Effect of Polyphosphorylation on Behavior of Protein Disordered Regions

Proteins interact with many charged biological macromolecules (polyelectrolytes), including inorganic polyphosphates. Recently a new protein post-translational modification, polyphosphorylation, or a covalent binding of polyphosphate chain to lysine, was demonstrated in human and yeast. Herein, we performed the first molecular modeling study of a possible effect of polyphosphorylation on behavior of the modified protein using replica exchange molecular dynamics simulations in atomistic force field with explicit water. Human endoplasmin (GRP-94), a member of heat shock protein 90 family, was selected as a model protein. Intrinsically disordered region in N-terminal domain serving as a charged linker between domains and containing a polyacidic serine and lysine-rich motif, was selected as a potent polyphosphorylation site according to literature data. Polyphosphorylation, depending on exact modification site, has been shown to influence on the disordered loop flexibility and induce its further expanding, as well as induce changes in interaction with ordered part of the molecule. As a result, polyphosphorylation in N-terminal domain might affect interaction of HSP90 with client proteins since these chaperones play a key role in protein folding.

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Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: A Force Field Comparison

International Journal of Molecular Sciences ◽

10.3390/ijms221810174 ◽

2021 ◽

Vol 22 (18) ◽

pp. 10174

Author(s):

Ellen Rieloff ◽

Marie Skepö

Keyword(s):

Force Field ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Conformational Ensemble ◽

Salt Bridges ◽

Post Translational Modification ◽

Intrinsically Disordered ◽

The Difference ◽

Disordered Peptides ◽

Dynamics Simulations

Phosphorylation is a common post-translational modification among intrinsically disordered proteins and regions, which helps regulate function by changing the protein conformations, dynamics, and interactions with binding partners. To fully comprehend the effects of phosphorylation, computer simulations are a helpful tool, although they are dependent on the accuracy of the force field used. Here, we compared the conformational ensembles produced by Amber ff99SB-ILDN+TIP4P-D and CHARMM36m, for four phosphorylated disordered peptides ranging in length from 14–43 residues. CHARMM36m consistently produced more compact conformations with a higher content of bends, mainly due to more stable salt bridges. Based on comparisons with experimental size estimates for the shortest and longest peptide, CHARMM36m appeared to overestimate the compactness. The difference between the force fields was largest for the peptide showing the greatest separation between positively charged and phosphorylated residues, in line with the importance of charge distribution. For this peptide, the conformational ensemble did not change significantly upon increasing the ionic strength from 0 mM to 150 mM, despite a reduction of the salt-bridging probability in the CHARMM36m simulations, implying that salt concentration has negligible effects in this study.

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Functional Regulation of the Anti-Apoptotic Protein BCL-xL through Post-Translational Modification of its Intrinsically Disordered Loop

Biophysical Journal ◽

10.1016/j.bpj.2011.11.3446 ◽

2012 ◽

Vol 102 (3) ◽

pp. 633a

Author(s):

Ariele Viacava Follis ◽

Richard W. Kriwacki

Keyword(s):

Post Translational Modification ◽

Intrinsically Disordered ◽

Apoptotic Protein ◽

Functional Regulation ◽

Disordered Loop

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Molecular Dynamics Simulations of the FtsZ mutant G105S

10.1101/280248 ◽

2018 ◽

Author(s):

Vidyalakshmi C Muthukumar

Keyword(s):

Molecular Dynamics ◽

Atpase Activity ◽

Molecular Dynamics Simulations ◽

Binding Site ◽

Homology Model ◽

Nucleotide Binding ◽

Intrinsically Disordered ◽

Terminal Domain ◽

Intrinsically Disordered Region ◽

Dynamics Simulations

AbstractIn our previous studies we simulated FtsZ monomer and dimer in different nucleotide binding states. In our simulations, we had used the E.coli FtsZ homology model including the FtsZ Intrinsically Disordered Region (IDR). Our simulations revealed that FtsZ dynamics involves a key stage in which GTP binds to monomeric FtsZ and opens its nucleotide binding site which in turn favours polymerization. During dimerization, the C-terminal of the top monomer rotates considerably towards the bottom monomer. Such a rotation of the C-terminal domain leads to capture of the nucleotide by its N-terminal domain. In this study we simulate the FtsZ G105S mutant to see if it may have ATPase activity which was reported in a previous study.

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Author Correction: Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations

Scientific Reports ◽

10.1038/s41598-020-72315-w ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Pablo Herrera-Nieto ◽

Adrià Pérez ◽

Gianni De Fabritiis

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Partially Ordered ◽

Intrinsically Disordered ◽

Terminal Domain ◽

Dynamics Simulations

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Sequence Specificity Despite Intrinsic Disorder: How a Disease-Associated Val/Met Polymorphism Shifts Tertiary Interactions in a Long Disordered Protein

10.26434/chemrxiv.8135777.v1 ◽

2019 ◽

Author(s):

Ruchi Lohia ◽

Reza Salari ◽

Grace Brannigan

Keyword(s):

Secondary Structure ◽

Electrostatic Interactions ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Sequence Specificity ◽

Intrinsically Disordered ◽

Specific Effects ◽

Heterogeneous Polymer ◽

Non Local ◽

Dynamics Simulations

<div>The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) encodes a hydrophobic-to-hydrophobic mutation at the midpoint of the prodomain of precursor brain-derived neurotrophic factor (BDNF), one of the earliest SNPs to be associated with neuropsychiatric disorders, for which the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence.</div><div>The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the local structure change is mediated via entropic and sequence specific effects. We show that the highly disordered prodomain can be meaningfully divided into domains based on sequence alone. Monte Carlo simulations of a self-excluding heterogeneous polymer, with monomers representing each domain, suggest the sequence would be effectively segmented by the long, highly disordered polyampholyte near the sequence midpoint. This is qualitatively consistent with observed interdomain contacts within the BDNF prodomain, although contacts between the two segments are enriched relative to the self-excluding polymer. The Val66Met mutation increases interactions across the boundary between the two segments, due in part to a specific Met-Met interaction with a Methionine in the other segment. This effect propagates to cause the non-local change in secondary structure around the second methionine, previously observed in NMR. The effect is not mediated simply via changes in inter-domain contacts but is also dependent on secondary structure formation around residue 66, indicating a mechanism for secondary structure coupling in disordered proteins. </div>

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Exploring PLAC1 Structure and Underlying Mechanisms to Design a Derivative Vaccine Against Breast Cancer Progression; In-Silico Study

Current Proteomics ◽

10.2174/1570164617666191203111451 ◽

2020 ◽

Vol 17 (5) ◽

pp. 379-391

Author(s):

Farzaneh Afzali ◽

Parisa Ghahremanifard ◽

Mohammad Mehdi Ranjbar ◽

Mahdieh Salimi

Keyword(s):

Breast Cancer ◽

Cancer Progression ◽

In Silico ◽

Tertiary Structure ◽

Specific Antigen ◽

Docking Simulation ◽

Post Translational Modification ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Underlying Mechanisms

Background: The tolerogenic homeostasis in Breast Cancer (BC) can be surpassed by rationally designed immune-encouraging constructs against tumor-specific antigens through immunoinformatics approach. Objective: Availability of high throughput data providing the underlying concept of diseases and awarded computational simulations, lead to screening the potential medications and strategies in less time and cost. Despite the extensive effects of Placenta Specific 1 (PLAC1) in BC progression, immune tolerance, invasion, cell cycle regulation, and being a tumor-specific antigen the fundamental mechanisms and regulatory factors were not fully explored. It is also worth to design an immune response inducing construct to surpass the hurdles of traditional anti-cancer treatments. Methods and Result: The study was initiated by predicting and modelling the PLAC1 secondary and tertiary structures and then engineering the fusion pattern of PLAC1 derived immunodominant predicted CD8+ and B-cell epitopes to form a multi-epitope immunogenic construct. The construct was analyzed considering the physiochemical characterization, safety, antigenicity, post-translational modification, solubility, and intrinsically disordered regions. After modelling its tertiary structure, proteinprotein docking simulation was carried out to ensure the attachment of construct with Toll-Like Receptor 4 (TLR4) as an immune receptor. To guarantee the highest expression of the designed construct in E. coli k12 as an expressional host, the codon optimization and in-silico cloning were performed. The PLAC1 related miRNAs in BC were excavated and validated through TCGA BC miRNA-sequencing and databases; the common pathways then were introduced as other probable mechanisms of PLAC1 activity. Conclusion: Regarding the obtained in-silico results, the designed anti-PLAC1 multi-epitope construct can probably trigger humoral and cellular immune responses and inflammatory cascades, therefore may have the potential of halting BC progression and invasion engaging predicted pathways.

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EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction

Nature Communications ◽

10.1038/s41467-021-21258-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Jing Zhao ◽

Alan Blayney ◽

Xiaorong Liu ◽

Lauren Gandy ◽

Weihua Jin ◽

...

Keyword(s):

Large Scale ◽

Molecular Mechanisms ◽

Epigallocatechin Gallate ◽

Cancer Drug ◽

Dynamic Interactions ◽

Cancer Drug Discovery ◽

Intrinsically Disordered ◽

Terminal Domain ◽

Cancerous Cells

AbstractEpigallocatechin gallate (EGCG) from green tea can induce apoptosis in cancerous cells, but the underlying molecular mechanisms remain poorly understood. Using SPR and NMR, here we report a direct, μM interaction between EGCG and the tumor suppressor p53 (KD = 1.6 ± 1.4 μM), with the disordered N-terminal domain (NTD) identified as the major binding site (KD = 4 ± 2 μM). Large scale atomistic simulations (>100 μs), SAXS and AUC demonstrate that EGCG-NTD interaction is dynamic and EGCG causes the emergence of a subpopulation of compact bound conformations. The EGCG-p53 interaction disrupts p53 interaction with its regulatory E3 ligase MDM2 and inhibits ubiquitination of p53 by MDM2 in an in vitro ubiquitination assay, likely stabilizing p53 for anti-tumor activity. Our work provides insights into the mechanisms for EGCG’s anticancer activity and identifies p53 NTD as a target for cancer drug discovery through dynamic interactions with small molecules.

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Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin

Nature Communications ◽

10.1038/s41467-021-24429-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Stephan Hirschi ◽

David Kalbermatter ◽

Zöhre Ucurum ◽

Thomas Lemmin ◽

Dimitrios Fotiadis

Keyword(s):

Proton Translocation ◽

Functional Characterization ◽

Green Light ◽

Proton Donor ◽

Molecular Organization ◽

Primary Proton ◽

Proton Pumps ◽

Model Protein ◽

Dynamics Simulations ◽

And Function

AbstractThe green-light absorbing proteorhodopsin (GPR) is the archetype of bacterial light-driven proton pumps. Here, we present the 2.9 Å cryo-EM structure of pentameric GPR, resolving important residues of the proton translocation pathway and the oligomerization interface. Superposition with the structure of a close GPR homolog and molecular dynamics simulations reveal conformational variations, which regulate the solvent access to the intra- and extracellular half channels harbouring the primary proton donor E109 and the proposed proton release group E143. We provide a mechanism for the structural rearrangements allowing hydration of the intracellular half channel, which are triggered by changing the protonation state of E109. Functional characterization of selected mutants demonstrates the importance of the molecular organization around E109 and E143 for GPR activity. Furthermore, we present evidence that helices involved in the stabilization of the protomer interfaces serve as scaffolds for facilitating the motion of the other helices. Combined with the more constrained dynamics of the pentamer compared to the monomer, these observations illustrate the previously demonstrated functional significance of GPR oligomerization. Overall, this work provides molecular insights into the structure, dynamics and function of the proteorhodopsin family that will benefit the large scientific community employing GPR as a model protein.

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