Metal-Binding Affinity and Selectivity of Nonstandard Natural Amino Acid Residues from DFT/CDM Calculations

Characterization of a Thermostable Endolysin of the Aeribacillus Phage AeriP45 as a Potential Staphylococcus Biofilm-Removing Agent

Multidrug-resistant Gram-positive bacteria, including bacteria from the genus Staphylococcus, are currently a challenge for medicine. Therefore, the development of new antimicrobials is required. Promising candidates for new antistaphylococcal drugs are phage endolysins, including endolysins from thermophilic phages against other Gram-positive bacteria. In this study, the recombinant endolysin LysAP45 from the thermophilic Aeribacillus phage AP45 was obtained and characterized. The recombinant endolysin LysAP45 was produced in Escherichia coli M15 cells. It was shown that LysAP45 is able to hydrolyze staphylococcal peptidoglycans from five species and eleven strains. Thermostability tests showed that LysAP45 retained its hydrolytic activity after incubation at 80 °C for at least 30 min. The enzymatically active domain of the recombinant endolysin LysAP45 completely disrupted biofilms formed by multidrug-resistant S. aureus, S. haemolyticus, and S. epidermidis. The results suggested that LysAP45 is a novel thermostable antimicrobial agent capable of destroying biofilms formed by various species of multidrug-resistant Staphylococcus. An unusual putative cell-binding domain was found at the C-terminus of LysAP45. No domains with similar sequences were found among the described endolysins.

Optimal density-functional theory method for zinc-amino acid complexes determined by analyzing structural and Fourier-transform infrared spectroscopy data

Metal-amino acid complexes are important compounds for the human body. Their nutritional value and anticancer, antibacterial, and catalytic properties are the focus of several studies. Density functional theory (DFT) can be used to predict their properties by optimizing their structures and performing electron population analyses. However, conventional computational methods cannot adequately determine the parameters of polymeric metal-amino acid complexes. Therefore, intermolecular interactions of polymers must be considered to correctly predict the properties of metal-amino acid and related metal complexes. In this study, different DFT protocols were used to acquire the infrared spectra and determine interatomic distances of two zinc-amino acid complexes, Zn(Gly)2 and Zn(Met)2. The results were compared to spectroscopic and X-ray crystallographic data, revealing that the M06 and M06-L functionals and the 6-311++G(d,p) basis set produced the smallest computational errors. Our results provide a foundation for future theoretical studies on other metal-amino acid and metal-organic complexes.

Complexation of Amino Acids with Cadmium and Their Application for Cadmium-Contaminated Soil Remediation

The interaction of amino acids with toxic heavy metals influences their immobilization and bioavailability in soils. However, the complexation ability of amino acids with Cd has not been well studied. The complexes of amino acids and cadmium were investigated by density functional theory (DFT) calculations and Fourier transform infrared spectrometry (FTIR) analyses. The complex structures were found to be [COc, COc] for fatty amino-cadmium and PheCd2+, [COc, COc, COs] for GluCd2+ and ThrCd2+, respectively. The complex energy of these conformers followed the order PheCd2+> AlaCd2+ > LeuCd2+ > GluCd2+ > GlyCd2+ > ThrCd2+. Importantly, all of the complex energy values were less than zero, indicating that these complexes could be easily dissolved in water. The Cd2+ concentration decreased with increasing amino acid concentration in aqueous solution. The complex stability constants (logβ) followed the order PheCd2+> AlaCd2+ > LeuCd2+ > GluCd2+ > GlyCd2+ > ThrCd2+, consistent with the order of the calculated complex energy values. The Cd removal efficiencies by Thr, Glu, Gly, Ala, Leu, and Phe were 38.88%, 37.47%, 35.5%, 34.72%, 34.04%, and 31.99%, respectively. In soil batch tests, the total Cd concentration in soil decreased in the presence of amino acids, while the Cd concentration in water increased from 231.97 μg/L to 652.94~793.51 μg/L. The results of sequential extraction showed that the acid-extractable fraction and the reducible fraction of Cd sharply decreased. Consequently, the significant features of amino acids along with their biocompatibility make them potentially applicable chelators in Cd-contaminated soil remediation processes.

Why Cellular Di/Triphosphates Preferably Bind Mg2+ and Not Ca2

Di/triphosphates perform a multitude of essential tasks, being important components of many vital organic cofactors such as adenosine/guanosine di/triphosphate (ADP/GDP, ATP/GTP), flavin adenine dinucleotide, and nicotinamide adenine dinucleotide and its phosphate derivative. They are generally bound to cations inside cells, in particular Mg²⁺ in the case of ATP/GTP. Yet how their metal-binding modes depend on the number, charge, and solvent exposure of the polyphosphate group and how Mg²⁺and Ca²⁺ dications that coexist in cellular fluids compete for di/triphosphates in biological systems remain elusive. Using density functional theory calculations combined with a polarizable continuum model, we have determined the relative free energies and stabilities of the different binding modes of di- and triphosphate groups to Mg²⁺ and Ca²⁺. We show that the thermodynamic outcome of the competition between Mg²⁺ and Ca²⁺ for cellular di/triphosphates depends mainly on the oligomericity/charge and metal-binding mode of the phosphate ligand as well as the solvent exposure of the binding site. Increasing the charge and thus denticity of the phosphate ligand from bi- to tridentate in a buried binding pocket enhances the affinity of the host system for the stronger charge acceptor, Mg²⁺. The cellular di/triphosphates's intrinsic properties and the protein matrix allowing them to bind a dication bi/tridentately, along with the higher cytosolic concentration of Mg²⁺ compared to Ca²⁺, enables Mg²⁺ to outcompete Ca²⁺ in binding to these highly charged anions. This suggests an explanation for why nature has chosen Mg²⁺ but not Ca²⁺ to perform most of the essential tasks associated with biological triphosphates.

Metal coordination in kinases and pseudokinases

Protein phosphorylation, mediated by protein kinases, is a key event in the regulation of eukaryotic signal transduction. The majority of eukaryotic protein kinases perform phosphoryl transfer, assisted by two divalent metal ions. About 10% of all human protein kinases are, however, thought to be catalytically inactive. These kinases lack conserved residues of the kinase core and are classified as pseudokinases. Yet, it has been demonstrated that pseudokinases are critically involved in biological functions. Here, we show how pseudokinases have developed strategies by modifying amino acid residues in order to achieve stable, active-like conformations. This includes binding of the co-substrate ATP in a two metal-, one metal- or even no metal-binding mode. Examples of the respective pseudokinases are provided on a structural basis and compared with a canonical protein kinase, Protein Kinase A. Moreover, the functional roles of both independent metal-binding sites, Me1 and Me2, are discussed. Lack of phosphotransferase activity does not implicate a loss of function and can easily point to alternative roles of pseudokinases, i.e. acting as switches or scaffolds, and having evolved as components crucial for cellular cross-talk and signaling. Interestingly, pseudokinases are present in all kingdoms of life and their specific roles remain enigmatic. More studies are needed to unravel the crucial functions of those interesting proteins.

Understanding the binding of inhibitors of matrix metalloproteinases by molecular docking, quantum mechanical calculations, molecular dynamics simulations, and a MMGBSA/MMBappl study

Matrix metalloproteinases (MMPs) consist of a class of proteins required for normal tissue function. Their over expression is associated with many disease states and hence the interest in MMPs as drug targets. Almost all MMP inhibitors have been reported to fail in clinical trials due to lack of specificity. Zinc in the binding site of metalloproteinases performs essential biological functions and contributes to the binding affinity of inhibitors. The multiple possibilities for coordination geometry and the consequent charge on the zinc atom indicate that parameters developed are not directly transferable across different families of zinc metalloproteinases with different zinc coordination geometries, active sites and ligand architectures which makes it difficult to evaluate metal-ligand interactions. In order to assist in drug design endeavors for MMP targets, a computationally tractable pathway is presented, comprising docking of small molecule inhibitors against the target MMPs, derivation of quantum mechanical charges on the zinc ion in the active site and the amino acids coordinating with zinc including the inhibitor molecule, molecular dynamics simulations on the docked ligand-MMP complexes and evaluation of binding affinities of the ligand-MMP complexes via an accurate scoring function for zinc containing metalloprotein-ligand complexes. The above pathway was applied to study the interaction of inhibitor Batimastat with MMPs, which resulted in a high correlation between the predicted binding free energies and experiment, suggesting the potential applicability of the pathway. We then proceeded to formulate a few design principles which identify the key protein residues for generating molecules with high affinity and specificity against each of the MMPs.

How simple is too simple? Computational perspective on importance of second-shell environment for metal-ion selectivity

The metal-ion selectivity in biomolecules represents one of the most important phenomena in bioinorganic chemistry. The open question to what extent is the selectivity in the complex bioinorganic structures such as metallopeptides determined by the first-shell ligands of the metal ion is answered herein using six model peptides complexed with the set of divalent metal ions (Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), and Hg(2+)) and their various first-shell representations. By calculating the differences among the free energies of complexation of metal ions in these peptides and their model (truncated) systems it is quantitatively shown that the definition of the first shell is paramount to this discussion and revolves around the chemical nature of the binding site. Despite the vast conceivable diversity of peptidic structures, that suggest certain fluidity of this definition, major contributing factors are identified and assessed based on their importance for capturing metal-ion selectivity. These factors include soft/hard character of ligands and various non-covalent interactions in the vicinity of the binding site. The relative importance of these factors is considered and specific suggestions for effective construction of the models are made. The relationship of first-shell models and their corresponding parent peptides is discussed thoroughly, both with respect to their chemical similarity and potential disparity introduced by generally "non-alignable" conformational flexibility of the two systems. It is concluded that, in special cases, this disparity can be negligible and that heeding the chemical factors contributing to selectivity during construction of the model can successfully result in models that retain the affinity profile for various metal ions with high fidelity.

Molecular mechanisms for generating transmembrane proton gradients

Membrane proteins use the energy of light or high energy substrates to build a transmembrane proton gradient through a series of reactions leading to proton release into the lower pH compartment (P-side) and proton uptake from the higher pH compartment (N-side). This review considers how the proton affinity of the substrates, cofactors and amino acids are modified in four proteins to drive proton transfers. Bacterial reaction centers (RCs) and photosystem II (PSII) carry out redox chemistry with the species to be oxidized on the P-side while reduction occurs on the N-side of the membrane. Terminal redox cofactors are used which have pKas that are strongly dependent on their redox state, so that protons are lost on oxidation and gained on reduction. Bacteriorhodopsin is a true proton pump. Light activation triggers trans to cis isomerization of a bound retinal. Strong electrostatic interactions within clusters of amino acids are modified by the conformational changes initiated by retinal motion leading to changes in proton affinity, driving transmembrane proton transfer. Cytochrome c oxidase (CcO) catalyzes the reduction of O2 to water. The protons needed for chemistry are bound from the N-side. The reduction chemistry also drives proton pumping from N- to P-side. Overall, in CcO the uptake of 4 electrons to reduce O2 transports 8 charges across the membrane, with each reduction fully coupled to removal of two protons from the N-side, the delivery of one for chemistry and transport of the other to the P-side.

Zwitterionic conformers of pyrrolysine and their interactions with metal ions--a theoretical study

A total of 16 pyrrolysine conformers in their zwitterionic forms are studied in gas and simulated aqueous phase using a polarizable continuum model (PCM). These conformers are selected on the basis of our study on the intrinsic conformational properties of non-ionic pyrrolysine molecule in gas phase [Das and Mandal (2013) J Mol Model 19:1695-1704]. In aqueous phase, the stable zwitterionic pyrrolysine conformers are characterized by full geometry optimization and vibrational frequency calculations using B3LYP/6-311++G(d,p) level of theory. Single point calculations are also carried out at MP2/6-311++G(d,p) level. Characteristic intramolecular hydrogen bonds present in each conformer, their relative energies, theoretically predicted vibrational spectra, rotational constants and dipole moments are systematically reported. The calculated relative energy range of the conformers at B3LYP/6-311++G(d,p) level is 5.19 kcal mol(-1) whereas the same obtained by single point calculations at MP2/6-311++G(d,p) level is 4.58 kcal mol(-1). A thorough analysis reveals that four types of intramolecular H-bonds are present in the conformers; all of which play key roles in determining the energetics and in imparting the observed conformations to the conformers. The vibrational frequencies are found to shift invariably toward the lower side of frequency scale corresponding to the presence of the H-bonds. This study also points out that conformers with diverse structural motifs may differ in their thermodynamical stability by a narrow range of relative energy. The effects of metal coordination on the relative stability order and structural features of the conformers are examined by complexing five zwitterionic conformers of pyrrolysine with Cu(+2) through their carboxylate groups. The interaction enthalpies and Gibbs energies, rotational constants, vibrational frequencies and dipole moments of the metal complexes calculated at B3LYP level are also reported. The zwitterionic conformers of pyrrolysine are not stable in gas phase; after geometry optimization they are converted to the non-ionic forms.

Structure of dipeptides having N-terminal selenocysteine residues: a DFT study in gas and aqueous phase

Over the last few decades, dipeptides as well as their analogues have served as important model systems for the computational studies concerning the structure of protein and energetics of protein folding. Here, we present a density functional structural study on a set of seven dipeptides having N-terminal selenocysteine residues (the component in the C-terminus is varied with seven different combinations viz. Ala, Phe, Glu, Thr, Asn, Arg and Sec) in gas and simulated aqueous phase using a polarizable continuum model (PCM). The molecular geometries of the dipeptides are fully optimized at B3LYP/6-311++G(d,p) level and subsequent frequency calculations confirm them as true minima. The effects of solvation and identity of the varying C-terminal residue on the energetics, structural features of the peptide planes, values of the ψ and ф dihedrals, geometry around the α-carbon atoms and theoretically predicted vibrational spectra of the dipeptides are investigated. Two types of intramolecular H-bonds, namely N…H-N and O…H-C, are found to play important roles in influencing the planarity of the peptide planes and geometry around the α-carbon atoms of the dipeptides. The identity of the varying C-terminal residue influences the values of ф, planarity of the peptide planes and geometry around the C₇ α-carbon atoms while the solvation effects are evident on the values of bond lengths and bond angles of the amide planes.

Investigations of dipeptide structures containing pyrrolysine as N-terminal residues: a DFT study in gas and aqueous phase

A set of six dipeptides containing pyrrolysine invariably at their N-terminal positions is studied in gas and aqueous phase using a polarizable continuum model (PCM). The molecular geometries of the dipeptides are fully optimized at B3LYP/6-31++G(d,p) level of theory and a second derivative (frequency) analysis confirms that all the optimized geometries are true minima. The effects of solvation and identity of the varying C-terminal residue on the energetics, structural features of the peptide planes, values of the ψ and ϕ dihedrals, geometry around the α-carbon atoms and theoretically predicted vibrational spectra of the dipeptides are thoroughly analyzed. Solvation effects are found to modify the gas phase conformation of the dipeptides around ψ dihedrals while the identity of the varying C-terminal residue affect the values of ϕ, planarity of the peptide planes and geometry around the α-carbon atoms. The presence or absence of three types of intramolecular H-bonds, namely O...H-N, N...H-N and O...H-C that leave noticeable signatures in the IR spectra, play crucial roles in influencing the geometry of the peptide planes and in determining the energetics of the dipeptides.

DFT studies on the intrinsic conformational properties of non-ionic pyrrolysine in gas phase

B3LYP/6-31G(d,p) level of theory is used to carry out a detailed gas phase conformational analysis of non-ionized (neutral) pyrrolysine molecule about its nine internal back-bone torsional angles. A total of 13 minima are detected from potential energy surface exploration corresponding to the nine internal back-bone torsional angles. These minima are then subjected to full geometry optimization and vibrational frequency calculations at B3LYP/6-31++G(d,p) level. Characteristic intramolecular hydrogen bonds present in each conformer, their relative energies, theoretically predicted vibrational spectra, rotational constants and dipole moments are systematically reported. Single point calculations are carried out at B3LYP/6-311++G(d,p) and MP2/6-31++G(d,p) levels. Six types of intramolecular H-bonds, viz. O...H-O, N...H-O, O...H-N, N...H-N, O...H-C and N...H-C, are found to exist in the pyrrolysine conformers; all of which contribute to the stability of the conformers. The vibrational frequencies are found to shift invariably toward the lower side of frequency scale corresponding to the presence of intramolecular H-bond interactions in the conformers.