scholarly journals Differential dehydration effects on globular proteins and intrinsically disordered proteins during film formation

2017 ◽  
Vol 26 (4) ◽  
pp. 718-726 ◽  
Author(s):  
Juliana Sakamoto Yoneda ◽  
Andew J. Miles ◽  
Ana Paula Ulian Araujo ◽  
B. A. Wallace
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Film Formation ◽  
Globular Proteins ◽  
Disordered Proteins ◽  
Intrinsically Disordered

scholarly journals Sequence Versus Composition: What Prescribes IDP Biophysical Properties?

Entropy ◽  
2019 ◽  
Vol 21 (7) ◽  
pp. 654 ◽  
Author(s):  
Jiří Vymětal ◽  
Jiří Vondrášek ◽  
Klára Hlouchová
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Intrinsically Disordered Proteins ◽  
Random Sequence ◽  
Bioinformatic Analysis ◽  
Globular Proteins ◽  
Disordered Proteins ◽  
Compositional Bias ◽  
Intrinsically Disordered ◽  
Sequence Versus

Intrinsically disordered proteins (IDPs) represent a distinct class of proteins and are distinguished from globular proteins by conformational plasticity, high evolvability and a broad functional repertoire. Some of their properties are reminiscent of early proteins, but their abundance in eukaryotes, functional properties and compositional bias suggest that IDPs appeared at later evolutionary stages. The spectrum of IDP properties and their determinants are still not well defined. This study compares rudimentary physicochemical properties of IDPs and globular proteins using bioinformatic analysis on the level of their native sequences and random sequence permutations, addressing the contributions of composition versus sequence as determinants of the properties. IDPs have, on average, lower predicted secondary structure contents and aggregation propensities and biased amino acid compositions. However, our study shows that IDPs exhibit a broad range of these properties. Induced fold IDPs exhibit very similar compositions and secondary structure/aggregation propensities to globular proteins, and can be distinguished from unfoldable IDPs based on analysis of these sequence properties. While amino acid composition seems to be a major determinant of aggregation and secondary structure propensities, sequence randomization does not result in dramatic changes to these properties, but for both IDPs and globular proteins seems to fine-tune the tradeoff between folding and aggregation.

scholarly journals Cyclic Ion Mobility – Collision Activation Experiments Elucidate Protein Behaviour in the Gas-Phase

2020 ◽  
Author(s):  
Charles Eldrid ◽  
Jakub Ujma ◽  
Hannah Britt ◽  
Tristan Cragnolini ◽  
Symeon Kalfas ◽  
...  
Keyword(s):  
Gas Phase ◽  
Ion Mobility ◽  
Protein Unfolding ◽  
Intrinsically Disordered Proteins ◽  
Conformational Dynamics ◽  
Globular Proteins ◽  
Disordered Proteins ◽  
Mass Selection ◽  
Intrinsically Disordered ◽  
Partially Folded States

<i>Elucidating the properties of intrinsically disordered proteins (IDPs) and unfolded and partially folded states of globular proteins is challenging owing to their heterogeneous and dynamic nature. Protein unfolding and misfolding is a key feature of a broad range of debilitating diseases, whilst the conformational propensities of intrinsically disordered proteins can play a significant role in modulating their activity, and the properties of unfolded states of globular proteins modulates their stability and tendency to aggregate. Ion mobility-mass spectrometry (IM-MS) is a powerful method for interrogating these systems, however limits in resolution and the difficulty in probing the energetics of interconversions amongst heterogeneous ensembles are major issues. Herein, using a quadrupole/cyclic-IM/ time-of-flight MS instrument, we show how the combination of precursor mass selection, mobility selection (IM<sup>n</sup>) and collisional activation (CA) allows the elucidation of complicated gas-phase dynamic behavior. The methodology employed is general and is demonstrated using a classic model globular protein, cytochrome C, and an aggregation-prone IDP, amylin. CA allows investigations of protein conformational dynamics and unfolding in the gas-phase for heterogeneous mixtures, whilst the additional precursor mass selection capability provides high resolution and selectivity, facilitating more in-depth investigation. Understanding protein dynamics in the gas-phase will allow greater insight into protein behaviour and allow application of gas-phase techniques to clinically relevant systems. </i>

Intrinsically disordered proteins: administration not executive

2012 ◽  
Vol 40 (5) ◽  
pp. 945-949 ◽  
Author(s):  
Mike P. Williamson ◽  
Jennifer R. Potts
Keyword(s):  
Executive Functions ◽  
Intrinsically Disordered Proteins ◽  
Globular Proteins ◽  
Disordered Proteins ◽  
Pharmaceutical Intervention ◽  
Intrinsically Disordered ◽  
Good Target ◽  
Eukaryotic Genomes

IDPs (intrinsically disordered proteins) are common in eukaryotic genomes and have regulatory roles. In the cell, they are disordered, although not completely random. They bind weakly, but specifically, often remaining partially disordered even when bound. Whereas folded globular proteins have ‘executive’ roles in the cell, IDPs have an essential administrative function, making sure that the executive functions are properly co-ordinated. This makes them a good target for pharmaceutical intervention.

scholarly journals Unraveling the Thermodynamics of Ultra-tight Binding of Intrinsically Disordered Proteins

2021 ◽  
Vol 8 ◽  
Author(s):  
Uroš Zavrtanik ◽  
San Hadži ◽  
Jurij Lah
Keyword(s):  
Protein Interactions ◽  
Intrinsically Disordered Proteins ◽  
Tight Binding ◽  
Bound State ◽  
Globular Proteins ◽  
Disordered Proteins ◽  
Prothymosin Α ◽  
Intrinsically Disordered ◽  
High Affinity ◽  
Entropy Optimization

Protein interactions mediated by the intrinsically disordered proteins (IDPs) are generally associated with lower affinities compared to those between globular proteins. Here, we characterize the association between the intrinsically disordered HigA2 antitoxin and its globular target HigB2 toxin from Vibrio cholerae using competition ITC experiments. We demonstrate that this interaction reaches one of the highest affinities reported for IDP-target systems (KD = 3 pM) and can be entirely attributed to a short, 20-residue-long interaction motif that folds into α-helix upon binding. We perform an experimentally based decomposition of the IDP-target association parameters into folding and binding contributions, which allows a direct comparison of the binding contribution with those from globular ultra-high affinity binders. We find that the HigA2-HigB2 interface is energy optimized to a similar extent as the interfaces of globular ultra-high affinity complexes, such as barnase-barstar. Evaluation of other ultra-high affinity IDP-target systems shows that a strategy based on entropy optimization can also achieve comparably high, picomolar affinities. Taken together, these examples show how IDP-target interactions achieve picomolar affinities either through enthalpy optimization (HigA2-HigB2), resembling the ultra-high affinity binding of globular proteins, or via bound-state fuzziness and entropy optimization (CcdA-CcdB, histone H1-prothymosin α).

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 Cyclic Ion Mobility – Collision Activation Experiments Elucidate Protein Behaviour in the Gas-Phase

2020 ◽  
Author(s):  
Charles Eldrid ◽  
Jakub Ujma ◽  
Hannah Britt ◽  
Tristan Cragnolini ◽  
Symeon Kalfas ◽  
...  
Keyword(s):  
Gas Phase ◽  
Ion Mobility ◽  
Protein Unfolding ◽  
Intrinsically Disordered Proteins ◽  
Conformational Dynamics ◽  
Globular Proteins ◽  
Disordered Proteins ◽  
Mass Selection ◽  
Intrinsically Disordered ◽  
Partially Folded States

<i>Elucidating the properties of intrinsically disordered proteins (IDPs) and unfolded and partially folded states of globular proteins is challenging owing to their heterogeneous and dynamic nature. Protein unfolding and misfolding is a key feature of a broad range of debilitating diseases, whilst the conformational propensities of intrinsically disordered proteins can play a significant role in modulating their activity, and the properties of unfolded states of globular proteins modulates their stability and tendency to aggregate. Ion mobility-mass spectrometry (IM-MS) is a powerful method for interrogating these systems, however limits in resolution and the difficulty in probing the energetics of interconversions amongst heterogeneous ensembles are major issues. Herein, using a quadrupole/cyclic-IM/ time-of-flight MS instrument, we show how the combination of precursor mass selection, mobility selection (IM<sup>n</sup>) and collisional activation (CA) allows the elucidation of complicated gas-phase dynamic behavior. The methodology employed is general and is demonstrated using a classic model globular protein, cytochrome C, and an aggregation-prone IDP, amylin. CA allows investigations of protein conformational dynamics and unfolding in the gas-phase for heterogeneous mixtures, whilst the additional precursor mass selection capability provides high resolution and selectivity, facilitating more in-depth investigation. Understanding protein dynamics in the gas-phase will allow greater insight into protein behaviour and allow application of gas-phase techniques to clinically relevant systems. </i>

scholarly journals Configurational Entropy of Folded Proteins and Its Importance for Intrinsically Disordered Proteins

2021 ◽  
Vol 22 (7) ◽  
pp. 3420
Author(s):  
Meili Liu ◽  
Akshaya K. Das ◽  
James Lincoff ◽  
Sukanya Sasmal ◽  
Sara Y. Cheng ◽  
...  
Keyword(s):  
Force Field ◽  
Intrinsically Disordered Proteins ◽  
Force Fields ◽  
Configurational Entropy ◽  
Globular Proteins ◽  
Disordered Proteins ◽  
Radius Of Gyration ◽  
Body Protein ◽  
Field Development ◽  
Intrinsically Disordered

Many pairwise additive force fields are in active use for intrinsically disordered proteins (IDPs) and regions (IDRs), some of which modify energetic terms to improve the description of IDPs/IDRs but are largely in disagreement with solution experiments for the disordered states. This work considers a new direction—the connection to configurational entropy—and how it might change the nature of our understanding of protein force field development to equally well encompass globular proteins, IDRs/IDPs, and disorder-to-order transitions. We have evaluated representative pairwise and many-body protein and water force fields against experimental data on representative IDPs and IDRs, a peptide that undergoes a disorder-to-order transition, for seven globular proteins ranging in size from 130 to 266 amino acids. We find that force fields with the largest statistical fluctuations consistent with the radius of gyration and universal Lindemann values for folded states simultaneously better describe IDPs and IDRs and disorder-to-order transitions. Hence, the crux of what a force field should exhibit to well describe IDRs/IDPs is not just the balance between protein and water energetics but the balance between energetic effects and configurational entropy of folded states of globular proteins.

scholarly journals Understanding the Binding Induced Folding of Intrinsically Disordered Proteins by Protein Engineering: Caveats and Pitfalls

2020 ◽  
Vol 21 (10) ◽  
pp. 3484 ◽  
Author(s):  
Francesca Malagrinò ◽  
Lorenzo Visconti ◽  
Livia Pagano ◽  
Angelo Toto ◽  
Francesca Troilo ◽  
...  
Keyword(s):  
Free Energy ◽  
Intrinsically Disordered Proteins ◽  
Three Dimensional ◽  
Globular Proteins ◽  
Disordered Proteins ◽  
Dimensional Structure ◽  
Value Analysis ◽  
Intrinsically Disordered ◽  
Induced Folding ◽  
Key Techniques

Many proteins lack a well-defined three-dimensional structure in isolation. These proteins, typically denoted as intrinsically disordered proteins (IDPs), may display a characteristic disorder-to-order transition when binding their physiological partner(s). From an experimental perspective, it is of great importance to establish the general grounds to understand how such folding processes may be explored. Here we discuss the caveats and the pitfalls arising when applying to IDPs one of the key techniques to characterize the folding of globular proteins, the Φ value analysis. This method is based on measurements of the free energy changes of transition and native states upon conservative, non-disrupting, mutations. On the basis of available data, we reinforce the validity of Φ value analysis in the study of IDPs and suggest future experiments to further validate this powerful experimental method.

scholarly journals Templated folding of intrinsically disordered proteins

2020 ◽  
Vol 295 (19) ◽  
pp. 6586-6593 ◽  
Author(s):  
Angelo Toto ◽  
Francesca Malagrinò ◽  
Lorenzo Visconti ◽  
Francesca Troilo ◽  
Livia Pagano ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Current Knowledge ◽  
Large Fraction ◽  
Globular Proteins ◽  
Order Transition ◽  
Disordered Proteins ◽  
Linear Free Energy Relationship ◽  
Intrinsically Disordered ◽  
Linear Free Energy ◽  
Induced Folding

Much of our current knowledge of biological chemistry is founded in the structure-function relationship, whereby sequence determines structure that determines function. Thus, the discovery that a large fraction of the proteome is intrinsically disordered, while being functional, has revolutionized our understanding of proteins and raised new and interesting questions. Many intrinsically disordered proteins (IDPs) have been determined to undergo a disorder-to-order transition when recognizing their physiological partners, suggesting that their mechanisms of folding are intrinsically different from those observed in globular proteins. However, IDPs also follow some of the classic paradigms established for globular proteins, pointing to important similarities in their behavior. In this review, we compare and contrast the folding mechanisms of globular proteins with the emerging features of binding-induced folding of intrinsically disordered proteins. Specifically, whereas disorder-to-order transitions of intrinsically disordered proteins appear to follow rules of globular protein folding, such as the cooperative nature of the reaction, their folding pathways are remarkably more malleable, due to the heterogeneous nature of their folding nuclei, as probed by analysis of linear free-energy relationship plots. These insights have led to a new model for the disorder-to-order transition in IDPs termed “templated folding,” whereby the binding partner dictates distinct structural transitions en route to product, while ensuring a cooperative folding.

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