It is known that water molecules play an important role in the biological functioning of proteins. The members of the ribonuclease A (RNase A) family of proteins, which are sequentially and structurally similar, are known to carry out the obligatory function of cleaving RNA and individually perform other diverse biological functions. Our focus is on elucidating whether the sequence and structural similarity lead to common hydration patterns, what the common hydration sites are and what the differences are. Extensive molecular dynamics simulations followed by a detailed analysis of protein-water interactions have been carried out on two members of the ribonuclease A superfamily-RNase A and angiogenin. The water residence times are analyzed and their relationship with the characteristic properties of the protein polar atoms, such as their accessible surface area and mean hydration, is studied. The capacity of the polar atoms to form hydrogen bonds with water molecules and participate in protein-water networks are investigated. The locations of such networks are identified for both proteins.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1002/prot.20114 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Electrostatic Interaction between SARS-CoV-2 and Charged Surfaces: Spike Protein Evolution Changed the Game.
J Chem Inf Model
December 2024
Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Spain.
Previous works show the key role of electrostatics in the SARS-CoV-2 virus in aspects such as virus-cell interactions or virus inactivation by ionic surfactants. Electrostatic interactions depend strongly on the variant since the charge of the Spike protein (responsible for virus-environment interactions) evolved across the variants from the highly negative Wild Type (WT) to the highly positive Omicron variant. The distribution of the charge also evolved from diffuse to highly localized.
View Article and Find Full Text PDFBenchmarking a dual-scale hybrid simulation framework for small globular proteins combining the CHARMM36 and Martini2 models.
J Mol Graph Model
December 2024
CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India. Electronic address:
Multi-scale models in which varying resolutions are considered in a single molecular dynamics simulation setup are gaining importance in integrative modeling. However, combining atomistic and coarse-grain resolutions, especially for coarse-grain force fields derived from top-down approaches, have not been well explored. In this study, we have implemented and tested a dual-resolution simulation approach to model globular proteins in atomistic detail (represented by the CHARMM36 model) with the surrounding solvent in Martini2 coarse-grain detail.
View Article and Find Full Text PDFStreamlining Linear Free Energy Relationships of Proteins through Dimensionality Analysis and Linear Modeling.
J Chem Inf Model
December 2024
Institute of Environmental Science and Engineering (IESE), School of Civil and Environmental Engineering (SCEE), National University of Sciences and Technology (NUST), H-12, Islamabad 44000, Pakistan.
Article Synopsis
- Linear free energy relationships (LFERs) help predict how proteins interact with water, moving from simple models to a complex multi-parameter approach to improve accuracy.
- A new two-parameter LFER model simplifies the process by focusing on octanol-water and air-water partition coefficients, providing strong predictive results for protein-water interactions.
- This model shows comparable performance to traditional one-parameter models and offers a reliable alternative for estimating chemical behaviors when other descriptors are not accessible.
Assessment of the impact of quinoa protein modification on silver carp surimi gel quality and its utilization in 3D printing.
J Food Sci
December 2024
SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Liaoning Province Collaborative Innovation Center for Marine Food Deep Processing, Dalian Technology Innovation Center for Chinese Prepared Food, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.
This study aims to investigate the effects of different modified quinoa proteins (MQP) on the gel quality of silver carp surimi, as well as to explore their feasibility for three-dimensional (3D) printing. Five different methods were employed to modify quinoa protein, water bath (WB), microwave (MW), ultrasonic (US), microwave followed by ultrasonic (M-U), and ultrasonic followed by microwave (U-M), to prepare compound surimi gels (MQPs). The results showed that the addition of quinoa protein improved the gel quality of surimi, while the MQP had an even better effect on enhancing the gel quality.
View Article and Find Full Text PDFLikely Overstabilization of Charge-Charge Interactions in CHARMM36m(w): A Case for a99SB-disp Water.
J Phys Chem B
November 2024
Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States.
Recent years have witnessed drastic improvements in general-purpose explicit solvent protein force fields, partially driven by the need to study intrinsically disordered proteins (IDPs), and yet the state-of-the-art force fields such as CHARMM36m (c36m) and a99SB-disp still provide different performances in simulating disordered protein states, where c36m has a bias toward overcompaction for large IDPs. Here, we examine the performance of c36m and a99SB-disp in describing the stabilities of a set of 46 amino acid backbone and side chain pairs in various configurations. The free energy results show that c36m systematically predicts stronger interactions compared to a99SB-disp by an average of 0.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!