Three-Dimensional Structure of p21 and Its Implications
Juan Carlos Lacal, Frank McCormick in The ras Superfamily of GTPases, 2017
The structures of several different wild-type and mutant p21 complexes have been determined by S. H. Kim and co-workers as well as in our laboratory. A list of the published structures is shown in Table 1 together with the resolutions obtained in the crystallographic analyses. For cellular and one oncogenic mutant p21 both the triphosphate and diphosphate structures have been determined. From these the mechanism of the conformational change could be deduced. For the triphosphate complex of p21 the noncleavable analogs GppNHp and Gpp(CH2)p were used, because GTP and even GTPγS are hydrolyzed by p21 during crystallization. A complex of p21 with a noncleavable GTP analog having a photolabile protecting group on γ-phosphate, which was named cagedGTP, has also been crystallized.32 This latter crystal type was used to determine the three-dimensional structure of the real p21-GTP complex after photolytic cleavage of the protecting group. Additionally, it also allowed us to directly follow the GTP hydrolysis reaction within the crystal and observe the conformational transition from the active to the inactive form of p21.20
Protein Phosphorylation of Prolactin Target Tissue: Mammary Gland
James A. Rillema in Actions of Prolactin on Molecular Processes, 1987
Calmodulin is a highly conserved, ubiquitous protein of the family that includes parvalbumin, the vitamin D-dependent calcium-binding protein, troponin C, and the S-100 proteins.25 Calmodulin contains four high-affinity binding sites for calcium (10−5 M affinity). Occupation of these sites promotes a conformational change in the protein structure.26 Calcium-loaded calmodulin binds to several protein kinases, including myosin light-chain kinase,27,28 a glycogen synthase kinase,29 tyrosine hydroxylase kinase,30 synapsin kinase,31 and tubulin kinase.32 Calmodulin is the δ subunit of phosphorylase kinase.33 Mammary tissue has recently been shown to contain calmodulin,34 and several calcium- and calmodulin-dependent protein kinases have been observed in mammary tissue,2,35 The calcium- and calmodulin-dependent enzymes, unlike the cyclic AMP-dependent kinases, have different subunit and holoenzyme structures with varying substrate specificities, although several of these enzymes are proving to be similar or perhaps identical.36
Tyrosine Phosphatases as New Treatment Targets in Acute Myeloid Leukemia
Gertjan J. L. Kaspers, Bertrand Coiffier, Michael C. Heinrich, Elihu Estey in Innovative Leukemia and Lymphoma Therapy, 2019
The hydrolysis of phosphoester bonds on tyrosine residues of proteins differs from threonine and serine in that it is metal-ion independent. Furthermore, the catalytic mechanism involves a two-step process with the formation and breakdown of a transient phosphoenzyme intermediate. The process starts with the stabilization of the negatively charged phosphate substrate by hydrogen bonds to residues of the phosphate binding loop (P-loop) and a highly conserved arginine group. A nearby-localized dipole of an α-helix stabilizes the phosphate. Upon binding of the substrate, the enzyme undergoes a conformational change. This event triggers interactions between residues and result in covering the substrate-binding pocket by the movable WPD loop, which is essential for substrate selectivity and catalytic activity. Subsequently, a deprotonated cysteine residue attacks the substrate, which results in a phosphor-enzyme intermediate (27). After transferring the phosphate to a catalytic cysteine residue, the dephosporylated substrate is expelled from the active site using an acidic amino-acid residue to protonate a tyrosine phenolic oxygen (28).
Changing paradigms for targeted therapies against diffuse infiltrative gliomas: tackling a moving target
Published in Expert Review of Neurotherapeutics, 2019
Candice D. Carpenter, Iyad Alnahhas, Javier Gonzalez, Pierre Giglio, Vinay K. Puduvalli
Heat-shock proteins are considered to be crucial to the survival of cancers such as glioblastoma due to their key roles in (a) stabilizing proteins, (b) facilitating protein conformational change, (c) protein trafficking and (d) breakdown as well as control of apoptosis [142]. They are activated by the ‘stress’ environment found in tumor beds and consisting mainly of hypoxia and inflammation [143]. A Phase I study in patients with recurrent GBM using an autologous heat-shock protein peptide complex-96 (HSPPC-96) vaccine, which utilized peptides bound to a chaperone protein isolated from glioma tissue, to immunize patients with recurrent disease, showed the potential for improved outcome in patients who had an immune response [144]. A subsequent phase II study further demonstrated the safety and potential efficacy of this approach in adults with recurrent GBM with the additional findings that patients who were lymphopenic at baseline had worse survival [145].
Unmasking allosteric-binding sites: novel targets for GPCR drug discovery
Published in Expert Opinion on Drug Discovery, 2022
Verònica Casadó-Anguera, Vicent Casadó
The concept of allostery was proposed 60 years ago when the term ‘allosteric inhibition’ was used by Jacques Monod and Francois Jacob to describe a mechanism in which ‘the inhibitor is not a steric analogue of the substrate.’ Allostery consists in ‘an interaction between two topographically distinct sites on an enzyme mediated indirectly by a conformational change’ transmitted between the sites [4]. Shortly after, the mechanism underlying this conformational change was proposed to be the conformational selection. This mechanism predicts that the macromolecule exists in a thermal equilibrium between active and inactive states that can be stabilized by the binding of orthosteric or allosteric ligands to their respective (non-overlapping) binding sites [5]. This mechanism is commonly known as the concerted MWC model by Monod, Wyman, and Changeux [6]. According to this concerted model, different protomers (dimers, tetramers, …) can exist in two different states in equilibrium: a tense (T) state, which has low affinity for the ligand and is the most abundant in its absence, and a relaxed (R) state, which has high affinity for the ligand. All protomers must be in the same state at any time and ligand binding induces a concerted change of conformation of all protomers. Thus, according to this model, all protomers must be in the same conformation and symmetry has to be conserved. The oligomeric nature of the model is also able to explain the phenomenon of positive cooperativity in ligand binding, since the same ligand can bind to different protomers within the oligomer [5].
Cell signal transduction: hormones, neurotransmitters and therapeutic drugs relate to purine nucleotide structure
Published in Journal of Receptors and Signal Transduction, 2018
Nucleotides are ideal as regulatory compounds, as they exist in syn and anti conformations, cyclized and dephosphorylated forms. The cyclic nucleotide form participates in a ligand-activated, phosphodiesterase-regulated, cross-talk signaling network [44]. The results presented here provide some insight into ligand directed effects on nucleotide structure. The potential of a ligand to promote conformational change of a nucleotide structure, by displacement of nucleotide or a component group from a receptor protein, is evident within the paired structures used in this study as molecular similarity. Ligand structures regulating Gs and Gi alpha subunits relate to the nucleotide cyclization process. Agonist and antagonist structures differentially alter the space-filling structure of nucleotides. Neurotransmitters may competitively replace a nucleotide structure, or part structure, with a more minimal form whereas antagonists provide a replacement structure that is more similar in size and shape. Ligands specific to the different voltage-gated channel classes relate to different components within the nucleotide structure. Relative molecular similarity within nucleotide and ligand structures of LGIC receptor classes identifies the potential for receptor cross-talk.