Preface of Special Issue “Protein-Ligand Interactions”

When we consider investigating function of macromole-cules, it is hardly possible to draw an experiment map without taking interactions of other molecules (ligands) into account, whether they could be metal ion, ATP, hormone, carbohydrate, lipid, nucleic acid, DNA, RNA, peptide and protein. In other words, no biological function can be elucidated without molecular interactions. Therefore, the study of protein-ligand interactions has been one of the long-standing fields in biophysics. Understanding in this field is, for example , a fundamental step for the rational design of a ligand to target a specific protein [1, 2]. The questions to be asked in this topic include mechanisms of selectivity, swift binding, and rapid turnover, if one concentrates on enzyme function, but different emphases can be placed on different aspects. These questions have been addressed both experimentally and computationally for a long time, but they are not fully resolved, hence more than 100 papers around this area is published every year, even when one just counts review litera ture. Recent progress in the methods for analysing protein-ligand interactions such as proteomics and other omics analyses, X-ray crystallography, NMR, mass spectro-metry (MS), computer simulation and so forth, is astonishing and all those methods, with combination, have a potential to completely revolutionise our understanding of this topic. The goal of this special issue is, therefore, to exchange the latest advances amongst the community and to inform researchers in related fields of its potential. In this special issue, we openly invited submission and finally have the following twelve papers; nine are based on computational study and three are based on wet-lab study. This special issue starts with the literature by Ishii et al. [3] that gave us a good review on the history of MS. Based on the background understanding, they demonstrated the power of MS for detecting conformational changes of protein with ligand, its stoichiometry and its dissociation constant. Then follow several papers focusing on protein structures. Iakovou et al. [4] developed a new virtual reality method for protein docking with haptics device. The software enables us to " feel " the docking process of two proteins and gave us a new insight in the mechanisms of protein-protein interactions. Uchikoga et al. [5] investigated the protein interfaces of protein-protein interactions, especially the one of hub proteins that has many different partners. Their computational analyses revealed that the composition of interacting amino acid residue pairs was sufficient …