Editorial [Hot topic: Predictions and Determinations of Protein and Peptide Structures (Guest Editor: Guo-Ping Zhou)]
Abstract:In recent decades, faced with global threats of SARS (severe acute respiratory syndrome) coronavirus and influenza A viruses on human life and health, scientists realize that studying methodologies for rapid and accurate structure determination of biomacromolecules is of utmost importance. The structural determination of viruses and their relevant enzymes and proteins will be helpful to understand the relationship between structures and functions, including the mechanisms of interactions between protein-protein, protein-DNA, and protein-ligands. Furthermore, it provides solid insights and footings for rational drug design. As is known, most membrane receptors are druggable target proteins, such as tyrosine kinase-linked receptors, peripheral membrane protein receptors, G-protein-coupled receptors, ion-channels and transporters. Many proteins, particularly membrane proteins are very difficult to crystallize for X-ray spectroscopy or solubilize for NMR spectroscopy to determine their 3D (three-dimensional) structures. Therefore, one of the highest priority tasks today for structural biologists is to timely and accurately determine the 3D structures of various biomacromolecules, either experimentally or theoretically, or by their combination. This special issue contains two systematic reviews, eight original research articles and a letter, reporting the recent progresses of this area from different angles.
The review article by Dr. Guo-Ping Zhou addressed that the interactions between cGKIα and MBS proteins are closely related to the pathological mechanisms of cardiovascular diseases including hypertension and atherosclerosis . A highresolution NMR facility and computational approaches were used in this study. Another remarkable feature in this review is that, rather than the traditional helix wheel diagrams widely used to represent helices in proteins, the wenxiang diagram [2,3] is for the first time adopted to study LZCC structures and LZCC-LZCC interaction mechanism, and stimulating insights are gained.
The review article by Dr. Takeshi Kikuchi et al. have elucidated that decoding amino acid sequences to extract information on the principles of protein folding is a significant but difficult problem. Based on the technique used to study the statistical average distances between inter-residues in proteins, they have showed the possibility to predict some useful information about protein 3D structures. Meanwhile, some relevant results derived from their approach were reported as well.
Dr. Chen-Yan Zhang et al. have developed an efficient approach to enhance the success rate of crystallizing proteins. According to their statistical analysis, a significant improvement was shown in crystal screening by using a convenient strategy called “composition modification”. Interestingly, with such a strategy, some new crystals were found in addition to a significant enhancement in the success rate of crystallisation.
Dr. Jing He et al. report a novel geometric approach for predicting protein-ligand binding sites. The method may be of use for drug design.
It is indicated in the article by Dr. Hui-Min Lv et al. that the accurate assessment of salvation free energy is important for molecules containing a lot of polar groups. Meanwhile, some examples are shown how the potential leading compounds bound to the protein target may affect the future drug design and screening.
In the article by Dr. Khader Shameer et al., a novel method called “3Dswap-pred” was proposed for predicting the 3D information of proteins based on the Random Forest approach using a positive sequence dataset. The corresponding web-server is accessible to the public at http://caps.ncbs.res.in/3dswap-pred.
Dr. Xu-Yuan Liu et al. have reported an interesting finding by means of molecular docking and molecular dynamics studies that the GlaxoSmithKline's compound sodelglitazar (GW677954) can activate PPARs (peroxisome proliferator-activated receptors), which play a critical role in treating metabolic diseases, especially the Type-2 diabetes mellitus.
Dr. Xing Zhou et al. reported that, based on the analysis of the 3-D molecular modeling, SI and its mutants can synthesize α-arbutin, where some important phenylalanine residues have been found. This finding may pave a new way to change the selectivity and specificity of sucrose isomerase and other enzymes, thereby extending the application fields for these enzymes.
The paper by Dr. Ibrahim et al. has presented a docking modeling of the protease MASPT-Mn2+. The model and structural analysis are very useful not only for the initial inferences about the enzyme's structure but also for the rational design of its improved derivatives.....
Document Type: Research Article
Publication date: October 1, 2011
More about this publication?
- Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.