Search results for "steric"
showing 10 items of 476 documents
The effect of β-methylation on the conformation of α, β-dehydrophenylalanine: a DFT study
2009
Dehydroamino acids are non-coded amino acids that offer unique conformational properties. Dehydrophenylalanine (ΔPhe) is most commonly used to modify bioactive peptides to constrain the topography of the phenyl ring in the side chain, which commonly serves as a pharmacophore. The Ramachandran maps (in the gas phase and in CHCl3 mimicking environments) of ΔPhe analogues with methyl groups at the β position of the side chain as well as at the C-terminal amide were calculated using the B3LYP/6-31 + G** method. Unexpectedly, β-methylation alone results in an increase of conformational freedom of the affected ΔPhe residue. However, further modification by introducing an additional methyl group a…
Furosemide interactions with brain GABAA receptors
1997
1. The loop diuretic furosemide is known to antagonize the function of gamma-aminobutyric acid type A (GABAA) receptors. The purpose of the present study was to examine the direct interaction of furosemide with the GABAA receptors by autoradiography and ligand binding studies with native rat and human receptors and with recombinant receptors composed of rat subunits. 2. Autoradiography with [35S]-t-butylbicyclophosphorothionate ([35S]-TBPS) as a ligand indicated that furosemide (0.1-1 mM) reversed the 5 microM GABA-induced inhibition of binding only in the cerebellar granule cell layer of rat brain sections. In all other regions studied, notably also in the hippocampal and thalamic areas, f…
The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption
2015
Fibrinogen is a serum multi-chain protein which, when activated, aggregates to form fibrin, one of the main components of a blood clot. Fibrinolysis controls blood clot dissolution through the action of the enzyme plasmin, which cleaves fibrin at specific locations. Although the main biochemical factors involved in fibrin formation and lysis have been identified, a clear mechanistic picture of how these processes take place is not available yet. This picture would be instrumental, for example, for the design of improved thrombolytic or anti-haemorrhagic strategies, as well as, materials with improved biocompatibility. Here, we present extensive molecular dynamics simulations of fibrinogen w…
A new automated plunger for cryopreparation of proteins in defined - even oxygen free - atmospheres
2009
We study the structure and function of hemocyanins. They are giant extracellular oxygen carriers in the hemolymph of many molluscs and arthropods. Since some of these blue, copper-containing proteins show the highest cooperativity in nature (h = 10), one of our goals is to understand the chemomechanical interaction between the different substructures during allosteric oxygen binding.
Highly regio- and stereoselective iodocyclization of chiral 3-alkoxycarbonyl-4-propenyl-2,2-dimethyl-1,3-oxazolidines: a computational investigation
1999
The iodocyclization of allylic carbamates 3a and 3b proceeded with high regio- and stereoselection to give 2-oxobicyclo[4.3.0]nonane 5a as the major product. Both the regio- and diastereoselection of the reaction were investigated with the help of molecular mechanics and quantomechanical calculations. The energetic difference between the competing transition states TS-5a and TS-5b is in good agreement with the experimental results and from the calculated transition structures it appears that steric factors direct the discrimination.
Proline-Based Allosteric Inhibitors of Zika and Dengue Virus NS2B/NS3 Proteases
2019
The NS2B/NS3 serine proteases of the Zika and Dengue flaviviruses are attractive targets for the development of antiviral drugs. We report the synthesis and evaluation of a new, proline-based compound class that displays allosteric inhibition of both proteases. The structural features relevant for protease binding and inhibition were determined to establish them as new lead compounds for flaviviral inhibitors. Based on our structure-activity relationship studies, the molecules were further optimized, leading to inhibitors with submicromolar IC50 values and improved lipophilic ligand efficiency. The allosteric binding site in the proteases was probed using mutagenesis and covalent modificati…
SAR of novel benzothiazoles targeting an allosteric pocket of DENV and ZIKV NS2B/NS3 proteases
2021
In recent years, dengue virus (DENV) and Zika virus (ZIKV), both mosquito-borne members of the Flaviviridae family, have emerged as intercontinental health issues since their vectors have spread from their tropical origins to temperate climate zones due to climate change and increasing globalization. DENV and ZIKV are positive-sense, single-stranded RNA viruses, whose genomes consist of three structural (capsid, membrane precursor, envelope) and seven non-structural (NS) proteins, all of which are initially expressed as a single precursor polyprotein. For virus maturation, the polyprotein processing is accomplished by host proteases and the viral NS2B/NS3 protease complex, whose inhibitors …
The molecular heterogeneity of hemocyanin: Structural and functional properties of the 4×6-meric protein of Upogebia pusilla (Crustacea)
2006
The structural properties of the hemocyanin isolated from the Mediterranean mud shrimp, Upogebia pusilla (Decapoda: Thalassinidea), were investigated. Our intent was to make use of the U. pusilla case to perform a structural comparison between crustacean and chelicerate 4×6-meric hemocyanins. The thalassinidean hemocyanin appears similar in size but different in structural organization compared to the chelicerate 4×6-mer. Ultracentrifuge analyses on the purified protein revealed a sedimentation coefficient of 39S, typical of 4×6 hemocyanins. Electron micrographs are in agreement with a model in which four 2×6-meric building blocks are arranged in a tetrahedron-like quaternary structure and …
Valence Topological Charge-Transfer Indices for Dipole Moments
2003
Valence topological charge-transfer (CT) indices are applied to the calculation of dipole moments. The dipole moments calculated by algebraic and vector semisums of the CT indices are defined. The combination of the CT indices allows the estimation of the dipole moments. The model is generalized for molecules with heteroatoms. The ability of the indices for the description of the molecular charge distribution is established by comparing them with the dipole moment of the valence-isoelectronic series of benzene and styrene. Two CT indices, μ v e c (vector semisum of vertex-pair dipole moments) and μ V v e c (valence μ v e c ) are proposed. μ v e c and μ V v e c are important for the predicti…
Subunits composition and allosteric control in Carcinus aestuarii hemocyanin
1998
Carcinus aestuarii hemocyanin (Hc) exists in two aggregation forms at pH 7.5 and 20 mM Ca2+: 24S accounting for 90% of total hemocyanin and 16S accounting for 10%. Removal of metal cations by EDTA at neutral pH causes the complete dissociation of 24S hemocyanin into two different 16S. At pH 9.2, 24S hemocyanin dissociates into a pH stable 16S and a 5S component. The 5S component consists of three monomeric fractions named CaeSS1 (10%), CaeSS2 (50%) and CaeSS3 (40%); the latter fraction consisting of two isoforms. The fractions CaeSS1, CaeSS2 and CaeSS3 have been studied as far as their reassociation properties to form hexamers are concerned. We investigated the oxygen-binding properties of …