Next-gen sequencing identifies non-coding variation disrupting miRNA-binding sites in neurological disorders

The protein kinase mammalian target of rapamycin (mTOR) is the central regulator of cell growth. Aberrant mTOR signaling is linked to cancer, diabetes, and neurological disorders. mTOR exerts its functions in two distinct multiprotein complexes, mTORC1 and mTORC2. Here, we report a 3.2-Å resolution cryo-EM reconstruction of mTORC2. It reveals entangled folds of the defining Rictor and the substrate-binding SIN1 subunits, identifies the carboxyl-terminal domain of Rictor as the source of the rapamycin insensitivity of mTORC2, and resolves mechanisms for mTORC2 regulation by complex destabilization. Two previously uncharacterized small-molecule binding sites are visualized, an inositol hexakisphosphate (InsP6) pocket in mTOR and an mTORC2-specific nucleotide binding site in Rictor, which also forms a zinc finger. Structural and biochemical analyses suggest that InsP6 and nucleotide binding do not control mTORC2 activity directly but rather have roles in folding or ternary interactions. These insights provide a firm basis for studying mTORC2 signaling and for developing mTORC2-specific inhibitors.

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Novel Inhibitors of Neuronal Nitric Oxide Synthase

Experimental Biology and Medicine ◽

10.1177/15353702-0322805-11 ◽

2003 ◽

Vol 228 (5) ◽

pp. 486-490 ◽

Cited By ~ 19

Author(s):

C. Di Giacomo ◽

V. Sorrenti ◽

L. Salerno ◽

V. Cardile ◽

F. Guerrera ◽

...

Keyword(s):

Nitric Oxide ◽

Nitric Oxide Synthase ◽

Mechanism Of Action ◽

Binding Sites ◽

Neurological Disorders ◽

Neuronal Nitric Oxide Synthase ◽

Partial Loss ◽

Interesting Compound ◽

Substrate Binding Sites ◽

Oxide Synthase

Selective inhibitors of neuronal nitric oxide synthase (nNOS), which are devoid of any effect on the endothelial isoform (eNOS), may be required for the treatment of some neurological disorders. In our search for novel nNOS inhibitors, we recently described some 1-[(Aryloxy)ethyl]-1 H-imidazoles as interesting molecules for their selectivity for nNOS against eNOS. This work reports a new series of 1-[(Aryloxy)alkyl]-1 H-imidazoles in which a longer methylene chain is present between the imidazole and the phenol part of molecule. Some of these molecules were found to be more potent nNOS inhibitors than the parent ethylenic compounds, although this increase in potency resulted in a partial loss of selectivity. The most interesting compound was investigated to establish its mechanism of action and was found to interact with the tetrahydrobiopterin (BH4) binding site of nNOS, without interference with any other cofactors or substrate binding sites.

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How Running Give Us a High Expectations to Overcome Neurological Disorders

10.47363/jnrrr/2021(3)144 ◽

2021 ◽

pp. 1-6

Author(s):

Ven Sumedh Thero ◽

◽

Kataria HB ◽

Aditya Suman ◽

◽

...

Keyword(s):

Binding Sites ◽

Neurological Disorders ◽

General Feature ◽

Regular Exercise ◽

Step Frequency ◽

Running Speed ◽

Physically Active ◽

High Expectations ◽

Transfemoral Amputees ◽

Bouncing Gaits

Whether chasing down dinner, pushing a stroller up a hill or running errands for a neighbor, we can take joy in the effort. And the more physically active you are, the more rewarding these experiences become. One of the ways that regular exercise changes your brain is by increasing the density of binding sites for endocannabinoids. Spring-like leg behavior is a general feature of mammalian bouncing gaits, such as running and hopping. Although increases in step frequency at a given running speed are known to increase the stiffness of the leg spring (kleg) in non-amputees, little is known about stiffness regulation in unilateral transfemoral amputees. Thus Consequently, the unilateral transfemoral amputees attained the desired step frequency in the unaffected limb, but were unable to match the three highest step frequencies using their affected limbs

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The 3.2Å resolution structure of human mTORC2

10.1101/2020.04.10.029835 ◽

2020 ◽

Cited By ~ 3

Author(s):

Alain Scaiola ◽

Francesca Mangia ◽

Stefan Imseng ◽

Daniel Boehringer ◽

Karolin Berneiser ◽

...

Keyword(s):

Binding Sites ◽

Neurological Disorders ◽

Mammalian Target Of Rapamycin ◽

Nucleotide Binding ◽

Ternary Interactions ◽

Firm Basis ◽

Biochemical Analyses ◽

Specific Inhibitors ◽

Specific Nucleotide ◽

Resolution Structure

AbstractThe protein kinase mammalian target of rapamycin (mTOR) is the central regulator of cell growth. Aberrant mTOR signaling is linked to cancer, diabetes and neurological disorders. mTOR exerts its functions in two distinct multiprotein complexes, mTORC1 and mTORC2. Here we report a 3.2 Å resolution cryo-EM reconstruction of mTORC2. It reveals entangled folds of the defining Rictor and the substrate-binding SIN1 subunits, identifies the C-terminal domain of Rictor as the source of the rapamycin insensitivity of mTORC2, and resolves mechanisms for mTORC2 regulation by complex destabilization. Two novel small molecule binding sites are visualized, an inositol hexakisphosphate (InsP6) pocket in mTOR and an mTORC2-specific nucleotide binding site in Rictor which also forms a zinc finger. Structural and biochemical analyses suggest that InsP6 and nucleotide binding do not control mTORC2 activity directly but rather have roles in folding or ternary interactions. These insights provide a firm basis for studying mTORC2 signaling and for developing mTORC2-specific inhibitors.

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Investigation of bovine serum albumin aggregation upon exposure to silver(i) and copper(ii) metal ions using Zetasizer

Open Chemistry ◽

10.1515/chem-2021-0089 ◽

2021 ◽

Vol 19 (1) ◽

pp. 987-997

Author(s):

Hassan A. Alhazmi ◽

Waquar Ahsan ◽

Angum M. M. Ibrahim ◽

Rawan Ali Yahya Khubrani ◽

Zainab Ali Abdullah Haddadi ◽

...

Keyword(s):

Bovine Serum Albumin ◽

Zeta Potential ◽

Serum Albumin ◽

Metal Ions ◽

Binding Sites ◽

Neurological Disorders ◽

Bovine Serum ◽

Protein Molecule ◽

Protein Aggregate ◽

Bsa Aggregation

Abstract Depending upon the metal coordination capacity and the binding sites of proteins, interaction between metal and proteins leads to a number of changes in the protein molecule which may include the change in conformation, unfolding, overall charge, and aggregation in some cases. In this study, Cu(ii) and Ag(i) metal ions were selected to investigate aggregation of bovine serum albumin (BSA) molecule upon interaction by measuring the size and charge of the aggregates using nano-Zetasizer instrument. Two concentrations of metal ions were made to interact with a specific concentration of BSA and the size and zeta potential of BSA aggregates were measured from 0 min upto 18 h. The Cu(ii) and Ag(i) metal ions showed almost similar behavior in inducing the BSA aggregation and the intensity of peak corresponding to the normal-sized protein decreased with time, whereas the peak corresponding to the protein aggregate increased. However, the effect on zeta potential of the aggregates was observed to be different with both metal ions. The aggregation of protein due to interaction of different metal ions is important to study as it gives insight to the pathogenesis of many neurological disorders and would result in developing effective ways to limit their exposure.

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Ligand recognition and gating mechanism through three ligand-binding sites of human TRPM2 channel

eLife ◽

10.7554/elife.50175 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 13

Author(s):

Yihe Huang ◽

Becca Roth ◽

Wei Lü ◽

Juan Du

Keyword(s):

Ligand Binding ◽

Binding Sites ◽

Neurological Disorders ◽

Transmembrane Domain ◽

Structural Rearrangements ◽

Channel Activation ◽

Physiological Processes ◽

Gating Mechanism ◽

Trpm2 Channel ◽

Ligand Binding Sites

TRPM2 is critically involved in diverse physiological processes including core temperature sensing, apoptosis, and immune response. TRPM2’s activation by Ca2+ and ADP ribose (ADPR), an NAD+-metabolite produced under oxidative stress and neurodegenerative conditions, suggests a role in neurological disorders. We provide a central concept between triple-site ligand binding and the channel gating of human TRPM2. We show consecutive structural rearrangements and channel activation of TRPM2 induced by binding of ADPR in two indispensable locations, and the binding of Ca2+ in the transmembrane domain. The 8-Br-cADPR—an antagonist of cADPR—binds only to the MHR1/2 domain and inhibits TRPM2 by stabilizing the channel in an apo-like conformation. We conclude that MHR1/2 acts as a orthostatic ligand-binding site for TRPM2. The NUDT9-H domain binds to a second ADPR to assist channel activation in vertebrates, but not necessary in invertebrates. Our work provides insights into the gating mechanism of human TRPM2 and its pharmacology.

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Conformation of Ribosomes from Escherichia Coli

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051062 ◽

1974 ◽

Vol 32 ◽

pp. 210-211

Author(s):

M. Boublik ◽

W. Hellmann ◽

F. Jenkins

Keyword(s):

Binding Sites ◽

Ribosomal Proteins ◽

Fluorescent Dyes ◽

Protein Biosynthesis ◽

Three Dimensional ◽

Spatial Arrangement ◽

Dimensional Structure ◽

Complete Understanding ◽

And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

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Electron Probe Analysis of Muscle

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100054583 ◽

1982 ◽

Vol 40 ◽

pp. 398-401

Author(s):

A. V. Somlyo ◽

H. Shuman ◽

A. P. Somlyo

Keyword(s):

Skeletal Muscle ◽

Smooth Muscle ◽

Sarcoplasmic Reticulum ◽

Resting State ◽

Binding Sites ◽

Electron Probe ◽

Frog Skeletal Muscle ◽

Electron Probe Analysis ◽

Probe Analysis

Electron probe analysis of frozen dried cryosections of frog skeletal muscle, rabbit vascular smooth muscle and of isolated, hyperpermeab1 e rabbit cardiac myocytes has been used to determine the composition of the cytoplasm and organelles in the resting state as well as during contraction. The concentration of elements within the organelles reflects the permeabilities of the organelle membranes to the cytoplasmic ions as well as binding sites. The measurements of [Ca] in the sarcoplasmic reticulum (SR) and mitochondria at rest and during contraction, have direct bearing on their role as release and/or storage sites for Ca in situ.

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Sites of Insulin Action Using Ferritin Labeling

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100066759 ◽

1971 ◽

Vol 29 ◽

pp. 540-541

Author(s):

Burton B. Silver ◽

Ronald S. Nelson

Keyword(s):

Electron Microscopy ◽

Binding Sites ◽

Anterior Pituitary ◽

Insulin Action ◽

Diabetic Rats ◽

Insulin Antibody ◽

Fat Pad ◽

Target Organs ◽

Uranium Salts ◽

Sugar Levels

Some investigators feel that insulin does not enter cells but exerts its influence in some manner on the cell surface. Ferritin labeling of insulin and insulin antibody was used to determine if binding sites of insulin to specific target organs could be seen with electron microscopy.Alloxanized rats were considered diabetic if blood sugar levels were in excess of 300 mg %. Test reagents included ferritin, ferritin labeled insulin, and ferritin labeled insulin antibody. Target organs examined were were diaphragm, kidney, gastrocnemius, fat pad, liver and anterior pituitary. Reagents were administered through the left common carotid. Survival time was at least one hour in test animals. Tissue incubation studies were also done in normal as well as diabetic rats. Specimens were fixed in gluteraldehyde and osmium followed by staining with lead and uranium salts. Some tissues were not stained.

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