scholarly journals Dimerization of the Trk receptors in the plasma membrane: effects of their cognate ligands

2018 ◽  
Vol 475 (22) ◽  
pp. 3669-3685 ◽  
Author(s):  
Fozia Ahmed ◽  
Kalina Hristova
Keyword(s):  
Plasma Membrane ◽  
Ligand Binding ◽  
Conformational Changes ◽  
Tyrosine Kinases ◽  
Structural Changes ◽  
Control Cell ◽  
Trk Receptors ◽  
Surface Receptors ◽  
Neuronal Tissues ◽  
Membrane Effects

Receptor tyrosine kinases (RTKs) are cell surface receptors which control cell growth and differentiation, and play important roles in tumorigenesis. Despite decades of RTK research, the mechanism of RTK activation in response to their ligands is still under debate. Here, we investigate the interactions that control the activation of the tropomyosin receptor kinase (Trk) family of RTKs in the plasma membrane, using a FRET-based methodology. The Trk receptors are expressed in neuronal tissues, and guide the development of the central and peripheral nervous systems during development. We quantify the dimerization of human Trk-A, Trk-B, and Trk-C in the absence and presence of their cognate ligands: human β-nerve growth factor, human brain-derived neurotrophic factor, and human neurotrophin-3, respectively. We also assess conformational changes in the Trk dimers upon ligand binding. Our data support a model of Trk activation in which (1) Trks have a propensity to interact laterally and to form dimers even in the absence of ligand, (2) different Trk unliganded dimers have different stabilities, (3) ligand binding leads to Trk dimer stabilization, and (4) ligand binding induces structural changes in the Trk dimers which propagate to their transmembrane and intracellular domains. This model, which we call the ‘transition model of RTK activation,’ may hold true for many other RTKs.

scholarly journals Capturing Peptide–GPCR Interactions and Their Dynamics

Molecules ◽  
2020 ◽  
Vol 25 (20) ◽  
pp. 4724
Author(s):  
Anette Kaiser ◽  
Irene Coin
Keyword(s):  
Ligand Binding ◽  
Conformational Changes ◽  
Structural Changes ◽  
Structural Heterogeneity ◽  
Receptor Interaction ◽  
Spectroscopic Techniques ◽  
Peptide Receptors ◽  
Physiological Processes ◽  
High Dynamics ◽  
G Protein Coupled

Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.

scholarly journals Molecular mechanisms of endothelial hyperpermeability: implications in inflammation

2009 ◽  
Vol 11 ◽  
Author(s):  
Puneet Kumar ◽  
Qiang Shen ◽  
Christopher D. Pivetti ◽  
Eugene S. Lee ◽  
Mack H. Wu ◽  
...  
Keyword(s):  
Tyrosine Kinases ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Therapeutic Potential ◽  
Control Cell ◽  
Cell Junctions ◽  
Ischaemia Reperfusion Injury ◽  
Signalling Molecules ◽  
Endothelial Hyperpermeability ◽  
Cell Cell

Endothelial hyperpermeability is a significant problem in vascular inflammation associated with trauma, ischaemia–reperfusion injury, sepsis, adult respiratory distress syndrome, diabetes, thrombosis and cancer. An important mechanism underlying this process is increased paracellular leakage of plasma fluid and protein. Inflammatory stimuli such as histamine, thrombin, vascular endothelial growth factor and activated neutrophils can cause dissociation of cell–cell junctions between endothelial cells as well as cytoskeleton contraction, leading to a widened intercellular space that facilitates transendothelial flux. Such structural changes initiate with agonist–receptor binding, followed by activation of intracellular signalling molecules including calcium, protein kinase C, tyrosine kinases, myosin light chain kinase, and small Rho-GTPases; these kinases and GTPases then phosphorylate or alter the conformation of different subcellular components that control cell–cell adhesion, resulting in paracellular hypermeability. Targeting key signalling molecules that mediate endothelial-junction–cytoskeleton dissociation demonstrates a therapeutic potential to improve vascular barrier function during inflammatory injury.

scholarly journals Ligand Binding to the Androgen Receptor Induces Conformational Changes That Regulate Phosphatase Interactions

2007 ◽  
Vol 27 (9) ◽  
pp. 3390-3404 ◽  
Author(s):  
Chun-Song Yang ◽  
Hong-Wu Xin ◽  
Joshua B. Kelley ◽  
Adam Spencer ◽  
David L. Brautigan ◽  
...  
Keyword(s):  
Androgen Receptor ◽  
Ligand Binding ◽  
Conformational Changes ◽  
Structural Changes ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
T Antigen ◽  
Phosphorylation Sites ◽  
A Subunit ◽  
Androgen Binding

ABSTRACT We describe a mechanism for protein phosphatase 2A (PP2A) targeting to the androgen receptor (AR) and provide insight into the more general issue of kinase and phosphatase interactions with AR. Simian virus 40 (SV40) small t antigen (ST) binding to N-terminal HEAT repeats in the PP2A A subunit induces structural changes transduced to C-terminal HEAT repeats. This enables the C-terminal HEAT repeats in the PP2A A subunit, including HEAT repeat 13, to discriminate between androgen- and androgen antagonist-induced AR conformations. The PP2A-AR interaction was used to show that an AR mutant in prostate cancer cells (T877A) is activated by multiple ligands without acquiring the same conformation as that induced by androgen. The correlation between androgen binding to AR and increased phosphorylation of the activation function 1 (AF-1) region implies that changes in AR conformation or chaperone composition are causal to kinase access to phosphorylation sites. However, AF-1 phosphorylation sites are kinase accessible prior to androgen binding. This suggests that androgens can enhance the phosphorylation state of AR either by negatively regulating the ability of the ligand-binding domain to bind phosphatases or by inducing an AR conformation that is resistant to phosphatase action. SV40 ST subverts this mechanism by promoting the direct transfer of PP2A onto androgen-bound AR, resulting in multisite dephosphorylation.

scholarly journals An Improved Free Energy Perturbation FEP+ Sampling Protocol for Flexible Ligand-Binding Domains

2019 ◽  
Author(s):  
Filip Fratev ◽  
suman sirimulla
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Conformational Changes ◽  
Structural Changes ◽  
Binding Mode ◽  
Sampling Time ◽  
Free Energy Perturbation ◽  
Sampling Protocol ◽  
Sampling Schemes ◽  
Energy Perturbation

Recent improvements to free energy perturbation (FEP) calculations, especiallyFEP+, established their utility for pharmaceutical lead optimization. However, to dateFEP has typically been helpful only when (1) high-quality X-ray data is available and(2) the target protein does not undergo significant conformational changes. Also, alack of systematic studies on determining an adequate sampling time is often one ofthe primary limitations of FEP calculations. Herein, we propose a modified versionof the FEP/REST (i.e., replica exchange with solute tempering) sampling protocol,based on systematic studies on several targets by probing a large number of permutations with different sampling schemes. Improved FEP+ binding affinity predictions for regular flexible-loop (F-loop) motions and considerable structural changes can be obtained by extending the pre-REST sampling time from 0.24 ns to 5 ns/λand 2×10 ns/λ, respectively. We obtained much more precise ∆∆G calculations of the individual perturbations, including the sign of the transformations and less error. We extended the REST simulations from 5 ns to 8 ns to achieve reasonable free energy convergence.Implementing REST to the entire ligand as opposed to solely the perturbed region, and also some important flexible protein residues (pREST region) in ligand binding domain (LBD) , also considerably improved the FEP+ results in most of the studied cases. Preliminary molecular dynamics (MD) runs were useful for establishing the correct binding mode of the compounds and thus precise alignment for FEP+.<br>

scholarly journals Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Van K Duesterberg ◽  
Irena T Fischer-Hwang ◽  
Christian F Perez ◽  
Daniel W Hogan ◽  
Steven M Block
Keyword(s):  
Ligand Binding ◽  
Long Range ◽  
Single Molecule ◽  
Conformational Changes ◽  
Structural Changes ◽  
Regulatory Element ◽  
Optical Trap ◽  
Resonance Energy ◽  
Thiamine Pyrophosphate ◽  
Tertiary Interactions

The thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in mRNA that modifies gene expression in response to TPP concentration. Its specificity is dependent upon conformational changes that take place within its aptamer domain. Here, the role of tertiary interactions in ligand binding was studied at the single-molecule level by combined force spectroscopy and Förster resonance energy transfer (smFRET), using an optical trap equipped for simultaneous smFRET. The ‘Force-FRET’ approach directly probes secondary and tertiary structural changes during folding, including events associated with binding. Concurrent transitions observed in smFRET signals and RNA extension revealed differences in helix-arm orientation between two previously-identified ligand-binding states that had been undetectable by spectroscopy alone. Our results show that the weaker binding state is able to bind to TPP, but is unable to form a tertiary docking interaction that completes the binding process. Long-range tertiary interactions stabilize global riboswitch structure and confer increased ligand specificity.

scholarly journals An Improved Free Energy Perturbation FEP+ Sampling Protocol for Flexible Ligand-Binding Domains

2019 ◽  
Author(s):  
Filip Fratev ◽  
suman sirimulla
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Conformational Changes ◽  
Structural Changes ◽  
Binding Mode ◽  
Sampling Time ◽  
Free Energy Perturbation ◽  
Sampling Protocol ◽  
Sampling Schemes ◽  
Energy Perturbation

Recent improvements to free energy perturbation (FEP) calculations, especiallyFEP+, established their utility for pharmaceutical lead optimization. However, to dateFEP has typically been helpful only when (1) high-quality X-ray data is available and(2) the target protein does not undergo significant conformational changes. Also, alack of systematic studies on determining an adequate sampling time is often one ofthe primary limitations of FEP calculations. Herein, we propose a modified versionof the FEP/REST (i.e., replica exchange with solute tempering) sampling protocol,based on systematic studies on several targets by probing a large number of permutations with different sampling schemes. Improved FEP+ binding affinity predictions for regular flexible-loop (F-loop) motions and considerable structural changes can be obtained by extending the pre-REST sampling time from 0.24 ns to 5 ns/λand 2×10 ns/λ, respectively. We obtained much more precise ∆∆G calculations of the individual perturbations, including the sign of the transformations and less error. We extended the REST simulations from 5 ns to 8 ns to achieve reasonable free energy convergence.Implementing REST to the entire ligand as opposed to solely the perturbed region, and also some important flexible protein residues (pREST region) in ligand binding domain (LBD) , also considerably improved the FEP+ results in most of the studied cases. Preliminary molecular dynamics (MD) runs were useful for establishing the correct binding mode of the compounds and thus precise alignment for FEP+.<br>

scholarly journals An Improved Free Energy Perturbation FEP+ Sampling Protocol for Flexible Ligand-Binding Domains

2018 ◽  
Author(s):  
Filip Fratev ◽  
Suman Sirimulla
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Conformational Changes ◽  
Structural Changes ◽  
Binding Mode ◽  
Sampling Time ◽  
Free Energy Perturbation ◽  
Sampling Protocol ◽  
Sampling Schemes ◽  
Energy Perturbation

Recent improvements to free energy perturbation (FEP) calculations, especiallyFEP+, established their utility for pharmaceutical lead optimization. However, to dateFEP has typically been helpful only when (1) high-quality X-ray data is available and(2) the target protein does not undergo significant conformational changes. Also, alack of systematic studies on determining an adequate sampling time is often one ofthe primary limitations of FEP calculations. Herein, we propose a modified versionof the FEP/REST (i.e., replica exchange with solute tempering) sampling protocol,based on systematic studies on several targets by probing a large number of permutations with different sampling schemes. Improved FEP+ binding affinity predictions for regular flexible-loop (F-loop) motions and considerable structural changes can be obtained by extending the pre-REST sampling time from 0.24 ns to 5 ns/λand 2×10 ns/λ, respectively. We obtained much more precise ∆∆G calculations of the individual perturbations, including the sign of the transformations and less error. We extended the REST simulations from 5 ns to 8 ns to achieve reasonable free energy convergence.Implementing REST to the entire ligand as opposed to solely the perturbed region, and also some important flexible protein residues (pREST region) in ligand binding domain (LBD) , also considerably improved the FEP+ results in most of the studied cases. Preliminary molecular dynamics (MD) runs were useful for establishing the correct binding mode of the compounds and thus precise alignment for FEP+.<br>

scholarly journals D3PM: A Comprehensive Database for Protein Motions Ranging from Residue to Domain

2020 ◽  
Author(s):  
Cheng Peng ◽  
Xinben Zhang ◽  
Zhijian Xu ◽  
Zhaoqiang Chen ◽  
Yanqing Yang ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Conformational Changes ◽  
Structural Changes ◽  
Small Scale ◽  
Motion Patterns ◽  
Protein Motions ◽  
Protein Functions ◽  
Binding Pockets ◽  
Local Residue ◽  
Domain Motions

Abstract Background: Knowledge of protein motions is significant to understand its functions. The currently available databases for protein motions, in general, are focused on overall domain motions, which pay little attention to local residue motions. Albeit with relatively small scale, the local residue motions may play crucial roles in protein functions and its binding with ligand, in particular for those residues within binding pockets. Results: A comprehensive protein motion database (D3PM) was constructed in this study to facilitate the analysis of protein motions. The D3PM has the motion information ranging from the overall structural changes of macromolecule to the local flip motion of the residues in ligand binding site. Currently, the D3PM has 5,339 entries of overall motions and 2,319 entries of pocket residues’ motions. The motion patterns in the database are classified into 4 types of overall structural change and 5 types of pocket residues’ shift. Impressively, it was found that less than 15% of the protein pairs have obvious overall conformational adaptations induced by ligand binding, while more than 50% of the protein pairs have significant structural changes in the ligand binding sites, indicating that ligand-induced conformational changes are drastic whereas they are mostly confined around the ligand. By the analysis of pocket residues’ preference, we classified amino acids into “pocketphilic” and “pocketphobic” residues, which is helpful to pocket prediction and ligand design.Conclusion: D3PM is a comprehenssive database about protein motions ranging from residue to domain, which should be useful for exploring diverse protein motions and for understanding protein functions. The database is freely available on www.d3pharma.com/D3PM/index.php.

Antigen Receptor Function in the Context of the Nanoscale Organization of the B Cell Membrane

2019 ◽  
Vol 37 (1) ◽  
pp. 97-123 ◽  
Author(s):  
Michael R. Gold ◽  
Michael G. Reth
Keyword(s):  
Plasma Membrane ◽  
B Cell ◽  
Conformational Changes ◽  
Clonal Selection ◽  
Selection Process ◽  
Antigen Receptor ◽  
Activation Mechanism ◽  
Surface Receptors ◽  
New Information ◽  
Cell Plasma

The B cell antigen receptor (BCR) plays a central role in the self/nonself selection of B lymphocytes and in their activation by cognate antigen during the clonal selection process. It was long thought that most cell surface receptors, including the BCR, were freely diffusing and randomly distributed. Since the advent of superresolution techniques, it has become clear that the plasma membrane is compartmentalized and highly organized at the nanometer scale. Hence, a complete understanding of the precise conformation and activation mechanism of the BCR must take into account the organization of the B cell plasma membrane. We review here the recent literature on the nanoscale organization of the lymphocyte membrane and discuss how this new information influences our view of the conformational changes that the BCR undergoes during activation.

scholarly journals Composition of receptor tyrosine kinase-mediated lipid micro-domains controlled by adaptor protein interaction

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arndt Rohwedder ◽  
Sabine Knipp ◽  
Lee D. Roberts ◽  
John E. Ladbury
Keyword(s):  
Signal Transduction ◽  
Plasma Membrane ◽  
Growth Factor ◽  
Ligand Binding ◽  
Tyrosine Kinases ◽  
Growth Factor Receptor ◽  
Adaptor Protein ◽  
Effector Proteins ◽  
Control Mechanisms ◽  
The Impact

AbstractReceptor tyrosine kinases (RTKs) are highly regulated, single pass transmembrane proteins, fundamental to cellular function and survival. Aberrancies in regulation lead to corruption of signal transduction and a range of pathological outcomes. Although control mechanisms associated with the receptors and their ligands are well understood, little is known with respect to the impact of lipid/lipid and lipid/protein interactions in the proximal plasma membrane environment. Given that the transmembrane regions of RTKs change in response to extracellular ligand binding, the lipid interactions have important consequences in influencing signal transduction. Fibroblast growth factor receptor 2 (FGFR2) is a highly regulated RTK, including under basal conditions. Binding of the adaptor protein, growth factor receptor-bound protein 2 (GRB2) to FGFR2 prevents full activation and recruitment of downstream signalling effector proteins in the absence of extracellular stimulation. Here we demonstrate that the FGFR2-GRB2 complex is sustained in a defined lipid environment. Dissociation of GRB2 from this complex due to ligand binding, or reduced GRB2 expression, facilitates the dispersion of FGFR2 into detergent-resistant membrane (DRM) micro-domains. This modification of the plasma membrane proximal to FGFR2 provides a further regulatory checkpoint which controls receptor degradation, recycling and recruitment of intracellular signalling proteins.

Sign in / Sign up

Export Citation Format

Share Document