Charged Side-chain Groups Research Articles

Changes in the Local Conformational States Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Seven Force Fields with and without NBFIX and ECC Corrections.

Electrostatic interactions have a determining role in the conformational and dynamic behavior of polyelectrolyte molecules. In this study, anionic polyelectrolyte molecules, poly(glutamic acid) (PGA) and poly(aspartic acid) (PASA), in a water solution with the most commonly used K+ or Na+ counterions, were investigated using atomistic molecular dynamics (MD) simulations. We performed a comparison of seven popular force fields, namely AMBER99SB-ILDN, AMBER14SB, AMBER-FB15, CHARMM22*, CHARMM27, CHARMM36m and OPLS-AA/L, both with their native parameters and using two common corrections for overbinding of ions, the non-bonded fix (NBFIX), and electronic continuum corrections (ECC). These corrections were originally introduced to correct for the often-reported problem concerning the overbinding of ions to the charged groups of polyelectrolytes. In this work, a comparison of the simulation results with existing experimental data revealed several differences between the investigated force fields. The data from these simulations and comparisons with previous experimental data were then used to determine the limitations and strengths of these force fields in the context of the structural and dynamic properties of anionic polyamino acids. Physical properties, such as molecular sizes, local structure, and dynamics, were studied using two types of common counterions, namely potassium and sodium. The results show that, in some cases, both the macroion size and dynamics depend strongly on the models (parameters) for the counterions due to strong overbinding of the ions and charged side chain groups. The local structures and dynamics are more sensitive to dihedral angle parameterization, resulting in a preference for defined monomer conformations and the type of correction used. We also provide recommendations based on the results.

Adsorption of Native Amino Acids on Nanocrystalline TiO2: Physical Chemistry, QSPR, and Theoretical Modeling.

The affinity of biomolecules, such as peptides and proteins, with inorganic surfaces, is a fundamental topic in biotechnology and bionanotechnology. Amino acids are often used as "model" bits of peptides or proteins for studying their properties in different environments and/or developing functional surfaces. Despite great demand for knowledge about amino acid interactions with metal oxide surfaces, studies on the issue represent a fragmentary picture. In this paper, we describe amino acid adsorption on nanocrystalline anatase systematically at uniform conditions. Analysis of the Gibbs free adsorption energy indicated how the aliphatic, aromatic, polar, and charged side chain groups affect the binding affinity of the amino acids. Thermodynamic features of the l-amino acid adsorption receive thorough interpretation with calculated molecular descriptors. Theoretical modeling shows that amino acids complex with TiO2 nanoparticles as zwitterions via ammonium group.

Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions.

Ions differ in their ability to salt out proteins from solution as expressed in the lyotropic or Hofmeister series of cations and anions. Since its first formulation in 1888, this series has been invoked in a plethora of effects, going beyond the original salting out/salting in idea to include enzyme activities and the crystallization of proteins, as well as to processes not involving proteins like ion exchange, the surface tension of electrolytes, or bubble coalescence. Although it has been clear that the Hofmeister series is intimately connected to ion hydration in homogeneous and heterogeneous environments and to ion pairing, its molecular origin has not been fully understood. This situation could have been summarized as follows: Many chemists used the Hofmeister series as a mantra to put a label on ion-specific behavior in various environments, rather than to reach a molecular level understanding and, consequently, an ability to predict a particular effect of a given salt ion on proteins in solutions. In this Feature Article we show that the cationic and anionic Hofmeister series can now be rationalized primarily in terms of specific interactions of salt ions with the backbone and charged side chain groups at the protein surface in solution. At the same time, we demonstrate the limitations of separating Hofmeister effects into independent cationic and anionic contributions due to the electroneutrality condition, as well as specific ion pairing, leading to interactions of ions of opposite polarity. Finally, we outline the route beyond Hofmeister chemistry in the direction of understanding specific roles of ions in various biological functionalities, where generic Hofmeister-type interactions can be complemented or even overruled by particular steric arrangements in various ion binding sites.

A potential mechanism for amino acid-controlled crystal growth of hydroxyapatite.

The mineral component of bone, dentin and calcified parts of avian tendon, hydroxyapatite (HAP), has non-stoichiometric composition (idealized as Ca10(PO4)6(OH)2), plate-like morphology and nanometer size. This unique crystal morphology contributes to the physico-chemical and biochemical properties of bone. Thus, understanding the mechanism for the controlled growth of plate-like HAP nanocrystals is significant in the study of bone biomineralization. Previous studies have shown that acidic non-collagenous proteins (ANCPs), which are enriched in the residues of acidic amino acids, may play an important role in HAP crystal growth modulation. In this study, glutamic acid (Glu) and phosphoserine (Ser-OPO3) were used as model compounds to modify the synthesis of HAP nanocrystals. To identify the mechanisms of amino acids as regulators, X-ray diffraction (XRD), transmission electron microscopy (TEM) and solid state nuclear magnetic resonance (ssNMR) were used. The crystals obtained in the inorganic controls were needle-like, while crystals synthesized in the presence of the amino acids presented a plate-like morphology. The plate-like crystals had a preferred crystal orientation on (300) face, which was lacking in the inorganically grown crystals, indicating preferential adsorption and suppression of growth in specific crystal directions. Ser-OPO3 was more efficient than Glu in modulating HAP nucleation and crystal growth. Furthermore, NMR revealed interactions between the charged side chain groups in amino acids and the crystal surfaces. These results were successfully explained through our MD simulations for the free energy calculation of amino acid binding on HAP crystal faces. The present study revealed that amino acids may act as effective regulators of HAP morphology without the need to invoke large NCPs in bone biomineralization and in designing bioinspired materials for orthopaedic and dental applications.

Effects of Arginine Residue Introduction upon Interaction and Complexation Behavior of Peptide Ribonucleic Acids (PRNAs) with RNA: Synthesis and Properties of -Containing Arginine

A novel nucleic acid model using alpha-peptide ribonucleic acid (alpha-PRNA) possessing alternative alpha-PRNA/arginine sequences, where the arginine residue would be expected to stabilize the complex not only by the conventional hydrogen-bonding interactions between the complementary nucleobase pairs but also through the electrostatic interactions between positively charged side-chain groups and RNA's phosphate anions on the backbone. These alpha-PRNA form stable sequence-specific complex with the complementary RNA.

High-Density Hydration Layer of Lysozymes: Molecular Dynamics Decomposition of Solution Scattering Data

A characterization of the physical properties of protein hydration water is critical for understanding protein structure and function. Recent small-angle X-ray and neutron scattering data indicate that the density of water on the surface of lysozyme is significantly higher than in bulk water. Here, we provide an interpretation of the scattering results using a molecular dynamics simulation, which allows us to make quantitative predictions about density variations in the first hydration shell. The perturbation relative to bulk water involves statistically significant changes in the average water structure in the first hydration layer. The water density in the first hydration shell is increased by 5% with respect to the bulk. In regions of higher water density, the water dipoles align more parallel to each other and the number of hydrogen bonds per water molecule is higher. Increased water density is found for water molecules interacting with hydrogen and carbon atoms in the backbone or with nonpolar or negatively charged side-chain groups.

Intercalation and groove binding of an acridine–spermine conjugate on DNA sequences: an FT–Raman and UV–visible absorption study

Acridine and acridine derivatives are known as powerful DNA intercalators. Interactions of the acridine–spermine conjugate N1-(Acridin-9-yl)-1,5,9,14,18-pentaazaoctadecane on two 16-mer oligonucleotides containing either alternating guanine–cytosine or adenine–thymine sequences were studied by optical spectroscopies. UV–visible absorption spectra of oligonucleotide/conjugate solutions at different molar ratios were recorded. The conjugate bands in the 350–500 nm region showed strong hypochromism and slight red shift in the presence of the oligonucleotides, thus indicating that the acridine moieties intercalate into adjacent base pairs of the oligonucleotides. These effects stopped near the 1:1 molar ratio, indicating that each oligonucleotide chain can only host one conjugate molecule. Raman spectra of solutions 60 mM (in phosphate) of the oligonucleotides and 3 mM of the conjugate were also recorded. Upon intercalation, the spectra showed relevant wavenumber shifts for skeletal and base vibrations, which have been largely attributed to the interactions of the positively charged side chain groups with the reactive sites of the base residues. Raman data suggested the existence of sequence selectivity induced by the spermine tail. Intercalation together to spermine interaction by the major groove was favoured for the guanine–cytosine sequence, while no groove preference was achieved for the adenine–thymine sequence.

Probing the Energetic and Structural Role of Amino Acid/Nucleobase Cation-π Interactions in Protein-Ligand Complexes

X-ray structures of proteins bound to ligand molecules containing a nucleic acid base were systematically searched for cation-pi interactions between the base and a positively charged or partially charged side chain group located above it, using geometric criteria. Such interactions were found in 38% of the complexes and are thus even more frequent than pi-pi stacking interactions. They are moreover well conserved in families of related proteins. The overwhelming majority of cation-pi contacts involve Ade bases, as these constitute by far the most frequent ligand building block; Arg-Ade is the most frequent cation-pi pair. Ab initio energy calculations at MP2 level were performed on all recorded pairs. Though cation-pi interactions involving the net positive charge carried by Arg or Lys side chains are the most favorable energetically, those involving the partial positive charge of Asn and Gln side chain amino groups (sometimes referred to as amino-pi interactions) are favorable too, owing to the electron correlation energy contribution. Chains of cation-pi interactions with a nucleobase bound simultaneously to two charged groups or a charged group sandwiched between two aromatic moieties are found in several complexes. The systematic association of these motifs with specific ligand molecules in unrelated protein sequences raises the question of their role in protein-ligand structure, stability, and recognition.

Self-association and backbone dynamics of the hck SH2 domain in the free and phosphopeptide-complexed forms.

Decreased dynamic motion in the peptide backbone of proteins may accompany ligand binding and influence the thermodynamic and kinetic stability of the resulting complexes. We have investigated the diffusional behavior and backbone dynamics of the free and phosphopeptide (EPQpYEEIPIYL) complexed Hck SH2 domain using NMR spectroscopy. Both the free domain and its phosphopeptide complex self-associate at higher protein concentrations. Diffusional measurements and surface analysis indicate that charged side-chain groups are probably responsible for self-association. Higher order aggregation, such as trimer and tetramer, also occurs at elevated protein concentrations. Dynamic motion in the peptide backbone of Hck SH2 was determined from 15N relaxation data fit using extended model-free parameters. The rotational correlation time (taum) for uncomplexed Hck SH2 was 6.8 ns while taum for peptide-bound Hck SH2 was 7.6 ns. Generalized order parameters (S2) increased for most residues upon binding of the phosphopeptide, consistent with peptide binding restricting motion of the NH bond vectors on the picosecond time scale. These studies suggest that complexation increases internal order in Hck SH2 and that internal dynamic motions contribute to the activation of Src-family kinases in vivo.

Ca(2+)-induced conformational transitions of phosphorylated peptides.

CD spectroscopic studies on protected peptides containing lysine and serine, or phosphoserine, and on serine-containing fragments of the neurofilament protein midsized subunit, both in the unphosphorylated and phosphorylated form, are reported. The introduction of the phosphoryl group was not found to have a significant spectral effect in aqueous solution. In trifluoroethanol (TFE), spectral shifts toward unordered (type U) spectra or the appearance of distorted spectra likely reflect the adoption of aperiodic polypeptide conformations due to salt bridge(s) between negatively charged phosphoserine and positive lysine side-chain groups. A turn-stabilizing effect of phosphorylation was also observed. CD-monitored titration experiments in TFE revealed a high conformational sensitivity of phosphopeptides toward Ca2+ ions. The appearance of the unordered spectra or spectral shifts were the sign of a bulk disordering effect of Ca2+ ions. Spectra with specific spectroscopic features reflect the formation of Ca2+ complexes and the adoption of ordered unique backbone conformations. When ordered structures were obtained on addition of Ca2+ ions, the observed CD curves showed a resemblance to the spectrum of beta-pleated sheets. This may originate from chain extension and the formation of beta-pleated sheet segments fixed by Ca2+ bridges between PO3H-1 groups of adjacent peptide chains. The data clearly show that the effect of the Ca2+ ions is highly specific: the sequence, chain length, presence and distribution of charged side-chain groups, degree and site of phosphorylation, and environmental factors appear to be determining in the process of chain extension or beta-sheet formation.

Photoinduced cross-linkage, in situ, of Escherichia coli 30S ribosomal proteins to 16S rRNA: identification of cross-linked proteins and relationships between reactivity and ribosome structure.

The kinetics of photoinduced cross-linkage of Escherichia coli 30S ribosomal proteins to the 16S-rRNA molecule in the intact Escherichia coli 30S ribosomal subunit was studied in this report. All of the 30S ribosomal proteins become cross-linked to the 16S rRNA before changes in the sedimentation characteristics of the 30S ribosomal subunit can be detected. The proteins exhibit different reactivities in the cross-linkage reaction. One group of proteins-S3, S7-S9, S11, S12, and S15-S19-is cross-linked to the 16S rRNA by single-hit kinetics, or by photoprocesses of nonunity but low multiplicities. A second group of proteins--S1, S2, S4-S6, S10, S13, S14, and S21--is cross-linked to the 16S rRNA by photoprocesses of a complex nature. A comparison of these data with other properties of the individual 30S ribosomal proteins related to ribosome structure indicated that most of the 30S ribosomal proteins cross-linked to the 16S rRNA by photoprocesses of low multiplicities had been classified rRNA-binding proteins by nonphotochemical methods, and most of the proteins cross-linked to the 16S rRNA by photoprocesses of large multiplicities had been classified as nonbinding proteins. There were certain exceptions to these correlations. Proteins S4 and S20, both RNA-binding proteins, become cross-linked to the 16S rRNA by photoprocessses of large multiplicities, and proteins S3, S11, S12, and S18, none of which have been classified RNA-binding proteins, exhibited low multiplicities in the cross-linkage reaction. All of these exceptions could be explained in terms of limitations inherent in the photochemical methods used in this study and in other types of methods that have been used to study RNA-protein interactions in the 30S ribosomal subunit. The data presented here also suggest that labile RNA-protein cross-links are present in the uv-irradiated 30S ribosomal subunits, and that neither peptide-bond cleavage nor photoinduced modification of the charged side-chain groups in the ribosomal proteins accompanied the cross-linkage reaction. However, some photoinduced RNA-chain breakage might have occurred.

Gravimetric study of the sorption of water vapour by bovine serum albumin

The sorption of water vapour in the relative vapour pressure range 0.05 to 0.95 by bovine serum albumin isolated at pH values of 2.0, 4.0, 7.5 and 10.2 has been studied using a vacuum microbalance. Water vapour sorption was dependent on the number of ionic sites, particularly charged carboxylate groups, present in the protein. The existence of intramolecular ion pair bonds between charged side chain groups inhibited the sorption of water. Water was also sorbed onto peptide groups in the main protein chain at high relative vapour pressures.

The biuret complex of gelatin and the mechanism of gelation.

THE gelation of gelatin results from a thermally reversible cross-linking process involving hitherto unknown functional groups. In studies of gelation–molecular weight correlations of chemically modified gelatins (amino-acetylated, carboxyl-esterified, hydroxyl-acetylated, guanidino-nitrated) and of hypo-bromite-treated gelatin we have found that the polar and charged side-chain groups are of little importance in gelation1. Further, by study of the effects of various electrolytes on the melting points of gels of gelatin and of chemically modified gelatins, we have found that binding of ions at the polar and charged side-chain groups is not the mechanism by which electrolytes affect gelation2. These results have directed our attention to the role of the peptide group.