Search results for "kyy"
showing 10 items of 296 documents
Molecular Mechanism of ATP Hydrolysis in an ABC Transporter
2018
Hydrolysis of nucleoside triphosphate (NTP) plays a key role for the function of many biomolecular systems. However, the chemistry of the catalytic reaction in terms of an atomic-level understanding of the structural, dynamic, and free energy changes associated with it often remains unknown. Here, we report the molecular mechanism of adenosine triphosphate (ATP) hydrolysis in the ATP-binding cassette (ABC) transporter BtuCD-F. Free energy profiles obtained from hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations show that the hydrolysis reaction proceeds in a stepwise manner. First, nucleophilic attack of an activated lytic water molecule at the ATP γ-…
Phosphorylated immunoreceptor tyrosine-based activation motifs and integrin cytoplasmic domains activate spleen tyrosine kinase via distinct mechanis…
2018
Spleen tyrosine kinase (Syk) is involved in cellular adhesion and also in the activation and development of hematopoietic cells. Syk activation induced by genomic rearrangement has been linked to certain T-cell lymphomas, and Syk inhibitors have been shown to prolong survival of patients with B-cell lineage malignancies. Syk is activated either by its interaction with a double-phosphorylated immunoreceptor tyrosine-based activation motif (pITAM), which induces rearrangements in the Syk structure, or by the phosphorylation of specific tyrosine residues. In addition to its immunoreceptor function, Syk is activated downstream of integrin pathways, and integrins bind to the same region in Syk a…
Structural and functional insights into lysostaphin–substrate interaction
2018
Lysostaphin from Staphylococcus simulans and its family enzymes rapidly acquire prominence as the next generation agents in treatment of S. aureus infections. The specificity of lysostaphin is promoted by its C-terminal cell wall targeting domain selectivity towards pentaglycine bridges in S. aureus cell wall. Scission of these cross-links is carried out by its N-terminal catalytic domain, a zinc-dependent endopeptidase. Understanding the determinants affecting the efficiency of catalysis and strength and specificity of interactions lies at the heart of all lysostaphin family enzyme applications. To this end, we have used NMR, SAXS and molecular dynamics simulations to characterize lysostap…
A Perspective : Active Role of Lipids in Neurotransmitter Dynamics
2019
AbstractSynaptic neurotransmission is generally considered as a function of membrane-embedded receptors and ion channels in response to the neurotransmitter (NT) release and binding. This perspective aims to widen the protein-centric view by including another vital component—the synaptic membrane—in the discussion. A vast set of atomistic molecular dynamics simulations and biophysical experiments indicate that NTs are divided into membrane-binding and membrane-nonbinding categories. The binary choice takes place at the water-membrane interface and follows closely the positioning of the receptors’ binding sites in relation to the membrane. Accordingly, when a lipophilic NT is on route to a m…
Kultapinnan S(CH2)xN3-adsorbaattien laskennallinen värähdysdynamiikka ja 2DIR-spektroskopia molekyylidynamiikkamenetelmin
2018
Tehtiin MD-simulaatiot kultapinnan siltapaikkoihin kahdella eri peitolla (1/3 ja 1/4) yksikerrokseksi asetetuille pitkä- ja lyhytketjuisille S(CH2)xN3-adsorbaateille (x = 2, 11). Kukin systeemi simuloitiin sekä tyhjiössä että vesiympäristössä. Simulaatioista määritettiin atsidiryhmien FFCF:t ja CLS:t odotusaikavälille t2 ∈ [0, 200] ps. Näihin sovitettiin multieksponentiaaliset funktiot ja havaittiin FFCF:n hitaiden komponenttien vastaavan CLS-komponentteja. Lisäksi tarkasteltiin mallia, joka esittää CLS:n ja FFCF:n välille suoraviivaisen yhteyden ja mahdollistaa Lorentzin ja Gaussin leveyksien määrittämisen. Malli todettiin hyvin toimivaksi simulaatioista saatujen tulosten tapauksessa. MD s…
Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome
2019
The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that …
Structure and function of human triceps surae muscle and tendon in aging
2016
Resistance training status modifies inflammatory response to explosive and hypertrophic resistance exercise bouts.
2017
The purpose of the present study was to examine the immediate and prolonged immune response in circulating cytokine and adipocytokine concentrations after two different resistance exercise bouts: hypertrophic (HYP1, 5 × 10, 80% of 1RM) and maximal explosive (POW1, 10 × 5, 60% of 1RM) resistance exercise bouts and how 12 weeks of resistance training (RT) modifies these responses (HYP2, POW2). Eight men completed the study. RE-induced interleukin-6 (IL-6), interleukin-1β (IL-1β), interleukin-1 receptor antagonist (IL-1ra), monocyte-chemoattractant protein-1 (MCP-1), leptin, resistin, and adiponectin were measured before (PRE) and immediately (POST0), 24 (POST24) and 48 (POST48) hours after RE…
Supramolecular systems based on gold(I) derivatives : molecular recognition of L-glutamine and polyQ
2017
L-glutamiinin ja polyglutamiinin molekyylintunnistuksessa käytettyjen uusien organometallikompleksien mielenkiintoiset luminesoivat ominaisuudet ovat peräisin 4-etynyylianiliiniligandista ja fosfaaniyksiköstä sekä molekyylien välisistä Au⋯Au vuorovaikutuksista. Heikkojen intermolekulaaristen vuorovaikutusten on havaittu johtavan kuitu- ja pallomaisten muotojen morfologisiin muutoksiin vierasmolekyylien läsnä ollessa. Muodostunut isäntä-vieras -kompleksi tuottaa erilaisen emission vierasmolekyylistä riippuen. Lisäksi [Au(4-etynyylianiliini)(PTA)]:n itsejärjestäytymisen termodynaamisia funktioita tutkittiin eri pitoisuuksissa ja lämpötiloissa NMR mittausten avulla. Nämä lineaariset kulta(I) -…
Age-related muscle activation profiles and joint stiffness regulation in repetitive hopping
2011
It is well documented that increasing effort during exercise is characterized by an increase in electromyographic activity of the relevant muscles. How aging influences this relationship is a matter of great interest. In the present study, nine young and 24 elderly subjects did repetitive hopping with maximal effort as well as with 50%, 65%, 75% and 90% intensities. During hopping joint kinematics were measured together with electromyographic activity (EMG) from the soleus, gastrocnemius medialis, gastrocnemius lateralis and tibialis anterior muscles. The results showed that agonist activation increased in both age groups with increasing intensity. The highest jumping efficiency (EMG ratio …