scholarly journals Correction: Corrigendum: Modulating protein activity using tethered ligands with mutually exclusive binding sites

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Alberto Schena ◽  
Rudolf Griss ◽  
Kai Johnsson
Keyword(s):  
Binding Sites ◽  
Protein Activity ◽  
Tethered Ligands

scholarly journals Modulating protein activity using tethered ligands with mutually exclusive binding sites

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Alberto Schena ◽  
Rudolf Griss ◽  
Kai Johnsson
Keyword(s):  
Small Molecules ◽  
Binding Sites ◽  
Protein A ◽  
Living Cells ◽  
Protein Activity ◽  
Research Areas ◽  
Specific Effector ◽  
Tethered Ligands ◽  
General Method

Abstract The possibility to design proteins whose activities can be switched on and off by unrelated effector molecules would enable applications in various research areas, ranging from biosensing to synthetic biology. We describe here a general method to modulate the activity of a protein in response to the concentration of a specific effector. The approach is based on synthetic ligands that possess two mutually exclusive binding sites, one for the protein of interest and one for the effector. Tethering such a ligand to the protein of interest results in an intramolecular ligand–protein interaction that can be disrupted through the presence of the effector. Specifically, we introduce a luciferase controlled by another protein, a human carbonic anhydrase whose activity can be controlled by proteins or small molecules in vitro and on living cells, and novel fluorescent and bioluminescent biosensors.

scholarly journals Photocontrollable PROTAC molecules: Structure and mechanism of action

2021 ◽  
Vol 71 (3) ◽  
pp. 161-176
Author(s):  
Mladen Koravović ◽  
Gordana Tasić ◽  
Milena Rmandić ◽  
Bojan Marković
Keyword(s):  
Protein Degradation ◽  
Ubiquitin Ligase ◽  
Binding Sites ◽  
E3 Ubiquitin Ligase ◽  
Drug Binding ◽  
Post Translational Modification ◽  
Protein Activity ◽  
Target Drug ◽  
Traditional Drug

Traditional drug discovery strategies are usually focused on occupancy of binding sites that directly affect functions of proteins. Hence, proteins that lack such binding sites are generally considered pharmacologically intractable. Modulators of protein activity, especially inhibitors, must be applied in appropriate dosage regimens that often lead to high systemic drug exposures in order to maintain sufficient protein inhibition in vivo. Consequently, there is a risk of undesirable off-target drug binding and side effects. Recently, PROteolysis TArgeting Chimera (PROTAC) technology has emerged as a new pharmacological modality that exploits PROTAC molecules for induced protein degradation. PROTAC molecule is a heterobifunctional structure consisting of a ligand that binds a protein of interest (POI), a ligand for recruiting an E3 ubiquitin ligase (an enzyme involved in the POI ubiquitination) and a linker that connects these two. After POI-PROTAC-E3 ubiquitin ligase ternary complex formation, the POI undergoes ubiquitination (an enzymatic post-translational modification in which ubiquitin is attached to the POI) and degradation. By merging the principles of photopharmacology and PROTAC technology, photocontrollable PROTACs for spatiotemporal control of induced protein degradation have recently emerged. The main advantage of photocontrollable over conventional PROTACs is the possible prevention of off-target toxicity thanks to local photoactivation.

Allosteric theory

Hemoglobin ◽  
2018 ◽  
pp. 42-57
Author(s):  
Jay F. Storz
Keyword(s):  
Active Site ◽  
Binding Sites ◽  
Allosteric Regulation ◽  
Theoretical Models ◽  
State Model ◽  
Regulatory Control ◽  
Indirect Interaction ◽  
Protein Activity ◽  
Conformational States ◽  
Two State Model

Chapter 3 provides a brief overview of allostery, the modulation of protein activity that is caused by an indirect interaction between structurally remote binding sites. In this mode of intramolecular regulatory control, the binding of ligand at a protein’s active site is influenced by the binding of another ligand at a different site in the same protein. This interaction at a distance is mediated by a ligation-induced transition between alternative conformational states. Hemoglobin is regarded as the “allosteric paradigm,” and the oxygenation-linked transition between alternative quaternary conformations provides a textbook example of how allostery works. This chapter reviews different theoretical models, such as the Monod-Wyman-Changeux “two-state” model, to explain the allosteric regulation of hemoglobin function.

scholarly journals Binding in vitro of multiple cellular proteins to immunoglobulin heavy-chain enhancer DNA.

1986 ◽  
Vol 6 (12) ◽  
pp. 4168-4178 ◽  
Author(s):  
C L Peterson ◽  
K Orth ◽  
K L Calame
Keyword(s):  
Heavy Chain ◽  
Protein Interactions ◽  
Binding Sites ◽  
Immunoglobulin Heavy Chain ◽  
Lymphoid Cells ◽  
Protein Protein Interactions ◽  
Protein Activity ◽  
Enhancer Element ◽  
Enhancer Sequences

Seven protein-binding sites on the immunoglobulin heavy-chain (IgH) enhancer element have been identified by exonuclease III protection and gel retardation assays. It appears that the seven sites bind a minimum of four separate proteins. Three of these proteins also bind to other enhancers or promoters, but one protein seems to recognize exclusively IgH enhancer sequences. A complex of four binding sites, recognized by different proteins, is located within one 80-base-pair region of IgH enhancer DNA. Close juxtaposition of enhancer proteins may allow protein-protein interactions or be part of a mechanism for modulating enhancer protein activity. All IgH enhancer-binding proteins identified in this study were found in extracts from nonlymphoid as well as lymphoid cells. These data provide the first direct evidence that multiple proteins bind to enhancer elements and that while some of these proteins recognize common elements of many enhancers, others have more limited specificities.

scholarly journals A Comparative Analysis of Punicalagin Interaction with PDIA1 and PDIA3 by Biochemical and Computational Approaches

Biomedicines ◽  
2021 ◽  
Vol 9 (11) ◽  
pp. 1533
Author(s):  
Giuliano Paglia ◽  
Lorenzo Antonini ◽  
Laura Cervoni ◽  
Rino Ragno ◽  
Manuela Sabatino ◽  
...  
Keyword(s):  
Binding Sites ◽  
Rational Design ◽  
Reductase Activity ◽  
Binding Mode ◽  
Protein Activity ◽  
Molecular Determinant ◽  
Set Up ◽  
Dynamics Simulations ◽  
Protein Disulfide ◽  
Similar Affinity

In a previous work, it was shown that punicalagin, an active ingredient of pomegranate, is able to bind to PDIA3 and inhibit its disulfide reductase activity. Here we provide evidence that punicalagin can also bind to PDIA1, the main expressed form of protein disulfide isomerase (PDI). In this comparative study, the affinity and the effect of punicalagin binding on each protein were evaluated, and a computational approach was used to identify putative binding sites. Punicalagin binds to either PDIA1 or PDIA3 with a similar affinity, but the inhibition efficacy on protein reductase activity is higher for PDIA3. Additionally, punicalagin differently affects the thermal denaturation profile of both proteins. Molecular docking and molecular dynamics simulations led to propose a punicalagin binding mode on PDIA1 and PDIA3, identifying the binding sites at the redox domains a’ in two different pockets, suggesting different effects of punicalagin on proteins’ structure. This study provides insights to develop punicalagin-based ligands, to set up a rational design for PDIA3 selective inhibitors, and to dissect the molecular determinant to modulate the protein activity.

Role of calcium in membrane interactions by PI(4,5)P2-binding proteins

2014 ◽  
Vol 42 (5) ◽  
pp. 1441-1446 ◽  
Author(s):  
Marina E. Monteiro ◽  
Maria J. Sarmento ◽  
Fábio Fernandes
Keyword(s):  
Binding Sites ◽  
Binding Proteins ◽  
Fine Tuning ◽  
Protein Activity ◽  
Calcium Dependent ◽  
Spatial Regulation ◽  
Target Membrane ◽  
Temporal And Spatial ◽  
Lateral Organization

Ca2+ and phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] are key agents in membrane-associated signalling events. Their temporal and spatial regulation is crucial for activation or recruitment of proteins in the plasma membrane. In fact, the interaction of several signalling proteins with PI(4,5)P2 has been shown to be tightly regulated and dependent on the presence of Ca2+, with co-operative binding in some cases. In these proteins, PI(4,5)P2 and Ca2+ binding typically occurs at different binding sites. In addition, several PI(4,5)P2-binding proteins are known targets of calmodulin (CaM), which, depending on the presence of calcium, can compete with PI(4,5)P2 for protein interaction, translating Ca2+ transient microdomains into variations of PI(4,5)P2 lateral organization in time and space. The present review highlights different examples of calcium-dependent PI(4,5)P2-binding proteins and discusses the possible impact of this dual regulation on fine-tuning of protein activity by triggering target membrane binding in the presence of subtle changes in the levels of calcium or PI(4,5)P2.

scholarly journals Characterization of Protein-Lipid Interactions in Biosystems Processes

2019 ◽  
pp. 93-99
Author(s):  
Dr. Chrysanthus Chukwuma Sr
Keyword(s):  
Membrane Proteins ◽  
Binding Sites ◽  
Systematic Investigation ◽  
Morphological Characterization ◽  
Protein Activity ◽  
Lipid Interactions ◽  
Cellular Processes ◽  
Normal Enzyme ◽  
Basic And Applied Research

Lipids correlate with membrane characteristics and functionalities as macromolecular constituentts in all cellular processes. Numerous aspects of lipid modulation of protein activity and structure are not completely understood and, thus a holistic systematic investigation activities will be pertinent. Protein-lipid interactions are the resultant impacts of membrane proteins on lipid physical states or vice versa. Encompassing research needs to be associated with strategies to elucidate whether proteins contain binding sites which are lipid specific, and that the protein-lipid complexes are ostensibly long-lived, on the time order necessary for the turnover of a normal enzyme. Biological membranes have since been determined as essential ingredients in an expansive array of cellular processes, such as photosynthesis, cell defence, signaling transduction, communication and motility. Therefore, they constitute multiple targets in both basic and applied research. Protein-lipid interactions are becoming increasingly relevant to the morphological characterization of membrane proteins as related to their functionalities. Excepting for simplified models, certain protein-lipid interactions specifically constitute remarkable challenges which require optimum experimental paradigm and design.

Binding in vitro of multiple cellular proteins to immunoglobulin heavy-chain enhancer DNA

1986 ◽  
Vol 6 (12) ◽  
pp. 4168-4178
Author(s):  
C L Peterson ◽  
K Orth ◽  
K L Calame
Keyword(s):  
Heavy Chain ◽  
Protein Interactions ◽  
Binding Sites ◽  
Immunoglobulin Heavy Chain ◽  
Lymphoid Cells ◽  
Protein Protein Interactions ◽  
Protein Activity ◽  
Enhancer Element ◽  
Enhancer Sequences

Seven protein-binding sites on the immunoglobulin heavy-chain (IgH) enhancer element have been identified by exonuclease III protection and gel retardation assays. It appears that the seven sites bind a minimum of four separate proteins. Three of these proteins also bind to other enhancers or promoters, but one protein seems to recognize exclusively IgH enhancer sequences. A complex of four binding sites, recognized by different proteins, is located within one 80-base-pair region of IgH enhancer DNA. Close juxtaposition of enhancer proteins may allow protein-protein interactions or be part of a mechanism for modulating enhancer protein activity. All IgH enhancer-binding proteins identified in this study were found in extracts from nonlymphoid as well as lymphoid cells. These data provide the first direct evidence that multiple proteins bind to enhancer elements and that while some of these proteins recognize common elements of many enhancers, others have more limited specificities.

Conformation of Ribosomes from Escherichia Coli

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.

Electron Probe Analysis of Muscle

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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