In particular, water molecules in solutions are divided into 1) internal water molecules that occupy cavities in the biomolecule structure and can be identified in crystallography 2) water molecules that interact with the molecular surface and 3) bulk water. In light of this, solvation water should be considered an integral part of biological macromolecules. In general, both hydrophobic and hydrophilic effects are dominant driving forces for several biochemical processes, such as protein folding, nucleic acid stability, molecular recognition, and binding ( Tanford, 1972 Brooks et al., 1998 Aftabuddin and Kundu, 2007 Moret and Zebende, 2007 Miotto et al., 2018). So we can extract information on the chemical nature and function of the solute by studying the attraction and repulsion of chemical compounds toward the water ( Chothia, 1976). In particular, the arrangement of the water molecules that hydrate compounds changes according to their properties ( Vagenende and Trout, 2012 Tomobe et al., 2017). Compounds immersed in water display different behaviors depending on their chemical characteristics. Hydration water molecules play a crucial role in living organisms as most biological processes occur in an aqueous environment ( Rothschild and Mancinelli, 2001), which actively influences the structure and function of biomolecules and their interactions ( Levy and Onuchic, 2006 Ball 2008). A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. 3Department of Molecular Medicine, Sapienza University, Rome, ItalyĪssessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction.2Department of Physics, Sapienza University, Rome, Italy.1Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy.So only these four are able to build up salt bridges to cross-stabilise tertiary structures and are thus classed as charged.Lorenzo Di Rienzo 1 †, Mattia Miotto 1,2 †, Leonardo Bò 1, Giancarlo Ruocco 1,2, Domenico Raimondo 3* and Edoardo Milanetti 1,2* In a peptide or protein, these amino acids’ non-polar side chains will usually act as non-polar domains within the tertiary structureĪ similar case can be made for the ‘charged’ amino acids (Glu, Asp, Lys, Arg): obviously and trivially, all amino acids have charged groups when dissolved in water but only those four have a charged side chain. Gly, Ala, Val, Leu, Ile), it is a non-polar residue and thus these amino acids are classified as ‘non-polar amino acids’ in simplistic terms. If the residue contains only carbon and hydrogen atoms (e.g. As all amino acids have a carboxylic and amino group and as these groups are connected in peptide bonds to form the peptide or protein backbone, these two groups alone are not able to distinguish between the different amino acids.įor this reason, the amino acids have been classified according to their residue R. However, it is desirable to categorise the different amino acids into various groups, to better explain their individual contributions to an overall peptide or protein structure. This is (obviously) due to the carboxylic acid and amino groups both of which are very polar functional groups and both of which are ionised in neutral aquaeous solution. Most of them are very polar, especially when compared to other organic molecules. When seen as molecules, all amino acids are polar to at least some degree. There are two things at play here and you need to mentally separate them.
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