scholarly journals PGRS Domain of Rv0297 of Mycobacterium tuberculosis Functions in A Calcium Dependent Manner

2021 ◽  
Vol 22 (17) ◽  
pp. 9390
Author(s):  
Tarina Sharma ◽  
Jasdeep Singh ◽  
Sonam Grover ◽  
Manjunath P. ◽  
Firdos Firdos ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Intrinsically Disordered Proteins ◽  
Therapeutic Interventions ◽  
Disordered Proteins ◽  
No Production ◽  
Dependent Manner ◽  
Pathogenic Potential ◽  
Binding Motifs ◽  
Calcium Dependent ◽  
Intrinsically Disordered

Mycobacterium tuberculosis (M.tb), the pathogen causing tuberculosis, is a major threat to human health worldwide. Nearly 10% of M.tb genome encodes for a unique family of PE/PPE/PGRS proteins present exclusively in the genus Mycobacterium. The functions of most of these proteins are yet unexplored. The PGRS domains of these proteins have been hypothesized to consist of Ca2+ binding motifs that help these intrinsically disordered proteins to modulate the host cellular responses. Ca2+ is an important secondary messenger that is involved in the pathogenesis of tuberculosis in diverse ways. This study presents the calcium-dependent function of the PGRS domain of Rv0297 (PE_PGRS5) in M.tb virulence and pathogenesis. Tandem repeat search revealed the presence of repetitive Ca2+ binding motifs in the PGRS domain of the Rv0297 protein (Rv0297PGRS). Molecular Dynamics simulations and fluorescence spectroscopy revealed Ca2+ dependent stabilization of the Rv0297PGRS protein. Calcium stabilized Rv0297PGRS enhances the interaction of Rv0297PGRS with surface localized Toll like receptor 4 (TLR4) of macrophages. The Ca2+ stabilized binding of Rv0297PGRS with the surface receptor of macrophages enhances its downstream consequences in terms of Nitric Oxide (NO) production and cytokine release. Thus, this study points to hitherto unidentified roles of calcium-modulated PE_PGRS proteins in the virulence of M.tb. Understanding the pathogenic potential of Ca2+ dependent PE_PGRS proteins can aid in targeting these proteins for therapeutic interventions.

scholarly journals Transient Secondary Structures as General Target-Binding Motifs in Intrinsically Disordered Proteins

2018 ◽  
Vol 19 (11) ◽  
pp. 3614 ◽  
Author(s):  
Do-Hyoung Kim ◽  
Kyou-Hoon Han
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Disordered Proteins ◽  
Ample Evidence ◽  
Binding Motifs ◽  
Intrinsically Disordered ◽  
Long Time ◽  
Science Community ◽  
Target Binding

Intrinsically disordered proteins (IDPs) are unorthodox proteins that do not form three-dimensional structures under non-denaturing conditions, but perform important biological functions. In addition, IDPs are associated with many critical diseases including cancers, neurodegenerative diseases, and viral diseases. Due to the generic name of “unstructured” proteins used for IDPs in the early days, the notion that IDPs would be completely unstructured down to the level of secondary structures has prevailed for a long time. During the last two decades, ample evidence has been accumulated showing that IDPs in their target-free state are pre-populated with transient secondary structures critical for target binding. Nevertheless, such a message did not seem to have reached with sufficient clarity to the IDP or protein science community largely because similar but different expressions were used to denote the fundamentally same phenomenon of presence of such transient secondary structures, which is not surprising for a quickly evolving field. Here, we summarize the critical roles that these transient secondary structures play for diverse functions of IDPs by describing how various expressions referring to transient secondary structures have been used in different contexts.

scholarly journals Multisite Phosphorylation and Binding Alter Conformational Dynamics of the 4E-BP2 Protein

2022 ◽  
Author(s):  
Spencer Smyth ◽  
Zhenfu Zhang ◽  
Alaji Bah ◽  
Thomas Tsangaris ◽  
Jennifer Dawson ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Intrinsically Disordered Proteins ◽  
Regulatory Protein ◽  
Conformational Dynamics ◽  
Correlation Spectroscopy ◽  
Terminal Region ◽  
Disordered Proteins ◽  
Initiation Factor ◽  
Dependent Manner ◽  
Intrinsically Disordered

Intrinsically disordered proteins (IDPs) play critical roles in regulatory protein interactions, but detailed structural/dynamics characterization of their ensembles remain challenging, both in isolation and they form dynamic fuzzy complexes. Such is the case for mRNA cap-dependent translation initiation, which is regulated by the interaction of the predominantly folded eukaryotic initiation factor 4E (eIF4E) with the intrinsically disordered eIF4E binding proteins (4E-BPs) in a phosphorylation-dependent manner. Single-molecule Forster resonance energy transfer showed that the conformational changes of 4E-BP2 induced by binding to eIF4E are non-uniform along the sequence; while a central region containing both motifs that bind to eIF4E expands and becomes stiffer, the C-terminal region is less affected. Fluorescence anisotropy decay revealed a nonuniform segmental flexibility around six different labelling sites along the chain. Dynamic quenching of these fluorescent probes by intrinsic aromatic residues measured via fluorescence correlation spectroscopy report on transient intra- and inter-molecular contacts on nanosecond-microsecond timescales. Upon hyperphosphorylation, which induces folding of ~40 residues in 4E-BP2, the quenching rates decreased at labelling sites closest to the phosphorylation sites and within the folded domain, and increased at the other sites. The chain dynamics around sites in the C-terminal region far away from the two binding motifs were significantly reduced upon binding to eIF4E, suggesting that this region is also involved in the highly dynamic 4E-BP2:eIF4E complex. Our time-resolved fluorescence data paint a sequence-level rigidity map of three states of 4E-BP2 differing in phosphorylation or binding status and distinguish regions that form contacts with eIF4E. This study adds complementary structural and dynamics information to recent studies of 4E-BP2, and it constitutes an important step towards a mechanistic understanding of this important IDP via integrative modelling.

scholarly journals Dynamical Oligomerisation of Histidine Rich Intrinsically Disordered Proteins Is Regulated through Zinc-Histidine Interactions

Biomolecules ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 168 ◽  
Author(s):  
Carolina Cragnell ◽  
Lasse Staby ◽  
Samuel Lenton ◽  
Birthe Kragelund ◽  
Marie Skepö
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Intrinsically Disordered Proteins ◽  
Divalent Cations ◽  
Disordered Proteins ◽  
Resonance Spectroscopy ◽  
Binding Motifs ◽  
Histatin 5 ◽  
X Ray ◽  
Intrinsically Disordered ◽  
X Ray Scattering

Intrinsically disordered proteins (IDPs) can form functional oligomers and in some cases, insoluble disease related aggregates. It is therefore vital to understand processes and mechanisms that control pathway distribution. Divalent cations including Zn2+ can initiate IDP oligomerisation through the interaction with histidine residues but the mechanisms of doing so are far from understood. Here we apply a multi-disciplinary approach using small angle X-ray scattering, nuclear magnetic resonance spectroscopy, calorimetry and computations to show that that saliva protein Histatin 5 forms highly dynamic oligomers in the presence of Zn2+. The process is critically dependent upon interaction between Zn2+ ions and distinct histidine rich binding motifs which allows for thermodynamic switching between states. We propose a molecular mechanism of oligomerisation, which may be generally applicable to other histidine rich IDPs. Finally, as Histatin 5 is an important saliva component, we suggest that Zn2+ induced oligomerisation may be crucial for maintaining saliva homeostasis.

scholarly journals Multivalency enables unidirectional switch-like competition between intrinsically disordered proteins

2022 ◽  
Vol 119 (3) ◽  
pp. e2117338119
Author(s):  
Rebecca B. Berlow ◽  
H. Jane Dyson ◽  
Peter E. Wright
Keyword(s):  
Transcriptional Control ◽  
Intrinsically Disordered Proteins ◽  
Binding Protein ◽  
Critical Role ◽  
Molecular Switch ◽  
Negative Regulator ◽  
Disordered Proteins ◽  
Creb Binding Protein ◽  
Binding Motifs ◽  
Intrinsically Disordered

Intrinsically disordered proteins must compete for binding to common regulatory targets to carry out their biological functions. Previously, we showed that the activation domains of two disordered proteins, the transcription factor HIF-1α and its negative regulator CITED2, function as a unidirectional, allosteric molecular switch to control transcription of critical adaptive genes under conditions of oxygen deprivation. These proteins achieve transcriptional control by competing for binding to the TAZ1 domain of the transcriptional coactivators CREB-binding protein (CBP) and p300 (CREB: cyclic-AMP response element binding protein). To characterize the mechanistic details behind this molecular switch, we used solution NMR spectroscopy and complementary biophysical methods to determine the contributions of individual binding motifs in CITED2 to the overall competition process. An N-terminal region of the CITED2 activation domain, which forms a helix when bound to TAZ1, plays a critical role in initiating competition with HIF-1α by enabling formation of a ternary complex in a process that is highly dependent on the dynamics and disorder of the competing partners. Two other conserved binding motifs in CITED2, the LPEL motif and an aromatic/hydrophobic motif that we term ϕC, function synergistically to enhance binding of CITED2 and inhibit rebinding of HIF-1α. The apparent unidirectionality of competition between HIF-1α and CITED2 is lost when one or more of these binding regions is altered by truncation or mutation of the CITED2 peptide. Our findings illustrate the complexity of molecular interactions involving disordered proteins containing multivalent interaction motifs and provide insight into the unique mechanisms by which disordered proteins compete for occupancy of common molecular targets within the cell.

scholarly journals Mechanisms of small-molecule binding to intrinsically disordered proteins

2012 ◽  
Vol 40 (5) ◽  
pp. 1004-1008 ◽  
Author(s):  
Rémi Cuchillo ◽  
Julien Michel
Keyword(s):  
Small Molecules ◽  
Intrinsically Disordered Proteins ◽  
Amyloid Β ◽  
Therapeutic Interventions ◽  
Disordered Proteins ◽  
Amyloid Β Peptide ◽  
Structure Based Drug Design ◽  
Intrinsically Disordered ◽  
Rational Drug ◽  
Aβ Amyloid

IDPs (intrinsically disordered proteins) play crucial roles in many important cellular processes such as signalling or transcription and are attractive therapeutic targets for several diseases. The considerable structural flexibility of IDPs poses a challenge for rational drug discovery approaches. Consequently, structure-based drug design efforts to date have mostly focused on inhibiting interactions of IDPs with other proteins whose structure can be solved by conventional biophysical methods. Yet, in recent years, several examples of small molecules that bind to monomeric IDPs in their disordered states have been reported, suggesting that this approach may offer new opportunities for therapeutic interventions. Further developments of this strategy will greatly benefit from an improved understanding of molecular recognition mechanisms between small molecules and IDPs. The present article summarizes findings from experimental and computational studies of the mechanisms of interaction between small molecules and three IDPs in their disordered states: c-Myc, Aβ (amyloid β-peptide) and α-synuclein.

scholarly journals On the specificity of protein–protein interactions in the context of disorder

2021 ◽  
Vol 478 (11) ◽  
pp. 2035-2050
Author(s):  
Kaare Teilum ◽  
Johan G. Olsen ◽  
Birthe B. Kragelund
Keyword(s):  
Protein Interactions ◽  
Intrinsically Disordered Proteins ◽  
Globular Proteins ◽  
Disordered Proteins ◽  
Protein Protein Interactions ◽  
Binding Motifs ◽  
Intrinsically Disordered ◽  
Binding Partners ◽  
Trimer Formation ◽  
Definition Of

With the increased focus on intrinsically disordered proteins (IDPs) and their large interactomes, the question about their specificity — or more so on their multispecificity — arise. Here we recapitulate how specificity and multispecificity are quantified and address through examples if IDPs in this respect differ from globular proteins. The conclusion is that quantitatively, globular proteins and IDPs are similar when it comes to specificity. However, compared with globular proteins, IDPs have larger interactome sizes, a phenomenon that is further enabled by their flexibility, repetitive binding motifs and propensity to adapt to different binding partners. For IDPs, this adaptability, interactome size and a higher degree of multivalency opens for new interaction mechanisms such as facilitated exchange through trimer formation and ultra-sensitivity via threshold effects and ensemble redistribution. IDPs and their interactions, thus, do not compromise the definition of specificity. Instead, it is the sheer size of their interactomes that complicates its calculation. More importantly, it is this size that challenges how we conceptually envision, interpret and speak about their specificity.

scholarly journals Interplay between allostery and intrinsic disorder in an ensemble

2012 ◽  
Vol 40 (5) ◽  
pp. 975-980 ◽  
Author(s):  
Hesam N. Motlagh ◽  
Jing Li ◽  
E. Brad Thompson ◽  
Vincent J. Hilser
Keyword(s):  
Metabolic Regulation ◽  
Intrinsically Disordered Proteins ◽  
Cell Signalling ◽  
Disordered Proteins ◽  
Dependent Manner ◽  
Intrinsically Disordered ◽  
Classical Models ◽  
A Cell ◽  
Action At A Distance ◽  
External Signals

Allostery is a biological phenomenon of critical importance in metabolic regulation and cell signalling. The fundamental premise of classical models that describe allostery is that structure mediates ‘action at a distance’. Recently, this paradigm has been challenged by the enrichment of IDPs (intrinsically disordered proteins) or ID (intrinsically disordered) segments in transcription factors and signalling pathways of higher organisms, where an allosteric response from external signals is requisite for regulated function. This observation strongly suggests that IDPs elicit the capacity for finely tunable allosteric regulation. Is there a set of transferable ground rules that reconcile these disparate allosteric phenomena? We focus on findings from the human GR (glucocorticoid receptor) which is a nuclear transcription factor in the SHR (steroid hormone receptor) family. GR contains an intrinsically disordered NTD (N-terminal domain) that is obligatory for transcription activity. Different GR translational isoforms have various lengths of NTD and by studying these isoforms we found that the full-length ID NTD consists of two thermodynamically distinct coupled regions. The data are interpreted in the context of an EAM (ensemble allosteric model) that considers only the intrinsic and measurable energetics of allosteric systems. Expansion of the EAM is able to reconcile the paradox that ligands for SHRs can be agonists and antagonists in a cell-context-dependent manner. These findings suggest a mechanism by which SHRs in particular, and IDPs in general, may have evolved to couple thermodynamically distinct ID segments. The ensemble view of allostery that is illuminated provides organizing principles to unify the description of all allosteric systems and insight into ‘how’ allostery works.

scholarly journals Therapeutic Interventions of Cancers Using Intrinsically Disordered Proteins as Drug Targets: c-Myc as Model System

2017 ◽  
Vol 16 ◽  
pp. 117693511769940 ◽  
Author(s):  
Deepak Kumar ◽  
Nitin Sharma ◽  
Rajanish Giri
Keyword(s):  
Drug Targets ◽  
Intrinsically Disordered Proteins ◽  
Hot Spot ◽  
Intrinsic Disorder ◽  
Therapeutic Interventions ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
In Vivo Experiments

The concept of protein intrinsic disorder has taken the driving seat to understand regulatory proteins in general. Reports suggest that in mammals nearly 75% of signalling proteins contain long disordered regions with greater than 30 amino acid residues. Therefore, intrinsically disordered proteins (IDPs) have been implicated in several human diseases and should be considered as potential novel drug targets. Moreover, intrinsic disorder provides a huge multifunctional capability to hub proteins such as c-Myc and p53. c-Myc is the hot spot for understanding and developing therapeutics against cancers and cancer stem cells. Our past understanding is mainly based on in vitro and in vivo experiments conducted using c-Myc as whole protein. Using the reductionist approach, c-Myc oncoprotein has been divided into structured and disordered domains. A wealth of data is available dealing with the structured perspectives of c-Myc, but understanding c-Myc in terms of disordered domains has just begun. Disorderness provides enormous flexibility to proteins in general for binding to numerous partners. Here, we have reviewed the current progress on understanding c-Myc using the emerging concept of IDPs.

scholarly journals Insight into Calcium-Binding Motifs of Intrinsically Disordered Proteins

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1173
Author(s):  
Estella A. Newcombe ◽  
Catarina B. Fernandes ◽  
Jeppe E. Lundsgaard ◽  
Inna Brakti ◽  
Kresten Lindorff-Larsen ◽  
...  
Keyword(s):  
Calcium Binding ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Binding Motif ◽  
Binding Motifs ◽  
Functional Roles ◽  
Intrinsically Disordered ◽  
Ef Hand ◽  
Folded Proteins ◽  
Affinity Quantification

Motifs within proteins help us categorize their functions. Intrinsically disordered proteins (IDPs) are rich in short linear motifs, conferring them many different roles. IDPs are also frequently highly charged and, therefore, likely to interact with ions. Canonical calcium-binding motifs, such as the EF-hand, often rely on the formation of stabilizing flanking helices, which are a key characteristic of folded proteins, but are absent in IDPs. In this study, we probe the existence of a calcium-binding motif relevant to IDPs. Upon screening several carefully selected IDPs using NMR spectroscopy supplemented with affinity quantification by colorimetric assays, we found calcium-binding motifs in IDPs which could be categorized into at least two groups—an Excalibur-like motif, sequentially similar to the EF-hand loop, and a condensed-charge motif carrying repetitive negative charges. The motifs show an affinity for calcium typically in the ~100 μM range relevant to regulatory functions and, while calcium binding to the condensed-charge motif had little effect on the overall compaction of the IDP chain, calcium binding to Excalibur-like motifs resulted in changes in compaction. Thus, calcium binding to IDPs may serve various structural and functional roles that have previously been underreported.

Sign in / Sign up

Export Citation Format

Share Document