97 research outputs found
Multisteric regulation by structural disorder in modular signaling proteins: An extension of the concept of allostery
Allostery is a classical regulatory mechanism of proteins in which a signal at 'another site' modifies the activity/function of a protein. In fact, with the recognition of the generality of the structural disorder of proteins and the landscape theory of protein structure, a 'new view' of allostery started to emerge, in which emphasis is placed on ligand-induced shifts in the conformational ensemble of the protein. The ensuing changes in ligand binding/catalytic activity might stem from coupled folding transitions of distinct binding sites or remodeling of the conformational landscape to entropically favor a particular downstream binding/catalytic event. The ensuing sigmoidal binding isotherm cannot be described by a simple saturation; rather, it shows signs of cooperation between ligands. If binding of one ligand weakens that of the others, one can also speak about negative cooperativity. To elucidate the underlying mechanistic changes, two models have been suggested, which, even today, form the basis of our textbook wisdom of this phenomenon
The Melting Diagram of Protein Solutions and Its Thermodynamic Interpretation
Here we present a novel method for the characterization of the hydration of protein solutions based on measuring and evaluating two-component wide-line 1H NMR signals. We also provide a description of key elements of the procedure conceived for the thermodynamic interpretation of such results. These interdependent experimental and theoretical treatments provide direct experimental insight into the potential energy surface of proteins. The utility of our approach is demonstrated through the examples of two proteins of distinct structural classes: the globular, structured ubiquitin; and the intrinsically disordered ERD10 (early response to dehydration 10). We provide a detailed analysis and interpretation of data recorded earlier by cooling and slowly warming the protein solutions through thermal equilibrium states. We introduce and use order parameters that can be thus derived to characterize the distribution of potential energy barriers inhibiting the movement of water molecules bound to the surface of the protein. Our results enable a quantitative description of the ratio of ordered and disordered parts of proteins, and of the energy relations of protein–water bonds in aqueous solutions of the proteins
Nmr relaxation studies on the hydrate layer of intrinsically unstructured proteins
Intrinsically unstructured/ disordered proteins (IUPs) exist in
a
disordered and largely solvent- exposed, still functional,
structural
state under physiological conditions. As their function is often
directly linked with structural disorder, understanding their
structure-function relationship in detail is a great challenge
to
structural biology. In particular, their hydration and residual
structure, both closely linked with their mechanism of action,
require
close attention. Here we demonstrate that the hydration of IUPs
can be
adequately approached by a technique so far unexplored with
respect to
IUPs, solid-state NMR relaxation measurements. This technique
provides
quantitative information on various features of hydrate water
bound to
these proteins. By freezing nonhydrate ( bulk) water out, we
have been
able to measure free induction decays pertaining to protons of
bound
water from which the amount of hydrate water, its activation
energy,
and correlation times could be calculated. Thus, for three IUPs,
the
first inhibitory domain of calpastatin, microtubule-associated
protein
2c, and plant dehydrin early responsive to dehydration 10, we
demonstrate that they bind a significantly larger amount of
water than
globular proteins, whereas their suboptimal hydration and
relaxation
parameters are correlated with their differing modes of
function. The
theoretical treatment and experimental approach presented in
this
article may have general utility in characterizing proteins that
belong
to this novel structural class
Protein delivery into plant cells: Toward in vivo structural biology
Understanding the biologically relevant structural and functional behavior of proteins inside living plant cells is only possible through the combination of structural biology and cell biology. The state-of-the-art structural biology techniques are typically applied to molecules that are isolated from their native context. Although most experimental conditions can be easily controlled while dealing with an isolated, purified protein, a serious shortcoming of such in vitro work is that we cannot mimic the extremely complex intracellular environment in which the protein exists and functions. Therefore, it is highly desirable to investigate proteins in their natural habitat, i.e., within live cells. This is the major ambition of in-cell NMR, which aims to approach structure-function relationship under true in vivo conditions following delivery of labeled proteins into cells under physiological conditions. With a multidisciplinary approach that includes recombinant protein production, confocal fluorescence microscopy, nuclear magnetic resonance (NMR) spectroscopy and different intracellular protein delivery strategies, we explore the possibility to develop in-cell NMR studies in living plant cells. While we provide a comprehensive framework to set-up in-cell NMR, we identified the efficient intracellular introduction of isotope-labeled proteins as the major bottleneck. Based on experiments with the paradigmatic intrinsically disordered proteins (IDPs) Early Response to Dehydration protein 10 and 14, we also established the subcellular localization of ERD14 under abiotic stress. © 2017 Cedeño, Pauwels and Tompa
The role of structural disorder in cell cycle regulation, related clinical proteomics, disease development and drug targeting
Understanding the molecular mechanisms of the regulation of cell cycle is a central issue in molecular cell biology, due to its fundamental role in the existence of cells. The regulatory circuits that make decisions on when a cell should divide are very complex and particularly subtly balanced in eukaryotes, in which the harmony of many different cells in an organism is essential for life. Several hundred proteins are involved in these processes, and a great deal of studies attests that most of them have functionally relevant intrinsic structural disorder. Structural disorder imparts many functional advantages on these proteins, and we discuss it in detail that it is involved in all key steps from signaling through the cell membrane to regulating transcription of proteins that execute timely responses to an ever-changing environment. © Informa Uk, Ltd
Design principles involving protein disorder facilitate specific substrate selection and degradation by the ubiquitin-proteasome system
The ubiquitin-proteasome system (UPS) regulates diverse cellular pathways by the timely removal (or processing) of proteins. Here we review the role of structural disorder and conformational flexibility in the different aspects of degradation. First, we discuss post-translational modifications within disordered regions that regulate E3 ligase localization, conformation, and enzymatic activity, and also the role of flexible linkers in mediating ubiquitin transfer and reaction processivity. Next we review well studied substrates and discuss that substrate elements (degrons) recognized by E3 ligases are highly disordered: short linear motifs recognized by many E3s constitute an important class of degrons, and these are almost always present in disordered regions. Substrate lysines targeted for ubiquitination are also often located in neighboring regions of the E3 docking motifs and are therefore part of the disordered segment. Finally, biochemical experiments and predictions show that initiation of degradation at the 26S proteasome requires a partially unfolded region to facilitate substrate entry into the proteasomal core. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc
Disordered regions in transmembrane proteins.
The functions of transmembrane proteins in living cells are widespread; they range from various transport processes to energy production, from cell-cell adhesion to communication. Structurally, they are highly ordered in their membrane-spanning regions, but may contain disordered regions in the cytosolic and extra-cytosolic parts. In this study, we have investigated the disordered regions in transmembrane proteins by a stringent definition of disordered residues on the currently available largest experimental dataset, and show a significant correlation between the spatial distributions of positively charged residues and disordered regions. This finding suggests a new role of disordered regions in transmembrane proteins by providing structural flexibility for stabilizing interactions with negatively charged head groups of the lipid molecules. We also find a preference of structural disorder in the terminal - as opposed to loop - regions in transmembrane proteins, and survey the respective functions involved in recruiting other proteins or mediating allosteric signaling effects. Finally, we critically compare disorder prediction methods on our transmembrane protein set. While there are no major differences between these methods using the usual statistics, such as per residue accuracies, Matthew's correlation coefficients, etc.; substantial differences can be found regarding the spatial distribution of the predicted disordered regions. We conclude that a predictor optimized for transmembrane proteins would be of high value to the field of structural disorder
Learning of Signaling Networks: Molecular Mechanisms
Molecular processes of neuronal learning have been well described. However, learning mechanisms of non-neuronal cells are not yet fully understood at the molecular level. Here, we discuss molecular mechanisms of cellular learning, including conformational memory of intrinsically disordered proteins (IDPs) and prions, signaling cascades, protein translocation, RNAs [miRNA and long noncoding RNA (lncRNA)], and chromatin memory. We hypothesize that these processes constitute the learning of signaling networks and correspond to a generalized Hebbian learning process of single, non-neuronal cells, and we discuss how cellular learning may open novel directions in drug design and inspire new artificial intelligence methods. © 2020 The Author
Globuláris szerkezetű fehérjék vizes oldatainak olvadásidiagramja és termodinamikai értelmezésük
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