Identification of hot spot residues at protein-protein interface
نویسندگان
چکیده
It is known that binding free energy of protein-protein interaction is mainly contributed by hot spot (high energy) interface residues. Here, we investigate the characteristics of hot spots by examining inter-atomic sidechain-sidechain interactions using a dataset of 296 alanine-mutated interface residues. Results show that hot spots participate in strong and energetically favorable sidechain-sidechain interactions. Subsequently, we describe a novel, yet simple 'hot spot' prediction model with an accuracy that is similar to many available approaches. The model is also shown to efficiently distinguish specific protein-protein interactions from non-specific interactions.
منابع مشابه
Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy
MOTIVATION Hot spots are residues comprising only a small fraction of interfaces yet accounting for the majority of the binding energy. These residues are critical in understanding the principles of protein interactions. Experimental studies like alanine scanning mutagenesis require significant effort; therefore, there is a need for computational methods to predict hot spots in protein interfac...
متن کاملHotRegion: a database of predicted hot spot clusters
Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Hot regions are important for the stability of protein complexes, as well as providing specificity to binding sites. We propose a database called HotRegion, which provides the hot region information of t...
متن کاملHotPoint: hot spot prediction server for protein interfaces
The energy distribution along the protein-protein interface is not homogenous; certain residues contribute more to the binding free energy, called 'hot spots'. Here, we present a web server, HotPoint, which predicts hot spots in protein interfaces using an empirical model. The empirical model incorporates a few simple rules consisting of occlusion from solvent and total knowledge-based pair pot...
متن کاملPCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces
Protein-protein interactions (PPIs) are ubiquitous in Biology, and thus offer an enormous potential for the discovery of novel therapeutics. Although protein interfaces are large and lack defining physiochemical traits, is well established that only a small portion of interface residues, the so-called hot spot residues, contribute the most to the binding energy of the protein complex. Moreover,...
متن کاملRelationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces
In the context of protein-protein interactions, the term "hot spot" refers to a residue or cluster of residues that makes a major contribution to the binding free energy, as determined by alanine scanning mutagenesis. In contrast, in pharmaceutical research, a hot spot is a site on a target protein that has high propensity for ligand binding and hence is potentially important for drug discovery...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Bioinformation
دوره 1 شماره
صفحات -
تاریخ انتشار 2006