Ligands are hydrophobic. Medical search. Frequent questions

A crevice of hydrophobic residues linking the polar edge of KAR1 and the helical domain insert suggests that KAI2-KAR1 creates a contiguous interface for binding signaling partners in a ligand-dependent manner. (nih.gov)
Full names of ligands, sites, non-standard residues. (powerandbulk.com)
The human nuclear pregnane X receptor has a hydrophobic ligand-binding cavity with a small number of polar residues that are critical for precise pharmacologic activation. (the-scientist.com)
They found that hPXR has a hydrophobic ligand-binding cavity that contains a small number of polar residues, permitting SR12813 to bind in three distinct orientations. (the-scientist.com)
Similar to endogenous ligands, HT1-0 needs hydrophobic and basic residues to bind hMC4R. (iric.ca)
Docking studies with these compounds against cyclooxygenase-2 receptor(PDB 1D: 1PXX) indicated that they exhibit specific interactions with key residues located in the site of the COX2 structure, which corroborates the hypothesis that these molecules are potential ligands of COX2. (ias.ac.in)
In solution, compstatin forms a β-turn at residues Gln-5-Gly-8 with the disulfide bridge Cys-2-Cys-12, residues Ile-1-Val-4 and Thr-13 forming a hydrophobic cluster (PCT Pub. (justia.com)
Moreover, hydrophobic and hydrophilic residues in the WFDC and Kunitz domains allow plasma membrane anchoring, orienting the EPPIN binding pocket to the solvent. (bvsalud.org)
Targeting EPPIN's essential residues for its biomolecular interactions may improve the rational design of EPPIN ligands as spermiostatic compounds. (bvsalud.org)
We also ran QM/MM simulations on casein-kinase 2 (CK2), where the ligand and a few surrounding residues were treated at the QM level, and the rest of the system at the MM level. (lu.se)

In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. (wikipedia.org)
In DNA-ligand binding studies, the ligand can be a small molecule, ion, or protein which binds to the DNA double helix. (wikipedia.org)
Ligand binding to a receptor protein alters the conformation by affecting the three-dimensional shape orientation. (wikipedia.org)
We probe the open conformation of human Hsp90α for druggable sites that overlap with these allosteric control elements, and identify three putative natural compound allosteric modulators: Cephalostatin 17, 20(29)-Lupene-3β-isoferulate and 3′-Bromorubrolide F. We assess the allosteric potential of these ligands by examining their effect on the conformational dynamics of the protein. (nature.com)
Furthermore, in the caprate complex, the ligand binds to the protein cavity in two orientations with equal occupancy. (rcsb.org)
During evolution,this protein diversified into numerous families with low sequencesimilarity but with a common fold that succeeded as a versatile scaffoldfor binding of bulky ligands. (embl.de)
The pheromone receptors have seven hydrophobic segments and are coupled to a heterotrimeric G protein. (berkeley.edu)
The encoded protein has been implicated in numerous functions including anti-inflammation, inhibition of phospholipase A2 and the sequestering of hydrophobic ligands. (antibodies-online.com)
Apomyoglobin (apoMb), a model protein in biochemistry , exhibits a strong propensity to bind various ligands, which makes it a good candidate as a carrier of bioactive hydrophobic drugs. (cea.fr)
High pressure (HP) is a potent tool for studying protein stability, revealing the specific role of hydrophobic cavities in unfolding. (cea.fr)
A synthetic, specially- designed oligonucleotide with the ability to recognize and bind a protein ligand molecule or molecules with high affinity and specificity. (genomicglossaries.com)
A dry ligand-binding cavity in a solvated protein. (lu.se)
In drug discovery, it is of utmost importance to accurately calculate the free energies of binding ligands to various protein targets, such as enzymes and receptors. (lu.se)
We mostly used molecular mechanics (MM) in order to model the protein-ligand interactions, which is more approximate than quantum-mechanical (QM) methods, but necessary to reduce the computational cost when doing calculations on protein-ligand systems, which often contain tens of thousand of atoms. (lu.se)
In one study of a large set of protein-ligand complexes, we tried to improve the free energies of binding by using MD simulations with QM-derived charges, which sometimes led to improved results, but not always. (lu.se)
This entropy largely stems from the fluctuation of the protein and ligand. (lu.se)
Additionally, we compared how MD and grand-canonical Monte Carlo (GCMC) can be used to assess dynamics and thermodynamics of protein-ligand binding for both buried and solvent-exposed binding sites. (lu.se)
Webb, J. H., Villoutreix, B. O., Dahlbäck, B. and Blom A. M. (2001) Localization of a hydrophobic binding site for protein S on the b-chain of C4BP. (lu.se)

A ligand that can bind to and alter the function of the receptor that triggers a physiological response is called a receptor agonist. (wikipedia.org)
Ligands that bind to a receptor but fail to activate the physiological response are receptor antagonists. (wikipedia.org)
In the example shown to the right, two different ligands bind to the same receptor binding site. (wikipedia.org)
CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. (nih.gov)
Active targeting involves use of targeting ligands such as antibodies, peptides (e.g cell penetrating peptides) which bind specifically to receptors, epitopes over-expressed on target site. (trialx.com)
The 11th and 12th EGF-like repeats, that bind ligands such as Jagged and Delta-like families in humans, correspond to aa 412-488 in mouse Notch-1 (6). (rndsystems.com)

The solvent provides a chemical environment for the ligand and receptor to adapt, and thus accept or reject each other as partners. (wikipedia.org)
In general, high-affinity ligand binding results from greater attractive forces between the ligand and its receptor while low-affinity ligand binding involves less attractive force. (wikipedia.org)
the residence time (lifetime of the receptor-ligand complex) does not correlate. (wikipedia.org)
High-affinity binding of ligands to receptors is often physiologically important when some of the binding energy can be used to cause a conformational change in the receptor, resulting in altered behavior for example of an associated ion channel or enzyme. (wikipedia.org)
Electrostatic and hydrophobic interactions between the peptide and the LBD stabilize the active receptor conformation. (rcsb.org)
The Aryl hydrocarbon receptor (AHR) is a member of the basic helix-loop-helix-PER- ARNT-SIM (bHLH-PAS) subgroup of the bHLH superfamily of transcription factors and is the only member of this family known to be activated by ligands. (biolegend.com)
The Notch-1 receptor undergoes post-translational furin-type proteolytic cleavage, generating a heterodimer through the interaction of a hydrophobic area C-terminal to the LNR on the extracellular region with the transmembrane/cytoplasmic portion (8, 9). (rndsystems.com)
RET consists of 3 domains, including a cysteine-rich extracellular receptor domain, a hydrophobic transmembrane domain, and an intracellular tyrosine kinase catalytic domain. (medscape.com)
These ligands-glial cell line-derived neurotrophic factor (GDNF), neurturin, persephin, and artemin-also interact with one of four coreceptors in the GDNF-family receptor-alpha family. (medscape.com)

Hydrophobic interactions drive the binding of nonpolar ligands to the oily pockets of proteins and supramolecular species in aqueous solution. (aiche.org)
Docking results showed interaction between the proteins individually into selected ligands, except for gelsemine and vitamin E no interactions were shown. (ijpsonline.com)
Furthermore, vitamin C showed hydrophobic interactions with both proteins, two bonds with Arg119, Glu120 of HA, and one bond with Arg74 of NA. (ijpsonline.com)
These specialized signalling filopodia transmit signal proteins between communicating cells and allow a high degree of control of propagation speed, direction and concentration of the transmitted ligand. (exeter.ac.uk)

We combined synchrotron small angle X-ray scattering, X-ray fluorescence and extended X-ray absorption fine structure spectroscopy to probe the structure of chemically synthesized CoPt 3 nanoparticles (NPs) after ligand removal via the commonly accepted solvent/nonsolvent approach. (osti.gov)
Also, we demonstrated that drastic compositional and structural transformation of water transferred CoPt 3 NPs was rather a result of extensive removal of native ligands via a solvent/nonsolvent approach than leaching of cobalt atoms in aqueous media. (osti.gov)

In order to gain a better understanding of the structural basis of the non-specific binding of hydrophobic ligands by nsLTPs and to investigate the plasticity of the fatty acid binding cavity in nsLTPs, seven high-resolution (between 1.3 A and 1.9 A) crystal structures have been determined. (rcsb.org)
The volume of the hydrophobic cavity in the nsLTP from maize shows some variation depending on the size of the bound ligands. (rcsb.org)
The structural plasticity of the ligand binding cavity and the predominant involvement of non-specific van der Waals interactions with the hydrophobic tail of the ligands provide a structural explanation for the non-specificity of maize nsLTP. (rcsb.org)
The hydrophobic cavity accommodates various ligands from C10 to C18. (rcsb.org)

The remaining five matrices comprised various synthetic low molecular weight ligands immobilised on hydrophilic porous supports and these included: MEP HyperCel, MabSorbent AlP, MabSorbent A2P, FastMabsA and Kaptiv-GY. (dtu.dk)
The analysis of the docking results, which takes into account the hydrophilic and hydrophobic interactions betweenthe ligands and the target, identified N-(4-bromophenyl)-4,5-bis(4 hydroxyphenyl)thiophene-2-carboxamide (6k) having high binding free energy of −11.67 kcal/mole (comparable with standard diclofenac sodium) and the best docking score, indicating effective binding of the compound 6k at the active site. (ias.ac.in)

The interaction of ligands with their binding sites can be characterized in terms of a binding affinity. (wikipedia.org)
Elongation of O-linked fucose chains by Fringe family members at a site within this region can inhibit the interaction of Notch with Jagged ligands, thereby promoting Delta-like ligand interactions (7). (rndsystems.com)

High-affinity ligand binding implies that a relatively low concentration of a ligand is adequate to maximally occupy a ligand-binding site and trigger a physiological response. (wikipedia.org)
Low-affinity binding (high Ki level) implies that a relatively high concentration of a ligand is required before the binding site is maximally occupied and the maximum physiological response to the ligand is achieved. (wikipedia.org)
Binding affinity is most commonly determined using a radiolabeled ligand, known as a tagged ligand. (wikipedia.org)
There is only one ligand binding pocket in the AHR (in the Per-ARNT-Sim-B domain), and the affinity of the best characterized high affinity ligand, TCDD (2,3,7,8-tetrachlorodibenzo-pdioxin), depends on only a few amino acids in that pocket. (biolegend.com)
Three of these materials featured rProtein A (rProtein A Sepharose Fast Flow, Mabselect, Prosep rProtein A) as the affinity ligand, and differed from one another primarily with respect to the underlying base matrix. (dtu.dk)
Here, we described a cone snail toxin, N-CTX-Ltg1a, with a nanomolar affinity for hMC4R but unrelated to any known toxins or melanocortin ligands. (iric.ca)

Liposomes can carry both hydrophobic and hydrophillic molecules inside them. (trialx.com)

In contrast to the definition of ligand in metalorganic and inorganic chemistry, in biochemistry it is ambiguous whether the ligand generally binds at a metal site, as is the case in hemoglobin. (wikipedia.org)

nevertheless, the 25-hydroxyl group at the end of the chain occupies the same position as that of the natural ligand, and the hydrogen bonds with histidines 301 and 393 are maintained. (rcsb.org)
ACD/Column Selector evaluates columns based on parameters such as ligand density, hydrophobic sensitivity, shape selectivity, hydrogen bonding capacity, and total and acidic ion-exchange capacity. (webwire.com)
Both of the models consisted of six features (hydrogen bond acceptors, hydrogen bond donor and hydrophobic feature) besides the exclusion volumes. (helsinki.fi)

Ligand affinities can also be measured directly as a dissociation constant (Kd) using methods such as fluorescence quenching, isothermal titration calorimetry or surface plasmon resonance. (wikipedia.org)
ligands, based on the measured ligand binding dissociation constant (Kd). (duke.edu)

Those ligands can be endogenous, naturally occurring, and/or anthropogenic. (biolegend.com)
For decades, synthetic ligands have been derived from MC4R endogenous agonists and antagonists, such as setmelanotide used to treat rare forms of genetic obesity. (iric.ca)

Receptors of this type are ubiquitous and transduce binding of a wide variety of extracellular ligands (peptide hormones, neurotransmitters and other bioactive compounds) into a physiological signal. (berkeley.edu)
The extracellular domain interacts with one of four ligands identified to date. (medscape.com)

2002). Mutational studies showed that the polar 3-turn and the hydrophobic cluster are essential for the inhibitory activity of compstatin (Furlong et al. (justia.com)

Ligand affinities are most often measured indirectly as an IC50 value from a competition binding experiment where the concentration of a ligand required to displace 50% of a fixed concentration of reference ligand is determined. (wikipedia.org)

All lipids are hydrophobic and mostly insoluble in blood, so they require transport within lipoproteins. (msdmanuals.com)

Hydrophobic aromatic compound. (biolegend.com)

Measurably irreversible covalent bonding between a ligand and target molecule is atypical in biological systems. (wikipedia.org)

Although O2 and NO are readily dissolved in membrane lipids, they migrate to the reduction site exclusively via a pre-formed hydrophobic tunnel. (illinois.edu)
Comparison of ligand bindingactivities of Bet v 1-like superfamily members revealed that theirfunctions were related to binding and metabolism of large, hydrophobiccompounds such as lipids, hormones, and antibiotics. (embl.de)

These chemical species often act as substrates of enzymes and/or as ligands modulating biochemical cascades, so elucidating their delivery and transport is imminent towards understanding cellular functions. (illinois.edu)
The difference between 11β-HSD1 and 2 ligand binding sites is unknown, which complicates the search of selective inhibitors to both of the enzymes. (helsinki.fi)
The difference between the enzymes could not be identified by visual inspections Therefore, seven compounds, of which six are 11β-HSD2 -selective, were docked both to 11β-HSD1 and 11β-HSD2 ligand binding sites using the program GOLD. (helsinki.fi)

The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure. (wikipedia.org)
Molecular dynamics (MD) simulations showed a preferred interacting crystallographic plane for both crystalline allomorphs that exposes the CH groups (100 and 010) and is therefore considered hydrophobic. (cea.fr)

The stability of its hydrophobic pocket determines its potential as a carrier of bioactive compounds. (cea.fr)

The ligand substitution reactions of hydrophobic vitamin B12 derivatives. (scielo.org.za)
The hydrophobic cobyrinic acid heptapropyl ester corrinoids XCbs-Pr (axial ligandX = CN - ,SO 3 2- ,CH 3 - and CH 3 CH 2 - ) have been prepared from vitamin B 12 by hydrolysis of the amide side chains and their conversion to propyl esters. (scielo.org.za)

However, the detailed structural basis of the non-specific binding of hydrophobic ligands by nsLTPs is still poorly understood. (rcsb.org)

Thermal signature of hydrophobic hydration dynamics. (lu.se)

In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. (wikipedia.org)

Upon ligand binding, additional sequential proteolysis by TNF-converting enzyme (ADAM17) and the presenilin-dependent gamma -secretase results in the release of the Notch intracellular domain (NICD) which translocates into the nucleus, activating transcription of Notch-responsive genes (10). (rndsystems.com)
Please, note that similar approaches have been suggested earliear, but primarily for ligand-binding studies, whereas our approach is directed towards studies of enzyme active sites, for which the QM system is covalently bound to the MM system. (lu.se)

Clinically approved AR antagonists compete with dihydrotestosterone (DHT) for binding to the ligand-binding domain (LBD) of AR, and patients eventually develop resistance to these treatments. (aacrjournals.org)

We find evidence for the selective allosteric activation and inhibition of Hsp90's conformational transition toward the closed state in response to ligand binding and shed valuable insight to further the understanding of allosteric drug design and Hsp90's complex allosteric mechanism of action. (nature.com)

These tasks were approached with computational methods: homology modeling, docking, ligand-based pharmacophore modeling and virtual screening. (helsinki.fi)
Here, we combined computational approaches to uncover key aspects underlying EPPIN binding to SEMG1 and small organic ligands. (bvsalud.org)

Anhydrous sodium propionate is a polymeric structure, featuring trigonal prismatic Na + centers bonded to six oxygen ligands provided by the carboxylates. (wikipedia.org)
A layered structure is observed, with the hydrophobic ethyl groups projecting into the layered galleries. (wikipedia.org)
For the Fe(II) carbene complexes investigated, small changes in the ligand structure influenced both what excited state (charge-transfer or metal-centred) that was mainly populated and the lifetime of the state. (lu.se)

For the Fe(III) carbene complexes investigated, there was instead one dominating charge-transfer excited state that was rather unaffected by changes to the ligand. (lu.se)

Prior to docking simulations using AutoDock, the drug likeness properties of the ligands were screened using in silico techniques. (ijpsonline.com)

Binding of the 2-carbon-modified analogues does not change the positions of the amino acids in the ligand binding site and has no effect on the interactions in the coactivator binding pocket. (rcsb.org)

The karrikin-1 (KAR1) ligand sits in the opening to the active site abutting a helical domain insert but distal from the canonical catalytic triad (Ser95-His246-Asp217) of α/β-hydrolases, consistent with the lack of detectable hydrolytic activity by purified KAI2. (nih.gov)
The CD ring of the superpotent analogue, 2MD, is tilted within the binding site relative to the other ligands in this study and to (20S)-1alpha,25-dihydroxyvitamin D(3) [Tocchini-Valentini et al. (rcsb.org)

By combining HP-fluorescence and HP-visible absorption spectroscopy , our strategy highlights the crucial role of tetrapyrrole-metal complexes in stabilising apoMb hydrophobic pocket. (cea.fr)

In vitro studies and gene expression profiles showed that the transcriptional changes by the activated Ahr are ligand specific and are highly cell specific. (biolegend.com)
The ligand-based pharmacophores were based on the six 11β-HSD2 selective compounds, which were also used for the docking studies. (helsinki.fi)

Our results also show that empty pockets are especially long lived compared to their filled counterparts which suggests that the emptying of hydrophobic pockets will play a key role in binding kinetics. (aiche.org)

Their main role is in cell-signaling, and, because they are hydrophobic, their main actions are limited to paracrine (cell-to-cell) or autocrine (same cell), rather than systemic, effects. (medscape.com)

Recently, animal venoms have demonstrated their capacity to provide melanocortin ligands with toxins from a scorpion and a spider. (iric.ca)

Some examples of targeting ligands used in nanoscale drug delivery systems include folate, transferrin. (trialx.com)

Anatomy26

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Chemicals and Drugs125

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