scholarly journals Role of pKA in Charge Regulation and Conformation of Various Peptide Sequences

Polymers ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 214
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Zdeněk Tošner ◽  
Miroslav Štěpánek ◽  
Peter Košovan
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Total Charge ◽  
Side Chains ◽  
Intrinsically Disordered ◽  
Acid And Base ◽  
Base Side

Peptides containing amino acids with ionisable side chains represent a typical example of weak ampholytes, that is, molecules with multiple titratable acid and base groups, which generally exhibit charge regulating properties upon changes in pH. Charged groups on an ampholyte interact electrostatically with each other, and their interaction is coupled to conformation of the (macro)molecule, resulting in a complex feedback loop. Their charge-regulating properties are primarily determined by the pKA of individual ionisable side-chains, modulated by electrostatic interactions between the charged groups. The latter is determined by the amino acid sequence in the peptide chain. In our previous work we introduced a simple coarse-grained model of a flexible peptide. We validated it against experiments, demonstrating its ability to quantitatively predict charge on various peptides in a broad range of pH. In the current work, we investigated two types of peptide sequences: diblock and alternating, each of them consisting of an equal number of amino acids with acid and base side-chains. We showed that changing the sequence while keeping the same overall composition has a profound effect on the conformation, whereas it practically does not affect total charge on the peptide. Nevertheless, the sequence significantly affects the charge state of individual groups, showing that the zero net effect on the total charge is a consequence of unexpected cancellation of effects. Furthermore, we investigated how the difference between the pKA of acid and base side chains affects the charge and conformation of the peptide, showing that it is possible to tune the charge-regulating properties by following simple guiding principles based on the pKA and on the amino acid sequence. Our current results provide a theoretical basis for understanding of the complex coupling between the ionisation and conformation in flexible polyampholytes, including synthetic polymers, biomimetic materials and biological molecules, such as intrinsically disordered proteins, whose function can be regulated by changes in the pH.

scholarly journals Roles, Characteristics, and Analysis of Intrinsically Disordered Proteins: A Minireview

Life ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 320
Author(s):  
Frederik Lermyte
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Neurological Disorders ◽  
Intrinsically Disordered Proteins ◽  
Intrinsic Disorder ◽  
Disordered Proteins ◽  
Dynamic Nature ◽  
Intrinsically Disordered ◽  
Unfolded State ◽  
Underlying Causes

In recent years, there has been a growing understanding that a significant fraction of the eukaryotic proteome is intrinsically disordered, and that these conformationally dynamic proteins play a myriad of vital biological roles in both normal and pathological states. In this review, selected examples of intrinsically disordered proteins are highlighted, with particular attention for a few which are relevant in neurological disorders and in viral infection. Next, the underlying causes for intrinsic disorder are discussed, along with computational methods used to predict whether a given amino acid sequence is likely to adopt a folded or unfolded state in solution. Finally, biophysical methods for the analysis of intrinsically disordered proteins will be discussed, as well as the unique challenges they pose in this context due to their highly dynamic nature.

scholarly journals Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence

2020 ◽  
Author(s):  
Simon M. Lichtinger ◽  
Adiran Garaizar ◽  
Rosana Collepardo-Guevara ◽  
Aleks Reinhardt
Keyword(s):  
Phase Separation ◽  
Amino Acid ◽  
Liquid Phase ◽  
Amino Acid Sequence ◽  
Amino Acid Sequences ◽  
Liquid Phase Separation ◽  
Computational Method ◽  
Coarse Grained ◽  
Intrinsically Disordered ◽  
Liquid Liquid Phase Separation

AbstractRationally and efficiently modifying the amino-acid sequence of proteins to control their ability to undergo liquid-liquid phase separation (LLPS) on demand is not only highly desirable, but can also help to elucidate which protein features are important for LLPS. Here, we propose an innovative computational method that couples a genetic algorithm to a sequence-dependent coarse-grained protein model to evolve the amino-acid sequences of phase-separating intrinsically disordered protein regions (IDRs), and purposely enhance or inhibit their capacity to phase-separate. We apply it to the phase-separating IDRs of three naturally occurring proteins, namely FUS, hnRNPA1 and LAF1, as prototypes of regions that exist in cells and undergo homotypic LLPS driven by different types of intermolecular interaction. We find that the evolution of amino-acid sequences towards enhanced LLPS is driven in these three cases, among other factors, by an increase in the average size of the amino acids. However, the direction of change in the molecular driving forces that enhance LLPS (such as hydrophobicity, aromaticity and charge) depends on the initial amino-acid sequence: the critical temperature can be enhanced by increasing the frequency of hydrophobic and aromatic residues, by changing the charge patterning, or by a combination of both. Finally, we show that the evolution of amino-acid sequences to modulate LLPS is strongly coupled to the composition of the medium (e.g. the presence or absence of RNA), which may have significant implications for our understanding of phase separation within the many-component mixtures of biological systems.

scholarly journals A predictive coarse-grained model for position-specific effects of post-translational modifications on disordered protein phase separation

2020 ◽  
Author(s):  
T. M. Perdikari ◽  
N. Jovic ◽  
G. L. Dignon ◽  
Y. C. Kim ◽  
N. L. Fawzi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Phase Separation ◽  
Phase Behavior ◽  
Intrinsically Disordered Proteins ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Post Translational Modifications ◽  
Coarse Grained Model ◽  
Intrinsically Disordered ◽  
Liquid Liquid Phase Separation

AbstractBiomolecules undergo liquid-liquid phase separation (LLPS) resulting in the formation of multicomponent protein-RNA membraneless organelles in cells. However, the physiological and pathological role of post translational modifications (PTMs) on the biophysics of phase behavior is only beginning to be probed. To study the effect of PTMs on LLPS in silico, we extend our transferable coarse-grained model of intrinsically disordered proteins to include phosphorylated and acetylated amino acids. Using the parameters for modified amino acids available for fixed charge atomistic forcefields, we parameterize the size and atomistic hydropathy of the coarse-grained modified amino acid beads, and hence the interactions between the modified and natural amino acids. We then elucidate how the number and position of phosphorylated and acetylated residues alter the protein’s single chain compactness and its propensity to phase separate. We show that both the number and the position of phosphorylated threonines/serines or acetylated lysines can serve as a molecular on/off switch for phase separation in the well-studied disordered regions of FUS and DDX3X, respectively. We also compare modified residues to their commonly used PTM mimics for their impact on chain properties. Importantly, we show that the model can predict and capture experimentally measured differences in the phase behavior for position-specific modifications, showing that the position of modifications can dictate phase separation. In sum, this model will be useful for studying LLPS of post-translationally modified intrinsically disordered proteins and predicting how modifications control phase behavior with position-specific resolution.Statement of SignificancePost-translational modifications are important regulators of liquid-liquid phase separation (LLPS) which drives the formation of biomolecular condensates. Theoretical methods can be used to characterize the biophysical properties of intrinsically disordered proteins (IDPs). Our recent framework for molecular simulations using a Cα-centered coarse-grained model can predict the effect of various perturbations such as mutations (Dignon et al. PloS Comput. Biol, 2018) and temperature (Dignon et al, ACS Cent. Sci., 2019) on LLPS. Here, we expand this framework to incorporate modified residues like phosphothreonine, phosphoserine and acetylysine. This model will prove useful for simulating the phase separation of post-translationally modified IDPs and predicting how position-specific modifications can control phase behavior across the large family of proteins known to be phosphorylated and acetylated.

scholarly journals Quantitative Prediction of Charge Regulation in Oligopeptides

2020 ◽  
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Weak Acid ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Quantitative Prediction ◽  
Bottom Up ◽  
Charge Regulation ◽  
Flexible Polymer ◽  
Acid And Base ◽  
Base Side

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their charge regulation and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Our model predicts differences in the charge states between oligopeptides and monomeric amino acids, showing that conformational flexibility and electrostatic interactions between weak acid and base side chains play a key role in the charge regulation. By comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the charge state of various peptide sequences. Ultimately, our model is the first step towards understanding the charge regualtion in flexible disordered proteins, and towards using predictive bottom-up design of responsive ampholytes to tailor their<br>properties as a function of charge and pH.<br>

scholarly journals Quantitative Prediction of Charge Regulation in Oligopeptides

2020 ◽  
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Weak Acid ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Quantitative Prediction ◽  
Bottom Up ◽  
Charge Regulation ◽  
Flexible Polymer ◽  
Acid And Base ◽  
Base Side

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their charge regulation and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Our model predicts differences in the charge states between oligopeptides and monomeric amino acids, showing that conformational flexibility and electrostatic interactions between weak acid and base side chains play a key role in the charge regulation. By comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the charge state of various peptide sequences. Ultimately, our model is the first step towards understanding the charge regualtion in flexible disordered proteins, and towards using predictive bottom-up design of responsive ampholytes to tailor their<br>properties as a function of charge and pH.<br>

scholarly journals Quantitative Prediction of Charge Regulation in Oligopeptides

2020 ◽  
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Weak Acid ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Quantitative Prediction ◽  
Bottom Up ◽  
Charge Regulation ◽  
Flexible Polymer ◽  
Acid And Base ◽  
Base Side

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their charge regulation and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Our model predicts differences in the charge states between oligopeptides and monomeric amino acids, showing that conformational flexibility and electrostatic interactions between weak acid and base side chains play a key role in the charge regulation. By comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the charge state of various peptide sequences. Ultimately, our model is the first step towards understanding the charge regualtion in flexible disordered proteins, and towards using predictive bottom-up design of responsive ampholytes to tailor their<br>properties as a function of charge and pH.<br>

scholarly journals Effects of Sequence Composition and Patterning on the Structure and Dynamics of Intrinsically Disordered Proteins

2020 ◽  
Author(s):  
Andrei Vovk ◽  
Anton Zilman
Keyword(s):  
Amino Acid ◽  
Intrinsically Disordered Proteins ◽  
Amino Acid Sequences ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Radius Of Gyration ◽  
Sequence Composition ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Polymer Models

AbstractUnlike the well defined structures of classical natively folded proteins, Intrinsically Disordered Proteins (IDP) and Intrinsically Disordered Regions (IDR) dynamically span large conformational and structural ensembles. This dynamic disorder impedes the study of the relationship between the amino acid sequences of the IDPs and their spatial structures, dynamics, and function. Multiple experimental and theoretical evidence points in many cases to the overall importance of the general properties of the amino acid sequence of the IPDs rather than their precise atomistic details. However, while different experimental techniques can probe aspects of the IDP conformations, often different techniques or conditions offer seemingly contradictory results. Using coarse-grained polymer models informed by experimental observations, we investigate the effects of several key variables on the dimensions and the dynamics of IDPs. The coarse-grained simulations are in a good agreement with the results of atomistic MD. We show that the sequence composition and patterning are well reflected in the global conformational variables such as the radius of gyration and hydrodynamic radius, while the end-to-end distance and dynamics are highly sequence specific. We identify the conditions that allow mapping of highly heterogeneous sequences of IDPs onto averaged minimal polymer models. We discuss the implications of these results for the interpretation of the recent experimental measurements, and for further development of appropriate mesoscopic models of IDPs.

scholarly journals Proteus: A Random Forest Classifier to Predict Disorder-to-Order Transitioning Binding Regions in Intrinsically Disordered Proteins

2016 ◽  
Author(s):  
Sankar Basu ◽  
Fredrik Söderquist ◽  
Björn Wallner
Keyword(s):  
Amino Acid ◽  
Random Forest ◽  
Amino Acid Sequence ◽  
Intrinsically Disordered Proteins ◽  
Random Forest Classifier ◽  
Amino Acid Sequences ◽  
Order Transition ◽  
Disordered Proteins ◽  
Data Set ◽  
Intrinsically Disordered

AbstractThe focus of the computational structural biology community has taken a dramatic shift over the past one-and-a-half decades from the classical protein structure prediction problem to the possible understanding of intrinsically disordered proteins (IDP) or proteins containing regions of disorder (IDPR). The current interest lies in the unraveling of a disorder-to-order transitioning code embedded in the amino acid sequences of IDPs / IDPRs. Disordered proteins are characterized by an enormous amount of structural plasticity which makes them promiscuous in binding to different partners, multi-functional in cellular activity and atypical in folding energy landscapes resembling partially folded molten globules. Also, their involvement in several deadly human diseases (e.g. cancer, cardiovascular and neurodegenerative diseases) makes them attractive drug targets, and important for a biochemical understanding of the disease(s). The study of the structural ensemble of IDPs is rather difficult, in particular for transient interactions. When bound to a structured partner, an IDPR adapts an ordered conformation in the complex. The residues that undergo this disorder-to-order transition are called protean residues, generally found in short contiguous stretches and the first step in understanding the modus operandi of an IDP / IDPR would be to predict these residues. There are a few available methods which predict these protean segments from their amino acid sequences; however, their performance reported in the literature leaves clear room for improvement. With this background, the current study presents 'Proteus', a random forest classifier that predicts the likelihood of a residue undergoing a disorder-to-order transition upon binding to a potential partner protein. The prediction is based on features that can be calculated using the amino acid sequence alone. Proteus compares favorably with existing methods predicting twice as many true positives as the second best method (55% vs. 27%) with a much higher precision on an independent data set. The current study also sheds some light on a possible 'disorder-to-order' transitioning consensus, untangled, yet embedded in the amino acid sequence of IDPs. Some guidelines have also been suggested for proceeding with a real-life structural modeling involving an IDPR using Proteus.Software Availabilityhttps://github.com/bjornwallner/proteus

scholarly journals Targeted modulation of protein liquid–liquid phase separation by evolution of amino-acid sequence

2021 ◽  
Vol 17 (8) ◽  
pp. e1009328
Author(s):  
Simon M. Lichtinger ◽  
Adiran Garaizar ◽  
Rosana Collepardo-Guevara ◽  
Aleks Reinhardt
Keyword(s):  
Phase Separation ◽  
Amino Acid ◽  
Liquid Phase ◽  
Amino Acid Sequence ◽  
Amino Acid Sequences ◽  
Liquid Phase Separation ◽  
Computational Method ◽  
Coarse Grained ◽  
Intrinsically Disordered ◽  
Liquid Liquid Phase Separation

Rationally and efficiently modifying the amino-acid sequence of proteins to control their ability to undergo liquid–liquid phase separation (LLPS) on demand is not only highly desirable, but can also help to elucidate which protein features are important for LLPS. Here, we propose a computational method that couples a genetic algorithm to a sequence-dependent coarse-grained protein model to evolve the amino-acid sequences of phase-separating intrinsically disordered protein regions (IDRs), and purposely enhance or inhibit their capacity to phase-separate. We validate the predicted critical solution temperatures of the mutated sequences with ABSINTH, a more accurate all-atom model. We apply the algorithm to the phase-separating IDRs of three naturally occurring proteins, namely FUS, hnRNPA1 and LAF1, as prototypes of regions that exist in cells and undergo homotypic LLPS driven by different types of intermolecular interaction, and we find that the evolution of amino-acid sequences towards enhanced LLPS is driven in these three cases, among other factors, by an increase in the average size of the amino acids. However, the direction of change in the molecular driving forces that enhance LLPS (such as hydrophobicity, aromaticity and charge) depends on the initial amino-acid sequence. Finally, we show that the evolution of amino-acid sequences to modulate LLPS is strongly coupled to the make-up of the medium (e.g. the presence or absence of RNA), which may have significant implications for our understanding of phase separation within the many-component mixtures of biological systems.

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