Molecular interactions, in biological systems

Interactions between macromolecules (protems, lipids, DNA,.. . ) or biological structures (e.g. membranes) are considerably more complex than the interactions described m the two preceding paragraphs. The sum of all biological mteractions at the molecular level is the basis of the complex mechanisms of life. In addition to computer simulations, direct force measurements [98], especially the surface forces apparatus, represent an invaluable tool to help understand the molecular interactions in biological systems. 

Motoc, I. and Dragomir, O. (1981). Molecular Interactions in Biological Systems. Steric Interactions. The SIBIS Algorithm. Math.Chem., 12,117-126. 

Solvation Methods. Because the polar, cohesive nature of water profoundly affects aU molecular interactions in biological systems [248], the effects of solvation on the conformation of a protein must be included in an accurate protein model. 

Section 2 mainly focuses on the current efforts to improve the accuracy of quantum calculations using simplified empirical model forms. McNamara and Hillier, in Chapter 5, summary their work on improving the description of the interactions in biological systems via their optimized semiempirical molecular models. Piquemal and co-workers present recent advances in the classical molecular methods, aiming at better reproduction of high-level quantum descriptions of the electtostatic interactions in Chapter 6. In Chatper 7, Cui and Elstner describe a different semiempir-... 

Varying the side groups X in 27b affects both the stability and selectivity of the complexes (lateral discrimination), and allows the receptor-substrate interactions in biological systems to be modelled, for instance, the interaction between nicotinamide and tryptophan [2.109b]. One may attach to 27b amino acid residues (leading to parallel peptides [2.109] as in 27c), nucleic acid bases or nucleosides, saccharides, etc. The structural features of 27 and its remarkable binding properties make it an attractive unit for the construction of macropolycyclic multisite receptors, molecular catalysts, and carriers for membrane transport. Such extensions require sepa-... 

The importance of non - covalent interactions in biological systems has motivated much of the current interest in supramolecular assemblies [1]. A classical example of a supermolecule has been provided by the rotaxanes [2,3], in which a molecular rotor is threaded by a threaded by a linear axle . Another examples have been previously included as cyclic crown ethers threaded by polymers, paraquat -hydroquinone complexes [4] and cyclodextrin complexes [5,6],... 

Molecular recognition, defined as the favored binding of a molecule (i.e., a substrate) to a specific site in a receptor over other structurally and chemically related molecules, is at the forefront of science.1 s Long before man walked on this earth, nature had succeeded in the creation of a series of biologically based recognition elements with unmatched specificity antibodies, enzymes, and receptors. Perhaps the simplest well-known example of this concept is the lock and key hypothesis that has been used to describe protein-substrate interactions in biological systems.5-7... 

Our approach to understanding the role of the hydrogen bond in determining the three-dimensional structure of molecular shapes and interactions in biological systems is analogous to the modern meaning of epidemiology. That is, the prediction of the most probable behavior by means of surveys of the behavior of similar species, or the same species in different habitats. 

It is well known that water-mediated interaction stabilizes structure of biomolecules [1, 138, 247-250]. Therefore, several model molecular systems have been chosen to probe the water-mediated interactions in biomolecules and a large amount of experimental and theoretical work has been published over the years on this subject [78, 138, 251-258]. Since phenol is the simplest aromatic alcohol resembling chromophore of an aromatic amino acid, hydration of phenol molecules has been studied to understand H-bonding and solute-solvent interaction in biological systems. Several experimental and theoretical calculations have been made on the phenol-water clusters [259-273]. Recently, we have made a comprehensive analysis on structure, stability, and H-bonding interaction in phenol (P1-4), water (W1-4), and phenol-water (PmW (w = 1-3, n = 1-3, w + n < 4)) clusters using ab initio and DFT methods [245]. In this section, electronic structure calculations combined with AIM analysis on phenol-water clusters are presented. 

It should be pointed out that H-bonding plays a fundamental role in molecular recognition in biological systems and in all systems associated with architecture of crystal or condensed state of matter [5, 6]. These kinds of interactions are in principle of a long-distant type but these aspects will not be discussed in this review. 

Politzer P, Murray JS, Peralta-Inga Z. Molecular surface electrostatic potentials in relation to noncovalent interactions in biological systems. Int J Quantum Chem 2001 85 676-684. 

In conclusion, it is clear that considerable information about a molecule s inherit stability, and its ability to interact with other chemical species, can be deduced from the electrostatic potential and some other well defined properties that reflect the molecular charge distribution. It should be emphasized that this approach only requires the wavefunction of the isolated molecule to be calculated, and it is therefore considerably more economical than the conventional supermolecule approach for calculation of intermolecular interaction energies. In particular, we believe that this methodology can be very useful for studying interactions in biological systems, since these often involve large molecules with several interaction sites. 

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