Structural Modeling of γ-Secretase Aβn Complex Formation and Substrate Processing

AbstractThe intra-membrane aspartyl protease γ-secretase (GSEC) cleaves single-span transmembrane helices including the C-terminal fragment of the amyloid precursor protein (APP). This substrate is initially cleaved at the ɛ-site followed by successive processing (trimming) events mostly in steps of three amino acids. GSEC is responsible for the formation of N-terminal APP amyloid-β (A β) peptides of different length (e.g. Aβ42) that can form aggregates involved in Alzheimer’s disease pathogenesis. The molecular mechanism of GSEC-APP substrate recognition is key for understanding how different peptide products are formed and could help in designing APP-selective modulators. Based on the known structure of apo GSEC and the APP-C99 fragment we have generated putative structural models of the initial binding in three different possible modes using extensive Molecular Dynamics (MD) simulations. The binding mode with the substrate helix located in a cleft between the transmembrane helices 2 and 3 of the presenilin subunit was identified as a most likely binding mode. Based on this arrangement the processing steps were investigated using restraint MD simulations to pull the scissile bond (for each processing step) into a transition like (cleavable) state. This allowed us to analyze in detail the motions and energetic contributions of participating residues. The structural model agrees qualitatively well with the influence of many mutations in GSEC and C99. It also explains the effects of inhibitors, cross-linking as well as spectroscopic data on GSEC substrate binding and can serve as working model for the future planning of structural and biochemical studies.

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Solvents to Fragments to Drugs: MD Applications in Drug Design

Molecules ◽

10.3390/molecules23123269 ◽

2018 ◽

Vol 23 (12) ◽

pp. 3269 ◽

Cited By ~ 7

Author(s):

Lucas Defelipe ◽

Juan Arcon ◽

Carlos Modenutti ◽

Marcelo Marti ◽

Adrián Turjanski ◽

...

Keyword(s):

Binding Free Energy ◽

Mixed Solvents ◽

Md Simulations ◽

Binding Mode ◽

Condensed State ◽

Protein Targets ◽

Drug Candidates ◽

Interaction Sites ◽

Aqueous Solvation ◽

The Common

Simulations of molecular dynamics (MD) are playing an increasingly important role in structure-based drug discovery (SBDD). Here we review the use of MD for proteins in aqueous solvation, organic/aqueous mixed solvents (MDmix) and with small ligands, to the classic SBDD problems: Binding mode and binding free energy predictions. The simulation of proteins in their condensed state reveals solvent structures and preferential interaction sites (hot spots) on the protein surface. The information provided by water and its cosolvents can be used very effectively to understand protein ligand recognition and to improve the predictive capability of well-established methods such as molecular docking. The application of MD simulations to the study of the association of proteins with drug-like compounds is currently only possible for specific cases, as it remains computationally very expensive and labor intensive. MDmix simulations on the other hand, can be used systematically to address some of the common tasks in SBDD. With the advent of new tools and faster computers we expect to see an increase in the application of mixed solvent MD simulations to a plethora of protein targets to identify new drug candidates.

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Unraveling Sugar Binding Modes to DC-SIGN by Employing Fluorinated Carbohydrates

Molecules ◽

10.3390/molecules24122337 ◽

2019 ◽

Vol 24 (12) ◽

pp. 2337 ◽

Cited By ~ 15

Author(s):

J. Daniel Martínez ◽

Pablo Valverde ◽

Sandra Delgado ◽

Cecilia Romanò ◽

Bruno Linclau ◽

...

Keyword(s):

Protein Interactions ◽

Viral Infections ◽

Md Simulations ◽

Binding Mode ◽

Intercellular Adhesion Molecule ◽

Binding Modes ◽

Binding Epitope ◽

First Time ◽

Biomedical Interest ◽

Specific Sugar

A fluorine nuclear magnetic resonance (19F-NMR)-based method is employed to assess the binding preferences and interaction details of a library of synthetic fluorinated monosaccharides towards dendritic cell-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN), a lectin of biomedical interest, which is involved in different viral infections, including HIV and Ebola, and is able to recognize a variety of self- and non-self-glycans. The strategy employed allows not only screening of a mixture of compounds, but also obtaining valuable information on the specific sugar–protein interactions. The analysis of the data demonstrates that monosaccharides Fuc, Man, Glc, and Gal are able to bind DC-SIGN, although with decreasing affinity. Moreover, a new binding mode between Man moieties and DC-SIGN, which might have biological implications, is also detected for the first time. The combination of the 19F with standard proton saturation transfer difference (1H-STD-NMR) data, assisted by molecular dynamics (MD) simulations, permits us to successfully define this new binding epitope, where Man coordinates a Ca2+ ion of the lectin carbohydrate recognition domain (CRD) through the axial OH-2 and equatorial OH-3 groups, thus mimicking the Fuc/DC-SIGN binding architecture.

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Surface Preparation of Single Crystal C(001) Substrates for Homoepitaxial Diamond Growth

MRS Proceedings ◽

10.1557/proc-339-51 ◽

1994 ◽

Vol 339 ◽

Cited By ~ 4

Author(s):

T. P. Humphreys ◽

J. B. Posthill ◽

D. P. Malta ◽

R. E. Thomas ◽

R. A. Rudder ◽

...

Keyword(s):

Electrochemical Etching ◽

Natural Diamond ◽

Surface Preparation ◽

Chemical Vapor ◽

Diamond Growth ◽

Rf Plasma ◽

Substrate Preparation ◽

Surface Plasmas ◽

Substrate Processing ◽

Processing Steps

ABSRACTA novel substrate preparation procedure which can be employed to remove the original surface from as-received C(001) natural diamond substrates has been developed. A description of the various substrate processing steps which includes, low-energy ion implantation of C and O, high-temperature annealing, electrochemical etching and surface plasmas treatments is presented. Also demonstrated is the growth of topographically excellent homoepitaxial films by rf-plasma-enhanced chemical vapor deposition using water/ethanol mixtures on C(001) substrates.

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A boosted unbiased molecular dynamics method for predicting ligands binding mechanisms: probing the binding pathway of dasatinib to Src-kinase

Bioinformatics ◽

10.1093/bioinformatics/btaa565 ◽

2020 ◽

Vol 36 (18) ◽

pp. 4714-4720

Author(s):

Farzin Sohraby ◽

Mostafa Javaheri Moghadam ◽

Masoud Aliyar ◽

Hassan Aryapour

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Md Simulation ◽

Src Kinase ◽

Deep Understanding ◽

Md Simulations ◽

Binding Mode ◽

Supplementary Information ◽

Computational Resources ◽

Binding Mechanisms

Abstract Summary Small molecules such as metabolites and drugs play essential roles in biological processes and pharmaceutical industry. Knowing their interactions with biomacromolecular targets demands a deep understanding of binding mechanisms. Dozens of papers have suggested that discovering of the binding event by means of conventional unbiased molecular dynamics (MD) simulation urges considerable amount of computational resources, therefore, only one who holds a cluster or a supercomputer can afford such extensive simulations. Thus, many researchers who do not own such resources are reluctant to take the benefits of running unbiased MD simulation, in full atomistic details, when studying a ligand binding pathway. Many researchers are impelled to be content with biased MD simulations which seek its validation due to its intrinsic preconceived framework. In this work, we have presented a workable stratagem to encourage everyone to perform unbiased (unguided) MD simulations, in this case a protein–ligand binding process, by typical desktop computers and so achieve valuable results in nanosecond time scale. Here, we have described a dynamical binding’s process of an anticancer drug, the dasatinib, to the c-Src kinase in full atomistic details for the first time, without applying any biasing force or potential which may lead the drug to artificial interactions with the protein. We have attained multiple independent binding events which occurred in the nanosecond time scales, surprisingly as little as ∼30 ns. Both the protonated and deprotonated forms of the dasatinib reached the crystallographic binding mode without having any major intermediate state during induction. Availability and implementation The links of the tutorial and technical documents are accessible in the article. Supplementary information Supplementary data are available at Bioinformatics online.

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Process Monitoring for Fabrication of Mercuric Iodide Room Temperature Radiation Detectors

MRS Proceedings ◽

10.1557/proc-324-65 ◽

1993 ◽

Vol 324 ◽

Cited By ~ 1

Author(s):

J. M. Van Scyoc ◽

T. E. Schlesinger ◽

H. Yao ◽

R. B. James ◽

M. Natarajan ◽

...

Keyword(s):

Room Temperature ◽

Radiation Detectors ◽

Electrical Contacts ◽

Careful Study ◽

Mercuric Iodide ◽

Optical Functions ◽

Processing Step ◽

Material Choice ◽

Temperature Radiation ◽

Processing Steps

AbstractIn the fabrication of mercuric iodide room temperature radiation detectors, as in any semiconductor process, the quality of the final device can be very sensitive to the details of the processing steps. Each processing step can either reduce the intrinsic defects and those extrinsic defects introduced by earlier steps, or it can introduce new defects. In mercuric iodide these defects can act as trapping and recombination centers, thereby degrading immediate device performance or leading to long-term reliability problems. With careful study and monitoring of each step, the process can be modified to improve the end product. In this work we used several techniques to study processing steps and their effects. Photoluminescence spectroscopy and photoionization revealed defects introduced during processing. One critical step is the formation of electrical contacts, as both the material choice and deposition method have an impact. Four point probe sheet resistance methods were used to characterize the loss of material from the contact as it reacted with or moved into the bulk semiconductor. Ellipsometry was used to characterize the intrinsic optical functions of the material, and to study the effects of surface aging on these functions. Results from this work provide suggestions for the modification and monitoring of the detector fabrication process.

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QM/MM calculations and MD simulations of acetolactate decarboxylase to reveal substrate R/S-acetolactate binding mode and stereoselective catalytic mechansim

RSC Advances ◽

10.1039/c6ra19346c ◽

2016 ◽

Vol 6 (94) ◽

pp. 91852-91859 ◽

Cited By ~ 6

Author(s):

Can-Bo Zhuang ◽

Qing-Chuan Zheng

Keyword(s):

Md Simulations ◽

Binding Mode

Acetolactate decarboxylase (ALDC) catalyzesR/S-acetolactate to make the same product, (R)-acetoin, with different processes.

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Substrate processing in intramembrane proteolysis by γ-secretase – the role of protein dynamics

Biological Chemistry ◽

10.1515/hsz-2016-0269 ◽

2017 ◽

Vol 398 (4) ◽

pp. 441-453 ◽

Cited By ~ 20

Author(s):

Dieter Langosch ◽

Harald Steiner

Keyword(s):

Transmembrane Helix ◽

Peptide Bond ◽

Common Denominator ◽

Transmembrane Helices ◽

Intramembrane Proteases ◽

Bond Scission ◽

Catalytic Sites ◽

Substrate Processing

Abstract Intramembrane proteases comprise a number of different membrane proteins with different types of catalytic sites. Their common denominator is cleavage within the plane of the membrane, which usually results in peptide bond scission within the transmembrane helices of their substrates. Despite recent progress in the determination of high-resolution structures, as illustrated here for the γ-secretase complex and its substrate C99, it is still unknown how these enzymes function and how they distinguish between substrates and non-substrates. In principle, substrate/non-substrate discrimination could occur at the level of substrate binding and/or cleavage. Focusing on the γ-secretase/C99 pair, we will discuss recent observations suggesting that global motions within a substrate transmembrane helix may be much more important for defining a substrate than local unraveling at cleavage sites.

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Discovery of novel sphingosine kinase 1 inhibitorsvia structure-based hierarchical virtual screening

MedChemComm ◽

10.1039/c4md00312h ◽

2015 ◽

Vol 6 (3) ◽

pp. 413-417 ◽

Cited By ~ 5

Author(s):

Xiaojian Wang ◽

Chenbin Sun ◽

Liang Fang ◽

Dali Yin

Keyword(s):

Virtual Screening ◽

Sphingosine Kinase ◽

Md Simulations ◽

Binding Pocket ◽

Binding Mode ◽

Positive Control ◽

Biological Evaluation ◽

U937 Cells ◽

Sphingosine Kinase 1 ◽

Inhibitory Activities

Hierarchical structure-based virtual screening against the sphingosine kinase 1(SphK1) binding pocket was performed. 25 compounds were selected for biological evaluation. Compound 25 exhibited comparable SphK1 and SphK2 inhibitory activities and anti-proliferative effects on U937 cells to the positive control N,N-dimethylsphingosine (DMS) 1. Further molecule dynamic (MD) simulations revealed the binding mode between SphK1 and 25.

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Insights into substrate-mediated assembly of the chloroplast TAT receptor complex

10.1101/2020.05.08.085019 ◽

2020 ◽

Author(s):

Qianqian Ma ◽

Christopher Paul New ◽

Carole Dabney-Smith

Keyword(s):

Structural Model ◽

Substrate Recognition ◽

Transmembrane Helix ◽

Complex Function ◽

Transmembrane Helices ◽

Translocation Event ◽

Active Substrate ◽

Tat System ◽

Folded Proteins ◽

Transport Complex

AbstractThe Twin Arginine Transport (TAT) system translocates fully folded proteins across the thylakoid membrane in the chloroplast (cp) and the cytoplasmic membrane of bacteria. In chloroplasts, cpTAT transport is achieved by three components: Tha4, Hcf106, and cpTatC. Hcf106 and cpTatC function as the substrate recognition/binding complex while Tha4 is thought to play a significant role in forming the translocation pore. Recent studies challenged this idea by suggesting that cpTatC-Hcf106-Tha4 function together in the active translocase. Here, we have mapped the inter-subunit contacts of cpTatC-Hcf106 during the resting state and built a cpTatC-Hcf106 structural model based on our crosslinking data. In addition, we have identified a substrate-mediated reorganization of cpTatC-Hcf106 contact sites during active substrate translocation. The proximity of Tha4 to the cpTatC-Hcf106 complex was also identified. Our data suggest a model for cpTAT function in which the transmembrane helices of Hcf106 and Tha4 may each contact the fifth transmembrane helix of cpTatC while the insertion of the substrate signal peptide may rearrange the cpTatC-Hcf106-Tha4 complex and initiate the translocation event.One sentence summaryProtein subunits of the thylakoidal twin arginine transport complex function together during substrate recognition and translocase assembly.

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Fentanyl binds to the μ-opioid receptor via the lipid membrane and transmembrane helices

10.1101/2021.02.04.429703 ◽

2021 ◽

Author(s):

Katy J Sutcliffe ◽

Robin A Corey ◽

Steven J Charlton ◽

Richard B Sessions ◽

Graeme Henderson ◽

...

Keyword(s):

Opioid Receptor ◽

Lipid Membrane ◽

Binding Mode ◽

Free Energy Calculations ◽

Coarse Grained ◽

Transmembrane Helices ◽

Opioid Agonist ◽

The Usa ◽

Μ Opioid Receptor ◽

Dynamics Simulations

AbstractOverdose deaths from synthetic opioids, such as fentanyl, have reached epidemic proportions in the USA and are increasing worldwide. Fentanyl is a potent opioid agonist, that is less well reversed by naloxone than morphine. Due to fentanyl’s high lipophilicity and elongated structure we hypothesised that its unusual pharmacology may be explained by a novel binding mode to the μ-opioid receptor (MOPr).By employing coarse-grained molecular dynamics simulations and free energy calculations, we determined the routes by which fentanyl and morphine access the orthosteric pocket of MOPr.Morphine accesses MOPr via the aqueous pathway; first binding to an extracellular vestibule, then diffusing into the orthosteric pocket. In contrast, fentanyl takes a novel route; first partitioning into the membrane, before accessing the orthosteric site by diffusing through a ligand-induced gap between the transmembrane helices.This novel lipophilic route may explain the high potency and lower susceptibility of fentanyl to reversal by naloxone.

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