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Search · four archives
24 papers · ranked by Valyu relevance
A Keith Dunker, Christopher J Oldfield, Jingwei Meng, Pedro Romero + 5 more
'Jack Y Yang' 'Jessica Walton Chen' 'Vladimir Vacic' 'Zoran Obradovic' 'Vladimir N Uversky'] Background Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK…
Rakesh Trivedi, Hampapathalu Adimurthy Nagarajaram, Josephine C. Ferreon, Allan Chris M. Ferreon
'Josephine C. Ferreon' 'Allan Chris M. Ferreon'] Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant…
April L. Darling, Boris Y. Zaslavsky, Vladimir N. Uversky
The visible outcome of liquid-liquid phase transitions (LLPTs) in cells is the formation and disintegration of various proteinaceous membrane-less organelles (PMLOs). Although LLPTs and related PMLOs have been observed in living cells for over 200 years, the physiological functions of these transitions (also known as…
Shelly DeForte, Vladimir N. Uversky, Derek J. McPhee
In addition to the “traditional” proteins characterized by the unique crystal-like structures needed for unique functions, it is increasingly recognized that many proteins or protein regions (collectively known as intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs)), being…
Florencio Pazos, Natalia Pietrosemoli, Juan A. García-Martín, Roberto Solano
'Roberto Solano'] To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially…
Sergio Forcelloni, Antonio Deiana, Andrea Giansanti
In a recent study, we have introduced an operational classification of the human proteome in three variants of disorder: ordered proteins (ORDPs), structured proteins with intrinsically disordered protein regions (IDPRs), intrinsically disordered proteins (IDPs). That classification was useful in functionally…
Antonio Deiana, Sergio Forcelloni, Alessandro Porrello, Andrea Giansanti
We propose a new, sequence-only, classification of intrinsically disordered human proteins which is based on two parameters: dr, the percentage of disordered residues, and Ld, the length of the longest disordered segment in the sequence. Depending on dr and Ld, we distinguish five variants: i) ordered proteins (ORDs)…
Sidra Ilyas, Abdul Manan
The contribution of redox active properties of cysteines in intrinsically disordered regions (IDRs) of proteins is not very well acknowledged. Despite of providing structural stability and rigidity, intrinsically disordered cysteines are exceptional redox sensors and the redox status of the protein defines its…
Michael Vincent, Mark Whidden, Santiago Schnell
Intrinsically disordered proteins fail to adopt a stable three-dimensional structure under physiological conditions. It is now understood that many disordered proteins are not dysfunctional, but instead engage in numerous cellular processes, including signaling and regulation. Disorder characterization from amino acid…
Antonio Deiana, Sergio Forcelloni, Alessandro Porrello, Andrea Giansanti
Many studies about classification and the functional annotation of intrinsically disordered proteins (IDPs) are based on either the occurrence of long disordered regions or the fraction of disordered residues in the sequence. Taking into account both criteria we separate the human proteome, taken as a case study, into…
Konda Mani Saravanan, A Keith Dunker, Sankaran Krishnaswamy
More than sixty prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the world-wide web. Nearly, all of these predictors give balanced accuracies in the ~65% to ~80% range. Since predictors are not perfect, further studies are required to…
Antonio Deiana, Andrea Giansanti
In this paper we propose a straightforward operational definition of variants of disordered proteins, taking the human proteome as a case study. The focus is on a distinction between mostly unstructured proteins and proteins which contain long unstructured regions accommodated in an overall folded structure. Two…
Zi Hao Liu, Maria Tsanai, Oufan Zhang, Julie D. Forman‐Kay + 1 more
'Teresa Head‐Gordon'] In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community has made significant strides in unraveling the intricate…
Swarnadeep Seth, Brandon Stine, Aniket Bhattacharya
We report simulation studies of 33 single intrinsically disordered proteins (IDPs) using coarsegrained (CG) bead-spring models where interactions among different amino acids are introduced through a hydropathy matrix and additional screened Coulomb interaction for the charged amino acid beads. Our simulation studies of…
Lunna Li, Tommaso Casalini, Paolo Arosio, Matteo Salvalaglio
Intrinsically disordered proteins (IDPs) play a key role in many biological processes, including the formation of biomolecular condensates within cells. A detailed characterization of their configurational ensemble and structure-function paradigm is crucial for understanding their biological activity and for exploiting…
Beatriz Seoane, Alessandra Carbone
The importance of unstructured biology has quickly grown during the last decades accompanying the explosion of the number of experimentally resolved protein structures. The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the literature, although the number of…
Zi Hao Liu, Maria Tsanai, Oufan Zhang, Teresa Head‐Gordon + 1 more
Disordered Protein Systems Authors: ['Zi Hao Liu' 'Maria Tsanai' 'Oufan Zhang' 'Teresa Head‐Gordon' 'Julie D. Forman‐Kay'] Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe…
Antonio Deiana, Andrea Giansanti
Intrinsically disordered proteins are fascinating the community of protein science since the last decade, at least. There is a well-established line of research that intends to reveal the crucial role played by intrinsically disordered proteins (IDPs) in the development of human diseases. The main argument is that IDPs…
Authors not listed
Intrinsically disordered proteins (IDPs) pose a challenge for structural characterization, as experimental methods lack the sub-nanometer/sub-nanosecond resolution to capture their dynamic conformational ensembles. Molecular dynamics (MD) simulations can, in principle, provide this information, but for the simulation…
Selene M.C. Cannelli, Ritvik Gupta, Tan Nguyen, Arunava Poddar + 3 more
Liquid-liquid phase separation (LLPS) is a process that often occurs due to binding between oppositely charged biopolymers, and has gained increasing attention recently due to their ubiquity in biological systems and ability to direct essential cellular processes. For example, aberrant biological LLPS can lead to the…
Ricky Nencini, Efstathia Mantzari, Amanda Sandelin, Samuli Ollila
Besides structure, protein dynamics is pivotal for their functions, particularly for intrinsically disordered proteins (IDPs) that do not fold to a fixed 3D structure. Rapid rotations of chemical bonds in proteins can be detected measuring NMR spin relaxation rates, but interpretation of protein dynamics from the…
Authors not listed
The formation and modulation of biomolecular condensates as well as their structural and dynamic properties are determined by an intricate interplay of different driving forces, which down at the microscopic scale involve molecular interactions of the biological macromolecules and the surrounding solvent and ions.…
Monika Michaelis, Lorenzo Cupellini, Carl Mensch, Carole C. Perry + 2 more
The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved. We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (Circular…
Hannah Britt, Aisha Ben-Younis, Nathanael Page, Konstantinos Thalassinos
Native top-down mass spectrometry is a powerful approach for analyzing proteoforms, but one which largely disregards protein conformation. We report a new ion mobility-enabled method for performing native top-down MS in a conformation-specific manner. Our approach identified conformation-linked differences in backbone…