Critical Role of Confinement in the NMR Surface Relaxation and Diffusion of n-Heptane in a Polymer Matrix Revealed by MD Simulations

Arjun Valiya Parambathu; Philip M. Singer; George J. Hirasaki; Walter G. Chapman; Dilipkumar Asthagiri

doi:10.1021/acs.jpcb.0c00711

Structural basis of the differential binding of engineered knottins 2.5F and 2.5D to integrins αVβ3 and α5β1

10.1101/565358 ◽

2019 ◽

Author(s):

Johannes F. Van Agthoven ◽

Hengameh Shams ◽

Frank V. Cochran ◽

José L. Alonso ◽

James R. Kintzing ◽

...

Keyword(s):

Cancer Therapy ◽

Critical Role ◽

Md Simulations ◽

Structural Basis ◽

Conformational Selection ◽

Drug Candidates ◽

Tumor Survival ◽

Differential Binding ◽

Integrin Ligand

AbstractIntegrins αVβ3 and α5β1 play critical roles in tumor survival, invasion, metastasis, and angiogenesis and are validated targets for cancer therapy and molecular imaging. Increasing evidence suggests that targeting both integrins simultaneously with antagonists is more effective in cancer therapy because of concerns about resistance and paradoxical promotion of tumor growth with use of agents highly selective for a single integrin. Engineered Arg-Gly-Asp (RGD)-containing 3.5 kDa cysteine-knot proteins (knottins 2.5F and 2.5D) are attractive drug candidates due to their exceptional structural stability and high affinity binding to certain integrins. 2.5F binds both αVβ3 and α5β1, whereas 2.5D is αVβ3-selective. To elucidate the structural basis of integrin selection, we determined the structures of 2.5F and 2.5D both as apo-proteins and in complex with αVβ3. These data, combined with MD simulations and mutational studies, revealed a critical role of two αVβ3-specific residues in the vicinity of the metal ion dependent adhesion site (MIDAS) in promoting an αVβ3-induced fit of 2.5D. In contrast, conformational selection accounted for the specificity of 2.5F to both integrins. These data provide new insights into the structural basis of integrin-ligand binding specificity, and could help in development of integrin-targeted therapeutics.

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In VivoEvidence of Increased nNOS Activity in Acute MPTP Neurotoxicity: A Functional Pharmacological MRI Study

BioMed Research International ◽

10.1155/2013/964034 ◽

2013 ◽

Vol 2013 ◽

pp. 1-7 ◽

Cited By ~ 4

Author(s):

Tiing Yee Siow ◽

Chiao-Chi V. Chen ◽

Nina Wan ◽

Kai-Ping N. Chow ◽

Chen Chang

Keyword(s):

Diffusion Weighted Imaging ◽

Critical Role ◽

No Synthase ◽

Resonance Spectroscopy ◽

Systemic Injection ◽

Mptp Toxicity ◽

Mri Study ◽

And Diffusion

1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is a neurotoxin commonly used to produce an animal model of Parkinson’s disease. Previous studies have suggested a critical role for neuronal nitric oxide (NO) synthase- (nNOS-) derived NO in the pathogenesis of MPTP. However, NO activity is difficult to assessin vivodue to its extremely short biological half-life, and soin vivoevidence of NO involvement in MPTP neurotoxicity remains scarce. In the present study, we utilized flow-sensitive alternating inversion recovery sequences,in vivolocalized proton magnetic resonance spectroscopy, and diffusion-weighted imaging to, respectively, assess the hemodynamics, metabolism, and cytotoxicity induced by MPTP. The role of NO in MPTP toxicity was clarified further by administering a selective nNOS inhibitor, 7-nitroindazole (7-NI), intraperitoneally to some of the experimental animals prior to MPTP challenge. The transient increase in cerebral blood flow (CBF) in the cortex and striatum induced by systemic injection of MPTP was completely prevented by pretreatment with 7-NI. We provide the firstin vivoevidence of increased nNOS activity in acute MPTP-induced neurotoxicity. Although the observed CBF change may be independent of the toxicogenesis of MPTP, this transient hyperperfusion state may serve as an early indicator of neuroinflammation.

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Dual role of strigolactone receptor signaling partner in inhibiting substrate hydrolysis

10.1101/2021.12.01.470725 ◽

2021 ◽

Author(s):

Briana L Sobecks ◽

Jiming Chen ◽

Diwakar Shukla

Keyword(s):

Active Site ◽

Conformational Stability ◽

Critical Role ◽

Md Simulations ◽

Binding Pocket ◽

Conformational Ensemble ◽

Downstream Signaling ◽

F Box Protein ◽

Substrate Hydrolysis

Plant branch and root growth relies on metabolism of the strigolactone (SL) hormone. The interaction between the SL molecule, Oryza sativa DWARF14 (D14) SL receptor, and D3 F-box protein has been shown to play a critical role in SL perception. Previously, it was believed that D3 only interacts with the closed form of D14 to induce downstream signaling, but recent experiments indicate that D3, as well as its C-terminal helix (CTH), can interact with the open form as well to inhibit strigolactone signaling. Two hypotheses for the CTH induced inhibition are that either the CTH affects the conformational ensemble of D14 by stabilizing catalytically inactive states, or the CTH interacts with SLs in a way that prevents them from entering the binding pocket. In this study, we have performed molecular dynamics (MD) simulations to assess the validity of these hypotheses. We used an apo system with only D14 and the CTH to test the active site conformational stability and a holo system with D14, the CTH, and an SL molecule to test the interaction between the SL and CTH. Our simulations show that the CTH affects both active site conformation and the ability of SLs to move into the binding pocket. In the apo system, the CTH allosterically stabilized catalytic residues into their inactive conformation. In the holo system, significant interactions between SLs and the CTH hindered the ability of SLs to enter the D14 binding pocket. These two mechanisms account for the observed decrease in SL binding to D14 and subsequent ligand hydrolysis in the presence of the CTH.

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Discovery of SARS-CoV-2 Mpro Peptide Inhibitors from Modelling Substrate and Ligand Binding

10.1101/2021.06.18.446355 ◽

2021 ◽

Author(s):

H. T. Henry Chan ◽

Marc A. Moesser ◽

Rebecca K. Walters ◽

Tika R. Malla ◽

Rebecca M. Twidale ◽

...

Keyword(s):

Critical Role ◽

Md Simulations ◽

Peptide Inhibitors ◽

Binding Modes ◽

Molecular Features ◽

Main Protease ◽

Modelling Studies ◽

Viral Lifecycle ◽

Computational Mutagenesis

The main protease (Mpro) of SARS-CoV-2 is central to its viral lifecycle and is a promising drug target, but little is known concerning structural aspects of how it binds to its 11 natural cleavage sites. We used biophysical and crystallographic data and an array of classical molecular mechanics and quantum mechanical techniques, including automated docking, molecular dynamics (MD) simulations, linear-scaling DFT, QM/MM, and interactive MD in virtual reality, to investigate the molecular features underlying recognition of the natural Mpro substrates. Analyses of the subsite interactions of modelled 11-residue cleavage site peptides, ligands from high-throughput crystallography, and designed covalently binding inhibitors were performed. Modelling studies reveal remarkable conservation of hydrogen bonding patterns of the natural Mpro substrates, particularly on the N-terminal side of the scissile bond. They highlight the critical role of interactions beyond the immediate active site in recognition and catalysis, in particular at the P2/S2 sites. The binding modes of the natural substrates, together with extensive interaction analyses of inhibitor and fragment binding to Mpro, reveal new opportunities for inhibition. Building on our initial Mpro-substrate models, computational mutagenesis scanning was employed to design peptides with improved affinity and which inhibit Mpro competitively. The combined results provide new insight useful for the development of Mpro inhibitors.

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Monitoring the microcirculation in the ICU

10.1093/med/9780199600830.003.0142 ◽

2016 ◽

Author(s):

Can Ince ◽

Alexandre Lima

Keyword(s):

Cardiovascular System ◽

Critical Role ◽

Passive Diffusion ◽

Peripheral Perfusion ◽

Organ Function ◽

Optical Techniques ◽

Microcirculatory Function ◽

Parenchymal Cells ◽

And Diffusion

The microcirculation is the key physiological compartment of the cardiovascular system where oxygen is delivered by convection and diffusion to respiring parenchymal cells to support cellular, and thereby organ, function. The microcirculation consists of microvessels less than 100 µmin diameter consisting of arterioles, capillaries, and venules. The smallest vessels (<6 µm) are the capillaries where most oxygen leaves the circulation by passive diffusion to cells. The critical role of the microcirculation has long been recognized, although it has recently been possible to image its function at the bedside, thus making it a clinically important compartment to monitor. Prior to this type of monitoring, peripheral perfusion was used as a surrogate before more advanced optical techniques were developed to image microcirculatory function both non-invasively and at the bedside. This chapter provides a brief overview of microcirculatory assessment.

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The Role of the SLP in Autism Spectrum Disorder Screening and Assessment

Perspectives on Language Learning and Education ◽

10.1044/lle15.2.50 ◽

2008 ◽

Vol 15 (2) ◽

pp. 50-59 ◽

Cited By ~ 1

Author(s):

Amy Philofsky

Keyword(s):

Language Development ◽

Critical Role ◽

Children With Autism ◽

Autism Spectrum ◽

Children With Asd ◽

Prevalence Estimates ◽

Notable Increase ◽

Screening Assessment ◽

Critical Components

AbstractRecent prevalence estimates for autism have been alarming as a function of the notable increase. Speech-language pathologists play a critical role in screening, assessment and intervention for children with autism. This article reviews signs that may be indicative of autism at different stages of language development, and discusses the importance of several psychometric properties—sensitivity and specificity—in utilizing screening measures for children with autism. Critical components of assessment for children with autism are reviewed. This article concludes with examples of intervention targets for children with ASD at various levels of language development.

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