Efficient Biosorption of Hexavalent Chromium from Water with Human Hair

The triphenyl group (trityl radical) possessing three-phenyl rings, self-assembled through aromatic π–π stacking interactions, can form interesting crystalline organic nano-flowers. In this work, we have synthesized a hybrid material of 1,2-bis(tritylthio)ethane and magnetite, which reduces toxic Cr(VI) to non-toxic Cr(III). We validated the efficacy of the hybrid in reducing toxic Cr(VI) along with three other adsorbent systems. Among the five adsorbent systems tested, we observed that human hair has higher Cr removal efficiency, which prompted us to explore further using different mechanical forms of human hair. Pulverized hair (PH), hair powder (HP), and raw hair (RH) were evaluated by employing different reaction factors such as the adsorbent dose, pH, initial Cr(VI) concentration, and contact time. The comparative evaluation showed that PH has greater adsorption capacity (15.14 mg/g), followed by RH (13.27 mg/g) and HP (10.5 mg/g). While investigating the adsorption mechanism, we observed that it follows pseudo-second-order kinetics suggesting chemisorption. The Freundlich isotherm model fitted well for Cr(VI) adsorption by human hair, suggesting a multi-layered adsorption process. Overall, this study promises a cost-effective and eco-friendly bio-adsorbent for Cr(VI), which may be scaled up to design automated industrial waste disposal systems

Existence of Specific “Folds” in Polyproline II Ensembles of an “Unfolded” Alanine Peptide Detected by Molecular Dynamics

Equilibrium ensembles of octaalanine (Ac−Ala8−NHMe) in water, prepared with MD, are analyzed for contributing microstates with an RMSD-based conformational clustering algorithm. The extracted ensemble-averaged properties are in excellent agreement with numerous spectroscopic measurements reported with small alanine model peptides in water. However, the dominantly polyproline II-like ensemble of the peptide is found to be populated with a handful of highly position-specific “folds”, including β-turns, β-hairpins, and helix nuclei, which could be the “seeds” that initiate proteins along their folding pathways

Symmetry-Directed Self-Organization in Peptide Nanoassemblies through Aromatic π–π Interactions

Almost all biological systems are assemblies of one or more biomolecules from nano- to macrodimensions. Unlike inorganic molecules, peptide systems attune with the conceptual framework of aggregation models when forming nanoassemblies. Three significant recent theoretical models have indicated that nucleation, end-to-end association, and geometry of growth are determined primarily by the size and electrostatics of the individual basic building blocks. In this study, we tested six model systems, differentially modulating the prominence of three design variables, namely, aromatic π–π interactions, local electrostatics, and overall symmetry of the basic building unit. Our results indicate that the crucial design elements in a peptide-based nanoassembly are (a) a stable extended π–π interaction network, (b) size, and (c) overall symmetry of the basic building blocks. The six model systems represent all of the design variables in the best manner possible, considering the complexity of a biomolecule. The results provide important directives in deciding the morphology and crystallinity of peptide nanoassemblies

The Link between Sequence and Conformation in Protein Structures Appears To Be Stereochemically Established

In search of the link between sequence and conformation in protein structures, we perform molecular dynamics analysis of the effect of stereochemical mutation in end-protected octa-alanine Ac-Ala8-NHMe from poly-l to an alternating-l,d structure. The mutation has a dramatic effect, transforming the peptide from a condition of extreme sensitivity to one of extreme insensitivity to solvent. Examining the molecular folds of poly-l and alternating-l,d structure in atomistic detail, we find them to differ in the relationship between peptide dipolar interactions at the local and nonlocal levels, either conflicting or harmonious depending upon the chain stereochemistry. The stereochemical transformation of interpeptide electrostatics from a condition of conflict to one of harmony explains the long-standing puzzle of why poly-l and alternating-l,d peptides strongly differ in properties such as “stiffness” and solvent sensitivity. Furthermore, it is possible that poly-l stereochemistry is also the fulcrum of protein sensitivity to the effects of amino acid side-chain structures via dielectric arbitrations in interpeptide electrostatics. Indeed the evidence is accumulating that the amino acid side chains differing in α-helix and β-sheet propensities also differ in their desolvating effects in the adjacent and nearest-neighbor peptides and thus possibly in the solvent screening of peptide dipolar interactions

Mapping the Geometric Evolution of Protein Folding Motor

<div><p>Polypeptide chain has an invariant main-chain and a variant side-chain sequence. How the side-chain sequence determines fold in terms of its chemical constitution has been scrutinized extensively and verified periodically. However, a focussed investigation on the directive effect of side-chain geometry may provide important insights supplementing existing algorithms in mapping the geometrical evolution of protein chains and its structural preferences. Geometrically, folding of protein structure may be envisaged as the evolution of its geometric variables: ϕ, and ψ dihedral angles of polypeptide main-chain directed by χ₁, and χ₂ of side chain. In this work, protein molecule is metaphorically modelled as a machine with 4 rotors ϕ, ψ, χ₁ and χ₂, with its evolution to the functional fold is directed by combinations of its rotor directions. We observe that differential rotor motions lead to different secondary structure formations and the combinatorial pattern is unique and consistent for particular secondary structure type. Further, we found that combination of rotor geometries of each amino acid is unique which partly explains how different amino acid sequence combinations have unique structural evolution and functional adaptation. Quantification of these amino acid rotor preferences, resulted in the generation of 3 substitution matrices, which later on plugged in the BLAST tool, for evaluating their efficiency in aligning sequences. We have employed BLOSUM62 and PAM30 as standard for primary evaluation. Generation of substitution matrices is a logical extension of the conceptual framework we attempted to build during the development of this work. Optimization of matrices following the conventional routines and possible application with biologically relevant data sets are beyond the scope of this manuscript, though it is a part of the larger project design.</p></div

MIDMAT 1 substitution matrix.

<p>MIDMAT 1 substitution matrix values are calculated based on basin statistics derived from the rotor combinations of amino acids in the structural dataset of 22,997 non-redundant structures from PISCES server. The amino acids are represented as their single letter codes.</p

MIDMAT 3 substitution matrix.

<p>MIDMAT3 substitution matrix constructed by following the third strategy (results section) for calculation of B_i, from the identical data set of 22,997 non-redundant structures from PISCES server.</p

Homochiral Stereochemistry: The Missing Link of Structure to Energetics in Protein Folding

The notion is tested that homochiral stereochemistry being ubiquitous to protein structure could be critical to protein folding as well, causing it to become frustrated energetically providing the basis for its solvent- and sequence-mediated control. The proof in support of the notion is found in a consensus of experiment and computation according to which suitable oligopeptides are in their folding−unfolding equilibria, at both macrostate and microstate levels, susceptible to dielectric because of the conflict of peptide-chain electrostatics with interpeptide hydrogen bonds when the structure is poly-l but not when it is alternating-l,d. The argument is thus made that homochiral stereochemistry may in protein folding provide the unifying basis for its solvent- and sequence-mediated control based on screening of peptide-chain electrostatics under conflict with folding of the chain due to homochiral stereochemistry. Dielectric is brought into spotlight as the effect comparatively obscure but presumably critical to the folding in protein structure for its control

Mapping the Geometric Evolution of Protein Folding Motor - Fig 1

Functional rotors involved in structure formation: a) The four rotors representing four dihedral angles of an amino acid residue in a polypeptide chain. b) Orientation of four rotor motions during formation and breaking of helix and sheet with positive sign indicating right handed or clockwise direction and negative sign indicating left handed or counter clockwise direction. c) Rotational patterns of rotors during helix formation (green) and helix breaking (red) are shown d) Orientation of rotors resulting in the formation and breaking of sheeted structures.</p

Similar and unique hits for MIDMATs compared to BLOSUM62 and PAM30: The number of total, common and unique hits scored by MIDMATs (MIDMAT 1, MIDMAT 2 and MIDMAT 3), against BLOSUM62 and PAM30 matrices when plugged into a BLAST program against PDB, using the CASP11 database as a query set, while maintaining the default parameters of BLAST.

Similar and unique hits for MIDMATs compared to BLOSUM62 and PAM30: The number of total, common and unique hits scored by MIDMATs (MIDMAT 1, MIDMAT 2 and MIDMAT 3), against BLOSUM62 and PAM30 matrices when plugged into a BLAST program against PDB, using the CASP11 database as a query set, while maintaining the default parameters of BLAST.</p