows access to new types of structures for SBDD, such as transmembrane proteins and difficult-to-crystalize complexes.New computational tools combined with cryoEM data provide key data for understanding ligand–protein interactions.Advances in cryoEM are rapidly improving accessibility and throughput, including increased automation in both hardware and software, and technical advances to improve signal to noise ratios and speed.New computational tools are unharnessing the ability of cryoEM to capture intermediate and equilibrium states of ligand–protein complexes.
Hallucinogens like lysergic acid diethylamide (LSD), psilocybin, and substituted N-benzyl phenylalkylamines are widely used recreationally with psilocybin being considered as a therapeutic for many ...neuropsychiatric disorders including depression, anxiety, and substance abuse. How psychedelics mediate their actions—both therapeutic and hallucinogenic—are not understood, although activation of the 5-HT2A serotonin receptor (HTR2A) is key. To gain molecular insights into psychedelic actions, we determined the active-state structure of HTR2A bound to 25-CN-NBOH—a prototypical hallucinogen—in complex with an engineered Gαq heterotrimer by cryoelectron microscopy (cryo-EM). We also obtained the X-ray crystal structures of HTR2A complexed with the arrestin-biased ligand LSD or the inverse agonist methiothepin. Comparisons of these structures reveal determinants responsible for HTR2A-Gαq protein interactions as well as the conformational rearrangements involved in active-state transitions. Given the potential therapeutic actions of hallucinogens, these findings could accelerate the discovery of more selective drugs for the treatment of a variety of neuropsychiatric disorders.
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•Cryo-EM 5-HT2A serotonin receptor structure complexed with hallucinogen and Gαq•The hallucinogen 25CN-NBOH displaces “toggle switch” tryptophan•Interactions essential for Gαq-specific signaling identified•X-ray crystal structure of LSD complexed with 5-HT2A elucidated
Roth et al. reveal structurally how psychedelics, including LSD, psilocin, mescaline, and various N-BOH analogs, mediate their therapeutic and hallucinogenic effects by binding to and activating their molecular target, the serotonin (5-HT) 2A receptor coupled with G-protein Gαq.
G protein-coupled receptors (GPCRs) and other membrane proteins are valuable drug targets, and their dynamic nature makes them attractive systems for study with molecular dynamics (MD) simulations ...and free energy approaches. Here, we report the development, implementation, and validation of OPLS-AA/M force field parameters to enable simulations of these systems. These efforts include the introduction of post-translational modifications including lipidations and phosphorylation. We also modify previously reported parameters for lipids to be more consistent with the OPLS-AA force field standard and extend their coverage. These new parameters are validated on a variety of test systems, with the results compared to high-level quantum mechanics calculations, experimental data, and simulations with other force fields. The results demonstrate that the new parameters reliably reproduce the behavior of membrane protein systems.
The origins of the RNA world Robertson, Michael P; Joyce, Gerald F
Cold Spring Harbor perspectives in biology,
05/2012, Letnik:
4, Številka:
5
Journal Article
Recenzirano
Odprti dostop
The general notion of an "RNA World" is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA and genetically encoded proteins were not ...involved as catalysts. There is now strong evidence indicating that an RNA World did indeed exist before DNA- and protein-based life. However, arguments regarding whether life on Earth began with RNA are more tenuous. It might be imagined that all of the components of RNA were available in some prebiotic pool, and that these components assembled into replicating, evolving polynucleotides without the prior existence of any evolved macromolecules. A thorough consideration of this "RNA-first" view of the origin of life must reconcile concerns regarding the intractable mixtures that are obtained in experiments designed to simulate the chemistry of the primitive Earth. Perhaps these concerns will eventually be resolved, and recent experimental findings provide some reason for optimism. However, the problem of the origin of the RNA World is far from being solved, and it is fruitful to consider the alternative possibility that RNA was preceded by some other replicating, evolving molecule, just as DNA and proteins were preceded by RNA.
Cannabis elicits its mood-enhancing and analgesic effects through the cannabinoid receptor 1 (CB1), a G protein-coupled receptor (GPCR) that signals primarily through the adenylyl cyclase-inhibiting ...heterotrimeric G protein Gi. Activation of CB1-Gi signaling pathways holds potential for treating a number of neurological disorders and is thus crucial to understand the mechanism of Gi activation by CB1. Here, we present the structure of the CB1-Gi signaling complex bound to the highly potent agonist MDMB-Fubinaca (FUB), a recently emerged illicit synthetic cannabinoid infused in street drugs that have been associated with numerous overdoses and fatalities. The structure illustrates how FUB stabilizes the receptor in an active state to facilitate nucleotide exchange in Gi. The results compose the structural framework to explain CB1 activation by different classes of ligands and provide insights into the G protein coupling and selectivity mechanisms adopted by the receptor.
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•3 Å cryo-EM structure of the CB1-Gi complex bound to potent agonist MDMB-Fubinaca•MDMB-Fubinaca locks “toggle switch” residues F2003.36/W3566.48 in active conformation•Quantum mechanics calculations reveal the mechanism for the high affinity of Fubinaca•Molecular dynamic simulations reveal a path for ligand entry between TM1 and TM7
Looking at how a toxic, synthetic ligand locks cannabinoid receptor 1 into a signaling conformation points to ways to understand and modulate receptor activity.
Worshipping Walt Robertson, Michael
2021, 2008, 2021-08-10
eBook
Despite his protests, Anne Gilchrist, distinguished woman of letters, moved her entire household from London to Philadelphia in an effort to marry him. John Addington Symonds, historian and theorist ...of sexual inversion, sent him avid fan mail for twenty years. And volunteer assistant Horace Traubel kept a record of their daily conversations, producing a nine-volume compilation. Who could inspire so much devotion? Worshipping Walt is the first book on the Whitman disciples--the fascinating, eclectic group of nineteenth-century men and women who regarded Walt Whitman not simply as a poet but as a religious prophet. Long before Whitman was established in the canon of American poetry, feminists, socialists, spiritual seekers, and supporters of same-sex passion saw him as an enlightened figure who fulfilled their religious, political, and erotic yearnings. To his disciples Whitman was variously an ideal husband, radical lover, socialist icon, or bohemian saint. In this transatlantic group biography, Michael Robertson explores the highly charged connections between Whitman and his followers, including Canadian psychiatrist R. M. Bucke, American nature writer John Burroughs, British activist Edward Carpenter, and the notorious Oscar Wilde. Despite their particular needs, they all viewed Whitman as the author of a new poetic scripture and prophet of a modern liberal spirituality. Worshipping Walt presents a colorful portrait of an era of intense religious, political, and sexual passions, shedding new light on why Whitman's work continues to appeal to so many.
Glucose is a primary energy source in living cells. The discovery in 1960s that a sodium gradient powers the active uptake of glucose in the intestine
heralded the concept of a secondary active ...transporter that can catalyse the movement of a substrate against an electrochemical gradient by harnessing energy from another coupled substrate. Subsequently, coupled Na
/glucose transport was found to be mediated by sodium-glucose cotransporters
(SGLTs). SGLTs are responsible for active glucose and galactose absorption in the intestine and for glucose reabsorption in the kidney
, and are targeted by multiple drugs to treat diabetes
. Several members within the SGLT family transport key metabolites other than glucose
. Here we report cryo-electron microscopy structures of the prototypic human SGLT1 and a related monocarboxylate transporter SMCT1 from the same family. The structures, together with molecular dynamics simulations and functional studies, define the architecture of SGLTs, uncover the mechanism of substrate binding and selectivity, and shed light on water permeability of SGLT1. These results provide insights into the multifaceted functions of SGLTs.
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