Potential influence of Asp in the Ca2+ coordination position 5 of parvalbumin on the calcium-binding affinity: A computational study

Effect of albumin on the transformation of dinitrosyl iron complexes with thiourea ligands

BSA binds the Fe(NO)₂⁺ fragment of DNIC and multiple molecules of [Fe(SC(NH₂)₂)₂(NO)₂]⁺ that prolongs NO donation by this DNIC.

Estimating affinities of calcium ions to proteins

Ca²⁺-ions have a range of affinities to different proteins, depending on the various functions of these proteins. This makes the determination of Ca²⁺-protein affinities an interesting subject for functional studies. We have investigated the performance of two methods – Fold-X and AutoDock vina – in the prediction of Ca²⁺-protein affinities. Both methods, although based on different energy functions, showed virtually the same correlation with experimental affinities. Guided by insight from experiment, we further derived a simple linear model based on the solvent accessible surface of Ca²⁺ that had practically the same performance in terms of absolute errors as the more complex docking methods.

Free energy calculations of glycosaminoglycan-protein interactions

Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.

Engineering aluminum binding affinity in an isolated EF-hand from troponin C: A computational site-directed mutagenesis study

Peptides with the ability to specifically bind aluminum would potentially be of great use in the fields of biochemistry and environmental chemistry. Unfortunately no such peptides are known. An aluminum-specific peptide may be used as an in vivo chelator, for metalloprotein design, for understanding metal-ion induced folding and metal-ion trafficking, and as an environmental sensor to monitor metal pollution in the environment. Plants genetically engineered to produce an aluminum binding peptide might be useful in environmental remediation in areas of high free aluminum ion concentration. In this paper, which is the theoretical complement to the experimental work, we analyzed crystallographic structures of EF-hands bound to various metals in order to determine the ligand distances and identities to compare to metal-ion size, charge, electronegativity, and coordination number and performed energy minimization calculations to identify possible mutations. We then constructed various mutant sequences in silico in an isolated EF-hand from troponin C and analyzed their binding behavior using molecular mechanics for binding to Tb(3+) as compared to Al(3+). As a result of these analyses we were able to isolate some characteristics that could lead to mutant peptides with enhanced aluminum activity that we plan to test experimentally in the future. We also performed metal-ion binding studies with the isolated EF-hand used in the computational work to examine the ability of Al(3+) and comparative metals to bind the peptide. In competition studies, the peptide demonstrated preference for Tb(3+) over Al(3+).