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.

Structural characterization of intrinsically disordered proteins by the combined use of NMR and SAXS

2012 ◽  
Vol 40 (5) ◽  
pp. 955-962 ◽  
Author(s):  
Nathalie Sibille ◽  
Pau Bernadó
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Dynamic Models ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Main Tool ◽  
Structural Features ◽  
Disordered Proteins ◽  
Dimensional Structure ◽  
Intrinsically Disordered ◽  
Conformational Preferences

In recent years, IDPs (intrinsically disordered proteins) have emerged as pivotal actors in biology. Despite IDPs being present in all kingdoms of life, they are more abundant in eukaryotes where they are involved in the vast majority of regulation and signalling processes. The realization that, in some cases, functional states of proteins were partly or fully disordered was in contradiction to the traditional view where a well defined three-dimensional structure was required for activity. Several experimental evidences indicate, however, that structural features in IDPs such as transient secondary-structural elements and overall dimensions are crucial to their function. NMR has been the main tool to study IDP structure by probing conformational preferences at residue level. Additionally, SAXS (small-angle X-ray scattering) has the capacity to report on the three-dimensional space sampled by disordered states and therefore complements the local information provided by NMR. The present review describes how the synergy between NMR and SAXS can be exploited to obtain more detailed structural and dynamic models of IDPs in solution. These combined strategies, embedded into computational approaches, promise the elucidation of the structure–function properties of this important, but elusive, family of biomolecules.

scholarly journals Disorder Atlas: web-based software for the proteome-based interpretation of intrinsic disorder predictions

2016 ◽  
Author(s):  
Michael Vincent ◽  
Santiago Schnell
Keyword(s):  
Large Scale ◽  
Intrinsically Disordered Proteins ◽  
Three Dimensional ◽  
Intrinsic Disorder ◽  
Query Protein ◽  
Disordered Proteins ◽  
Dimensional Structure ◽  
Web Based ◽  
Intrinsically Disordered ◽  
Eukaryotic Proteomes

AbstractIntrinsically disordered proteins lack a stable three-dimensional structure under physiological conditions. While this property has gained considerable interest within the past two decades, disorder poses substantial challenges to experimental characterization efforts. In effect, numerous computational tools have been developed to predict disorder from primary sequences, however, interpreting the output of these algorithms remains a challenge. To begin to bridge this gap, we present Disorder Atlas, web-based software that facilitates the interpretation of intrinsic disorder predictions using proteome-based descriptive statistics. This service is also equipped to facilitate large-scale systematic exploratory searches for proteins encompassing disorder features of interest, and further allows users to browse the prevalence of multiple disorder features at the proteome level. As a result, Disorder Atlas provides a user-friendly tool that places algorithm-generated disorder predictions in the context of the proteome, thereby providing an instrument to compare the results of a query protein against predictions made for an entire population. Disorder Atlas currently supports ten eukaryotic proteomes and is freely available for non-commercial users at http://www.disorderatlas.org.

scholarly journals Function, Regulation, and Dysfunction of Intrinsically Disordered Proteins

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 140
Author(s):  
Giuliana Fusco ◽  
Stefano Gianni
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Three Dimensional ◽  
Disordered Proteins ◽  
Dimensional Structure ◽  
Native State ◽  
Three Dimensional Structure ◽  
Considerable Fraction ◽  
Intrinsically Disordered ◽  
Eukaryotic Proteins

The discovery that a considerable fraction of the eukaryotic proteins lacks a well-defined three-dimensional structure in their native state has revolutionised our general understanding of proteins [...]

scholarly journals Exclusively heteronuclear NMR experiments for the investigation of intrinsically disordered proteins: focusing on proline residues

2021 ◽  
Author(s):  
Isabella C. Felli ◽  
Wolfgang Bermel ◽  
Roberta Pierattelli
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Heteronuclear Nmr ◽  
Three Dimensional ◽  
Spectroscopic Technique ◽  
Disordered Proteins ◽  
Amide Proton ◽  
Dimensional Structure ◽  
Intrinsically Disordered ◽  
Valuable Complement ◽  
Polypeptide Chains

Abstract. NMR represents a key spectroscopic technique to contribute to the emerging field of highly flexible, intrinsically disordered proteins (IDPs) or protein regions (IDRs) that lack a stable three-dimensional structure. A set of exclusively heteronuclear NMR experiments tailored for proline residues, highly abundant in IDPs/IDRs, are presented here. They provide a valuable complement to the widely used approach based on amide proton detection, filling the gap introduced by the lack of amide protons in prolines within polypeptide chains. The novel experiments have very interesting properties for the investigations of IDPs/IDRs of increasing complexity.

scholarly journals Exclusively heteronuclear NMR experiments for the investigation of intrinsically disordered proteins: focusing on proline residues

2021 ◽  
Vol 2 (1) ◽  
pp. 511-522
Author(s):  
Isabella C. Felli ◽  
Wolfgang Bermel ◽  
Roberta Pierattelli
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Heteronuclear Nmr ◽  
Three Dimensional ◽  
Spectroscopic Technique ◽  
Disordered Proteins ◽  
Amide Proton ◽  
Dimensional Structure ◽  
Intrinsically Disordered ◽  
Valuable Complement ◽  
Polypeptide Chains

Abstract. NMR represents a key spectroscopic technique that contributes to the emerging field of highly flexible, intrinsically disordered proteins (IDPs) or protein regions (IDRs) that lack a stable three-dimensional structure. A set of exclusively heteronuclear NMR experiments tailored for proline residues, highly abundant in IDPs/IDRs, are presented here. They provide a valuable complement to the widely used approach based on amide proton detection, filling the gap introduced by the lack of amide protons in proline residues within polypeptide chains. The novel experiments have very interesting properties for the investigations of IDPs/IDRs of increasing complexity.

scholarly journals Molecular chaperones: guardians of the proteome in normal and disease states

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 1448 ◽  
Author(s):  
Wilson Jeng ◽  
Sukyeong Lee ◽  
Nuri Sung ◽  
Jungsoon Lee ◽  
Francis T.F. Tsai
Keyword(s):  
Molecular Chaperones ◽  
Protein Unfolding ◽  
Intrinsically Disordered Proteins ◽  
Protein Quality ◽  
Three Dimensional ◽  
Forward Direction ◽  
Disordered Proteins ◽  
Dimensional Structure ◽  
Functional Protein ◽  
Intrinsically Disordered

Proteins must adopt a defined three-dimensional structure in order to gain functional activity, or must they? An ever-increasing number of intrinsically disordered proteins and amyloid-forming polypeptides challenge this dogma. While molecular chaperones and proteases are traditionally associated with protein quality control inside the cell, it is now apparent that molecular chaperones not only promote protein folding in the “forward” direction by facilitating folding and preventing misfolding and aggregation, but also facilitate protein unfolding and even disaggregation resulting in the recovery of functional protein from aggregates. Here, we review our current understanding of ATP-dependent molecular chaperones that harness the energy of ATP binding and hydrolysis to fuel their chaperone functions. An emerging theme is that most of these chaperones do not work alone, but instead function together with other chaperone systems to maintain the proteome. Hence, molecular chaperones are the major component of the proteostasis network that guards and protects the proteome from damage. Furthermore, while a decline of this network is detrimental to cell and organismal health, a controlled perturbation of the proteostasis network may offer new therapeutic avenues against human diseases.

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.

scholarly journals Disorder in a two-domain neuronal Ca2+-binding protein regulates domain stability and dynamics using ligand mimicry

2020 ◽  
Author(s):  
Lasse Staby ◽  
Katherine R. Kemplen ◽  
Amelie Stein ◽  
Michael Ploug ◽  
Jane Clarke ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Three Dimensional ◽  
Life Time ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Order And Disorder ◽  
C Terminus ◽  
Close Relationship ◽  
Stability Dynamics ◽  
And Function

Abstract Understanding the interplay between sequence, structure and function of proteins has been complicated in recent years by the discovery of intrinsically disordered proteins (IDPs), which perform biological functions in the absence of a well-defined three-dimensional fold. Disordered protein sequences account for roughly 30% of the human proteome and in many proteins, disordered and ordered domains coexist. However, few studies have assessed how either feature affects the properties of the other. In this study, we examine the role of a disordered tail in the overall properties of the two-domain, calcium-sensing protein neuronal calcium sensor 1 (NCS-1). We show that loss of just six of the 190 residues at the flexible C-terminus is sufficient to severely affect stability, dynamics, and folding behavior of both ordered domains. We identify specific hydrophobic contacts mediated by the disordered tail that may be responsible for stabilizing the distal N-terminal domain. Moreover, sequence analyses indicate the presence of an LSL-motif in the tail that acts as a mimic of native ligands critical to the observed order–disorder communication. Removing the disordered tail leads to a shorter life-time of the ligand-bound complex likely originating from the observed destabilization. This close relationship between order and disorder may have important implications for how investigations into mixed systems are designed and opens up a novel avenue of drug targeting exploiting this type of behavior.

An intrinsically disordered protein, CP12: jack of all trades and master of the Calvin cycle

2012 ◽  
Vol 40 (5) ◽  
pp. 995-999 ◽  
Author(s):  
Brigitte Gontero ◽  
Stephen C. Maberly
Keyword(s):  
Amino Acids ◽  
Stress Responses ◽  
Intrinsically Disordered Proteins ◽  
Calvin Cycle ◽  
Intrinsically Disordered Protein ◽  
Disulfide Bridge ◽  
Co2 Assimilation ◽  
Disordered Proteins ◽  
Dimensional Structure ◽  
Intrinsically Disordered

Many proteins contain disordered regions under physiological conditions and lack specific three-dimensional structure. These are referred to as IDPs (intrinsically disordered proteins). CP12 is a chloroplast protein of approximately 80 amino acids and has a molecular mass of approximately 8.2–8.5 kDa. It is enriched in charged amino acids and has a small number of hydrophobic residues. It has a high proportion of disorder-promoting residues, but has at least two (often four) cysteine residues forming one (or two) disulfide bridge(s) under oxidizing conditions that confers some order. However, CP12 behaves like an IDP. It appears to be universally distributed in oxygenic photosynthetic organisms and has recently been detected in a cyanophage. The best studied role of CP12 is its regulation of the Calvin cycle responsible for CO2 assimilation. Oxidized CP12 forms a supramolecular complex with two key Calvin cycle enzymes, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and PRK (phosphoribulokinase), down-regulating their activity. Association–dissociation of this complex, induced by the redox state of CP12, allows the Calvin cycle to be inactive in the dark and active in the light. CP12 is promiscuous and interacts with other enzymes such as aldolase and malate dehydrogenase. It also plays other roles in plant metabolism such as protecting GAPDH from inactivation and scavenging metal ions such as copper and nickel, and it is also linked to stress responses. Thus CP12 seems to be involved in many functions in photosynthetic cells and behaves like a jack of all trades as well as being a master of the Calvin cycle.

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