Molecular dynamics simulations of pro-apoptotic BH3 peptide helices in aqueous medium: relationship between helix stability and their binding affinities to the anti-apoptotic protein Bcl-X<Subscript>L</Subscript>

The B-cell lymphoma 2 (Bcl-2) family of proteins regulates the intrinsic pathway of apoptosis. Interactions between specific anti- and pro-apoptotic Bcl-2 proteins determine the fate of a cell. Anti-apoptotic Bcl-2 proteins have been shown to be over-expressed in certain cancers and they are attractive targets for developing anti-cancer drugs. Peptides from the BH3 region of pro-apoptotic proteins have been shown to interact with anti-apoptotic Bcl-2 proteins and induce biological activity similar to that observed in parent proteins. However, the specificity of BH3 peptides derived from different pro-apoptotic proteins differ for different anti-apoptotic Bcl-2 proteins. In this study, we have investigated the relationship between the stable helical nature of BH3 peptides and their affinities to Bcl-X_L, an anti-apoptotic Bcl-2 protein. We have carried out molecular dynamics simulations of six BH3 peptides derived from Bak, Bad and Bim pro-apoptotic proteins for a period of 50 ns each in aqueous medium. Due to the amphipathic nature of BH3 peptides, the hydrophobic residues on the hydrophobic face tend to cluster together in all BH3 peptides. While this process resulted in a complete loss of helical structure in 16-mer Bak and 16-mer Bad wild type peptides, stabilizing interactions in the hydrophilic face of the BH3 peptides and capping interactions helped to maintain partial helical character in 16-mer Bad mutant and 16-mer Bim peptides. The latter two 16-mer peptides exhibit higher affinity for Bcl-X_L. Similarly the longer BH3 peptides, 25-mer Bad and 33-mer Bim, also resulted in smaller and stable helical fragments and their helical conformation is stabilized by interactions between residues in the solvent-exposed hydrophilic half of the peptide. The stable nature of helical segment in a BH3 peptide can be directly correlated to its binding affinity and the helical region encompassed the highly conserved Leu residue. We propose that upon approaching the hydrophobic groove of anti-apoptotic proteins, a longer helix will be induced in high affinity BH3 peptides by extending the smaller stable helical segments around the conserved Leu residue in both N- and C-terminal regions. The results reported in this study will have implications in developing peptide-based inhibitors for anti-apoptotic Bcl-2 proteins.     

Effect of molecular association and reactivity on substitution in chromium(III)–salprn complexes

A new chromium(III)–Schiff base complex, [Cr(5-chlorosalprn)(H₂O)₂]ClO₄, where salprn = N,N-propylenebis(salicylideneimine) has been prepared and characterized by electrospray ionization mass spectrometric (ESIMS) analysis and other spectroscopic techniques. Single crystal X-ray data reveal that the complex assumes a trans-diaquo structure, [Cr(C₁₇H₁₈Cl₂N₂O₄)]ClO₄ · H₂O. The effect of phenyl ring substituents on the rate of formation of [O=Cr^V Schiff base]⁺ has been investigated. The bimolecular rate constant for the formation of O=Cr^V species by the [Cr(Schiff base)(H₂O)₂]ClO₄, where the Schiff base = salprn, (1) and 5-chlorosalprn, (2) with PhOI was compared. In the case of (2) the rate was found to be faster by an order of magnitude at pH = 4 compared to (1). The introduction of a chloro-substituent on the phenyl ring not only influences the rate of redox reactivity but also the pKa values of aquo ligands of the complexes, indicating the difference in the electronic environment around the metal ion in both (1) and (2).     

Membranes,immobilization, and protective strategies for enzyme fuel cell stability

Enzymatic biofuel cells (EBFCs) for direct biochemical energy conversion are a promising candidate for addressing the growing power demands for low-power implantable and wearable devices. EBFCs comprise electrodes modified with biorecognition elements that produce bioelectrical energy from the redox activity of an organic fuel (sugars, alcohols) and an oxidant at the surface of the anode and cathode. The biorecognition layers are carefully constructed using enzymes immobilized on the electrode via surface modification strategies to increase the enzyme loading and hence the turnover rate. In addition, a polymer encapsulation membrane is implemented to create a protective microenvironment for the enzymes to enhance the biofuel cell's productivity. In this brief review, the different methods carried out to improve the stability of the EBFC system are discussed. New trends and key challenges are presented to illustrate the importance of the various materials implemented in extending the operational lifetime of EBFCs.     

First Example of a Modular Porphyrinoid Assembly Capable of Stabilizing Different Metal Ions in a Single Molecular Scaffold

We report the synthesis and characterization of porphyrin–corrole–porphyrin (Por‐Cor‐Por) hybrids directly linked at the meso–meso positions for the first time. The stability and solubility of the trimer are carefully balanced by adding electron‐withdrawing substituents to the corrole ring and sterically bulky groups on the porphyrins. The new hybrids are capable of stabilizing more than one metal ion in a single molecular scaffold. The versatility of the triad has been demonstrated by successfully stabilizing homo‐ (Ni) and heterotrinuclear (Ni‐Cu‐Ni) coordination motifs. The solid‐state structure of the NiPor‐CuCor‐PorNi hybrid was revealed by single‐crystal X‐ray diffraction studies. The Ni^II porphyrins are significantly ruffled and tilted by 83° from the plane of corrole. The robustness of the synthesized hybrids was reflected in the electrochemical investigations and the redox behaviour of the hybrids show that the oxidation processes are mostly corrole‐centred. In particular it is worth noting that the Por‐Cor‐Por hybrid can further be manipulated due to the presence of substituent‐free meso‐positions on both the terminals.     

Close contacts between carbonyl oxygen atoms and aromatic centers in protein structures: pi...pi or lone-pair...pi interactions?

Lone-pair...pi and, more recently, pi...pi interactions have been studied in small molecule crystal structures, and they are the focus of attention in some biomolecules. In this study, we have systematically analyzed 500 high-resolution protein structures (resolution < or =1.8 A) and identified 286 examples in which carbonyl oxygen atoms approach the aromatic centers within a distance of 3.5 A. Contacts involving backbone carbonyl oxygens are frequently observed in helices and, to some extent, in strands. Geometrical characterization indicates that these contacts have geometry in between that of an ideal pi...pi and a lone-pair...pi interaction. Quantum mechanical calculations using 6-311++G** basis sets reveal that these contacts give rise to energetically favorable interactions and, along with MD simulations, indicate that such interactions could stabilize secondary structures.     

Photoinduced electron transfer reactions at methylene blue adsorbed nafion and clay coated electrodes

Nafion and montmorillonite clay adsorbed methylene blue coated onto platinum electrode were prepared. These dye modified electrodes were used as photoelectrodes in a photogalvanic cell in the presence of Fe²⁺ ions. The photoelectrochemical investigations showed that the dye coated electrodes behaved as cathode upon irradiation whereas the plain platinum electrode dipped in a homogeneous solution containing methylene blue and Fe²⁺ ions behaved as anode. It is suggested that the intermediate complex formed between the photoreduced methylene blue and ferric ion lead to the reductive reaction at the coated electrode.     

Dynamics of noncovalent interactions in all-α and all-β class proteins: implications for the stability of amyloid aggregates

A fully folded functional protein is stabilized by several noncovalent interactions. When a protein undergoes conformational motions, the existing noncovalent interactions may be maintained. They may also break or new interactions may be formed. Knowledge of the dynamical nature of the different types of noncovalent interactions is extremely important to understand the structural stability, function, and folding of a protein. There are experimental limitations to investigate the dynamics of different noncovalent interactions simultaneously in a biomolecule. We have carried out molecular dynamics simulations on four different proteins, two belonging to all-α class proteins and the other two are representatives of all-β class proteins. The dynamical nature of eight different noncovalent interactions was studied by monitoring the maximum residence time (MRT) and lifetime (LT). The conventional hydrogen bonds are the dominant interactions in all four proteins, and the majority of those formed between the main-chain atoms were maintained during most of the simulation time with MRT greater than 10 ns. Such interactions with more than 1 ns lifetime provide stability to the secondary structures, and hence they are responsible for the overall stability of the protein. The weak C-H···O hydrogen bond is the next major type of interactions. However, a large number of such interactions are observed between the main-chain atoms only in all-β proteins as interstrand interactions, and, surprisingly, they are observed during most part of the simulation although their average lifetime is only about 20 to 30 ps. The strong cation···π and salt-bridge interactions are present few in number. However, in many cases they are almost uninterrupted indicating the higher strength of these interactions. Four other interactions involving the π-electron cloud of aromatic rings are very small in number, and, in many cases, their presence is not maintained throughout the simulation. Our results clearly indicate that the weak C-H···O interactions between the main-chain atoms are the distinguishing factor between the all-α and all-β class of proteins, and these interstrand interactions can provide additional stability to all-β protein structures. Based on these results, we hypothesize that such weak C-H···O interstrand interactions could play a major role in providing stability to amyloid type of aggregates that are responsible for the pathological state of many proteins.     

Enzyme catalyzed reactions: From experiment to computational mechanism reconstruction

The traditional experimental practice in enzyme kinetics involves the measurement of substrate or product concentrations as a function of time. Advances in computing have produced novel approaches for modeling enzyme catalyzed reactions from time course data. One example of such an approach is the selection of appropriate chemical reactions that best fit the data. A common limitation of this approach resides in the number of chemical species considered. The number of possible chemical reactions grows exponentially with the number of chemical species, which makes difficult to select reactions that uniquely describe the data and diminishes the efficiency of the methods. In addition, a method’s performance is also dependent on several quantitative and qualitative properties of the time course data, of which we know very little. This information is important to experimentalists as it could allow them to setup their experiments in ways that optimize the network reconstruction. We have previously described a method for inferring reaction mechanisms and kinetic rate parameters from time course data. Here, we address the limitations in the number of chemical reactions by allowing the introduction of information about chemical interactions. We also address the unknown properties of the input data by determining experimental data properties that maximize our method’s performance. We investigate the following properties: initial substrate–enzyme concentration ratios; initial substrate–enzyme concentration variation ranges; number of data points; number of different experiments (time courses); and noise. We test the method using data generated in silico from the Michaelis–Menten and the Hartley–Kilby reaction mechanisms. Our results demonstrate the importance of experimental design for time course assays that has not been considered in experimental protocols. These considerations can have far reaching implications for the computational mechanism reconstruction process.