Role of water molecules and ion pairs in Dps and related ferritin-like structures

Ranjani, C. Vasuki; Rangarajan, S.K.; Michael, Daliah; Roy, Siddhartha; Sekar, K.

doi:10.1016/j.ijbiomac.2008.06.012

Cited by 5 publications

(4 citation statements)

References 26 publications

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“…They play a critical role in the folding, stability, and dynamics of 3D structures at all levels, from secondary and tertiary structures to supramolecular assemblies, and have been studied for multiple aspects: their energetic contribution or electrostatic strength, especially with respect to secondary, tertiary, or quaternary structure as well as stability; − a strong correlation is observed between the secondary structure and salt bridge formation . Furthermore, salt bridges form complex networks, , which are suspected to have a stabilizing effect on the protein structure, following the observed relation between the increased number of salt bridges and thermal stability; − their geometrical characteristics; for example, salt bridges between aspartate and glutamate and histidine, arginine, or lysine display extremely well defined geometric preferences; their environment and their location (within monomers or at the interface between monomers as well as their solvent accessibility); salt bridges display preferential formation in an environment of 30% solvent-accessible surface area; the separation of the amino acids; intrachain salt bridges are mainly separated by three or four residue salt bridges; their fluctuations and nuclear magnetic resonance (NMR) conformer ensembles show that salt bridges may break and new salt bridges are formed, in good correlation with crystallographic B-factors; water molecules have important roles to play toward the stability of molecular complexes, for example, conformational stability or stabilization or mediation of ion pairs. , …”

Section: Introductionmentioning

confidence: 99%

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Characterization of Ionizable Groups’ Environments in Proteins and Protein–Ligand Complexes through a Statistical Analysis of the Protein Data Bank

2017

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We conduct a statistical analysis of the molecular environment of common ionizable functional groups in both protein–ligand complexes and inside proteins from the Protein Data Bank (PDB). In particular, we characterize the frequency, type, and density of the interacting atoms as well as the presence of a potential counterion. We found that for ligands, most guanidinium groups, half of primary and secondary amines, and one-fourth of imidazole neighbor a carboxylate group. Tertiary amines bind more rarely near carboxylate groups, which may be explained by a crowded neighborhood and hydrophobic character. In comparison to the environment seen by the ligands, inside proteins, an environment enriched in main-chain atoms is found, and the prevalence of direct charge neutralization by carboxylate groups is different. When the ionizable character of water molecules and phenolic or hydroxyl groups is accounted, considering a high-resolution dataset (less than 1.5 Å), charge neutralization could occur for well above 80% of the ligand functional groups considered, but for tertiary amines.

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Section: Introductionmentioning

confidence: 99%

“…water molecules have important roles to play toward the stability of molecular complexes, for example, conformational stability or stabilization or mediation of ion pairs. , …”

Section: Introductionmentioning

confidence: 99%

Characterization of Ionizable Groups’ Environments in Proteins and Protein–Ligand Complexes through a Statistical Analysis of the Protein Data Bank

2017

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“…For example, the transfer of water molecules is involved in protein gating in certain enzymes (Wikstrom et al 2005). The hubs observed between the dimers of Dps and its related ferritin-like structures helps in the conformational stability of the protein molecule (Ranjani et al 2008).…”

Section: Hubs: a Special Case Of Networkmentioning

confidence: 99%

Water-mediated ionic interactions in protein structures

et al. 2011

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It is well known that water molecules play an indispensable role in the structure and function of biological macromolecules. The water-mediated ionic interactions between the charged residues provide stability and plasticity and in turn address the function of the protein structures. Thus, this study specifically addresses the number of possible water-mediated ionic interactions, their occurrence, distribution and nature found in 90% non-redundant protein chains. Further, it provides a statistical report of different charged residue pairs that are mediated by surface or buried water molecules to form the interactions. Also, it discusses its contributions in stabilizing various secondary structural elements of the protein. Thus, the present study shows the ubiquitous nature of the interactions that imparts plasticity and flexibility to a protein molecule.

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“…The quality of the data present in the PDB is required to be extremely high (Dodson et al, 1998) as these data serve as input to create various powerful tools and knowledgebases/ databases, which are in turn useful for researchers working in the areas of structural bioinformatics, biochemistry and biophysics (Carugo & Pongor, 2002;Hemavathi et al, 2010;Uthayakumar et al, 2011). Further, these data (sequence and structure) are used heavily in data-mining studies to percolate useful information to derive more knowledge to solve unknown structures (Gowri Shankar et al, 2007;Ranjani et al, 2008;Kanaujia & Sekar, 2009;Sabarinathan et al, 2011;Dhanasekaran et al, 2013). Missing regions in a protein structure create problems as they may produce misleading results, for example, misinterpretation of electrostatic potentials at the protein surface due to missing regions in the protein structure.…”

Section: Introductionmentioning

confidence: 99%

MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

et al. 2019

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Missing regions in protein crystal structures are those regions that cannot be resolved, mainly owing to poor electron density (if the three‐dimensional structure was solved using X‐ray crystallography). These missing regions are known to have high B factors and could represent loops with a possibility of being part of an active site of the protein molecule. Thus, they are likely to provide valuable information and play a crucial role in the design of inhibitors and drugs and in protein structure analysis. In view of this, an online database, Missing Regions in Polypeptide Chains (MRPC), has been developed which provides information about the missing regions in protein structures available in the Protein Data Bank. In addition, the new database has an option for users to obtain the above data for non‐homologous protein structures (25 and 90%). A user‐friendly graphical interface with various options has been incorporated, with a provision to view the three‐dimensional structure of the protein along with the missing regions using JSmol. The MRPC database is updated regularly (currently once every three months) and can be accessed freely at the URL http://cluster.physics.iisc.ac.in/mrpc.

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Role of water molecules and ion pairs in Dps and related ferritin-like structures

Cited by 5 publications

References 26 publications

Characterization of Ionizable Groups’ Environments in Proteins and Protein–Ligand Complexes through a Statistical Analysis of the Protein Data Bank

Characterization of Ionizable Groups’ Environments in Proteins and Protein–Ligand Complexes through a Statistical Analysis of the Protein Data Bank

Water-mediated ionic interactions in protein structures

MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

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