Influence of Ion Specificity and Concentration on the Conformational Transition of Intrinsically Disordered Sheep Prion Peptide

Singh, Omkar; Das, Bratin Kumar; Chakraborty, Debashree

doi:10.1002/cphc.202200211

Cited by 4 publications

(4 citation statements)

References 88 publications

(116 reference statements)

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“…This was seen in mixed ion solutions, where some ions may preferentially occupy the area around the nucleic acid sample. Comparing this to other studies, the findings of an atomistic molecular dynamics simulation study with intrinsically disordered proteins and metal ions suggest that the stability of the protein depends on intrapeptide and peptide–water hydrogen bonds coupled with the heterogeneity of hydration water around the peptide in the presence of various ions . It is likely that similar interactions are involved with nucleic acids in ion solutions, but more experiments are needed to confirm.…”

Section: Discussionmentioning

confidence: 99%

“…Comparing this to other studies, the findings of an atomistic molecular dynamics simulation study with intrinsically disordered proteins and metal ions suggest that the stability of the protein depends on intrapeptide and peptide−water hydrogen bonds coupled with the heterogeneity of hydration water around the peptide in the presence of various ions. 118 It is likely that similar interactions are involved with nucleic acids in ion solutions, but more experiments are needed to confirm. A myriad of variables need to be considered when performing benchtop or computational studies involving nucleic acids and metal ions.…”

Section: T H Imentioning

confidence: 99%

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Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability

Arteaga,

Dolenz,

Znosko

2023

ACS Omega

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The nonspecific atmosphere around nucleic acids, often termed the ion atmosphere, encompasses a collection of weak ion−nucleic acid interactions. Although nonspecific, the ion atmosphere has been shown to influence nucleic acid folding and structural stability. Studies investigating the composition of the ion atmosphere have shown competitive occupancy of the atmosphere between metal ions in the same solution. Many studies have investigated single ion effects on nucleic acid secondary structure stability; however, no comprehensive studies have investigated how the competitive occupancy of mixed ions in the ion atmosphere influences nucleic acid secondary structure stability. Here, six oligonucleotides were optically melted in buffers containing molar quantities, or mixtures, of either XCl (X = Li, K, Rb, or Cs) or NaCl. A correction factor was developed to better predict RNA duplex stability in solutions containing mixed XCl/NaCl. For solutions containing a 1:1 mixture of XCl/NaCl, one alkali metal chloride contributed more to duplex stability than the other. Overall, there was a 54% improvement in predictive capabilities with the correction factor compared with the standard 1.0 M NaCl nearest-neighbor models. This correction factor can be used in models to better predict RNA secondary structure in solutions containing mixed XCl/NaCl.

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Section: Discussionmentioning

confidence: 99%

Section: T H Imentioning

confidence: 99%

Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability

Arteaga,

Dolenz,

Znosko

2023

ACS Omega

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“…One such good example of proteins undergoing conformational transition is the Intrinsically disordered proteins (IDPs). These proteins undergo conformational transitions due to the effect of the temperature, pH, solvents, presence of ions, and many more. IDPs/IDP regions are commonly present in all living organisms, and it is found that the amount of disorderliness increases proportionately to the complexity of the organism.…”

Section: Introductionmentioning

confidence: 99%

Study of Correlated Motions to Detect the Conformational Transitions of the Intrinsically Disordered Sheep Prion Peptide

Chakraborty,

Singh,

Parameswaran

2024

J. Chem. Inf. Model.

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Intrinsically disordered proteins (IDPs) are known for their random structural changes throughout their sequence based on the environment. The mechanism underlying these structural changes is difficult to explain. All biological processes are known to follow the direction through which they act. A study of the correlated motion can help to understand the direction of the change. Herein, we introduced the multivariate statistical analysis (MSA) technique to study the correlated motion of the peptide. The correlated motion of the sheep prion peptide was studied with the change in the temperature and solvent. These techniques helped to identify the contributing residual motions that helped to form the different secondary structures of the protein and also the triggering factors that drive these sorts of residual motions. The structural details match the experimentally reported data. It was found that the direction of the change of the secondary structure for this peptide shifted from the C-terminal to the N-terminal with an increase in the temperature. It was found that the involvement of the hydrophobic residues present at the C-terminal and the middle residues (residues 12–17) is responsible for forming a β-sheet at the normal temperature. Hydration water was found to play an important role in this change. Insights gained from this study can be used to design strategies for desirable structural changes in the IDPs.

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“…They are also linked to pathological misfolded states in those suffering from neurological disorders [ 18 , 19 , 20 ], cancer [ 18 , 21 , 22 ], cardiovascular diseases [ 18 , 23 ], or diabetes [ 24 , 25 ]. As such, the study of their interaction with solvents and ions is of crucial importance to understanding their dynamics and characterization for possible pharmacological intervention [ 26 , 27 ].…”

Section: Introductionmentioning

confidence: 99%

SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories

Bruyn

Dorn

Zimmermann

et al. 2023

Biology

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The disordered nature of Intrinsically Disordered Proteins (IDPs) makes their structural ensembles particularly susceptible to changes in chemical environmental conditions, often leading to an alteration of their normal functions. A Radial Distribution Function (RDF) is considered a standard method for characterizing the chemical environment surrounding particles during atomistic simulations, commonly averaged over an entire or part of a trajectory. Given their high structural variability, such averaged information might not be reliable for IDPs. We introduce the Time-Resolved Radial Distribution Function (TRRDF), implemented in our open-source Python package SPEADI, which is able to characterize dynamic environments around IDPs. We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion–residue interactions play an important role in the structures and behaviors of IDPs.

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Influence of Ion Specificity and Concentration on the Conformational Transition of Intrinsically Disordered Sheep Prion Peptide

Cited by 4 publications

References 88 publications

Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability

Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability

Study of Correlated Motions to Detect the Conformational Transitions of the Intrinsically Disordered Sheep Prion Peptide

SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories

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