Energetic Selection of Topology in Ferredoxins

Models of early protein evolution posit the existence of short peptides that bound metals and ions and served as transporters, membranes or catalysts. The Cys-X-X-Cys-X-X-Cys heptapeptide located within bacterial ferredoxins, enclosing an Fe4S4 metal center, is an attractive candidate for such an early peptide. Ferredoxins are ancient proteins and the simple α+β fold is found alone or as a domain in larger proteins throughout all three kingdoms of life. Previous analyses of the heptapeptide conformation in experimentally determined ferredoxin structures revealed a pervasive right-handed topology, despite the fact that the Fe4S4 cluster is achiral. Conformational enumeration of a model CGGCGGC heptapeptide bound to a cubane iron-sulfur cluster indicates both left-handed and right-handed folds could exist and have comparable stabilities. However, only the natural ferredoxin topology provides a significant network of backbone-to-cluster hydrogen bonds that would stabilize the metal-peptide complex. The optimal peptide configuration (alternating αL,αR) is that of an α-sheet, providing an additional mechanism where oligomerization could stabilize the peptide and facilitate iron-sulfur cluster binding

Organization of Bio-Molecules in Bulk and Over the Nano-Substrate: Perspective to the Molecular Dynamics Simulations

The properties of bio-molecules are explicitly influenced by their organization in bulk and vicinity of substrate. Organization of bio-molecules can be of various kinds such as folded, unfolded, helix, swollen, globule, and so forth. These organizations of bio-molecule also depend on the local surrounding environmental conditions like temperature, solvency, adsorption, and encapsulation. Variation in environmental conditions helps to manipulate and control the organizations for the desired applications. Adsorption and encapsulation of bio-molecule over substrate have many applications in the area of drug delivery, design and development of bio-sensors, advance bio-separation process, etc. Molecular dynamics simulation is a very powerful tool to investigate the molecular structures, synthesis process and optimum properties, etc. A large number of efficient force field parameters and molecular dynamics simulators are available for large-scale simulation