Aromatic-Aromatic Interactions in Proteins: Beyond the Dimer

نویسندگان

  • Esteban Lanzarotti
  • Rolf R. Biekofsky
  • Dario A. Estrin
  • Marcelo A. Marti
  • Adrian Gustavo Turjanski
چکیده

Aromatic residues are key widespread elements of protein structures and have been shown to be important for structure stability, folding, protein-protein recognition, and ligand binding. The interactions of pairs of aromatic residues (aromatic dimers) have been extensively studied in protein structures. Isolated aromatic molecules tend to form higher order clusters, like trimers, tetramers, and pentamers, that adopt particular well-defined structures. Taking this into account, we have surveyed protein structures deposited in the Protein Data Bank in order to find clusters of aromatic residues in proteins larger than dimers and characterized them. Our results show that larger clusters are found in one of every two unique proteins crystallized so far, that the clusters are built adopting the same trimer motifs found for benzene clusters in vacuum, and that they are clearly nonlocal brining primary structure distant sites together. We extensively analyze the trimers and tetramers conformations and found two main cluster types: a symmetric cluster and an extended ladder. Finally, using calmodulin as a test case, we show aromatic clsuters possible role in folding and protein-protein interactions. All together, our study highlights the relevance of aromatic clusters beyond the dimer in protein function, stability, and ligand recognition.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions.

The ability to design and fine-tune non-covalent interactions between organic ligands and proteins is indispensable to rational drug development. Aromatic stacking has long been recognized as one of the key constituents of ligand-protein interfaces. In this communication, we employ a two-parameter geometric model to conduct a large-scale statistical analysis of aromatic contacts in the experime...

متن کامل

Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases

Aromatic molecules with π electrons are commonly involved in chemical and biological recognitions. For example, nucleobases play central roles in DNA/RNA structure and their interactions with proteins. The delocalization of the π electrons is responsible for the high polarizability of aromatic molecules. In this work, the AMOEBA force field has been developed and applied to 5 regular nucleobase...

متن کامل

Chiral porphyrin dimer with a macrocyclic cavity for intercalation of aromatic guests.

Chiral diporphyrin receptor 1, which has a macrocyclic cavity to sandwich aromatic guest molecules via double π-π stacking interactions, enabled the naked-eye detection of an aromatic explosive as well as chiral discrimination in NMR.

متن کامل

Comparison of Quantum Mechanics and Molecular Mechanics Dimerization Energy Landscapes for Pairs of Ring-Containing Amino Acids in Proteins

A promising approach to developing improved potential functions for modeling macromolecular interactions consists of combining protein structural analysis, quantum mechanical calculations on small molecule models, and molecular mechanics potential decomposition. Here we apply this approach to the interactions of pairs of ring-containing amino acids in proteins. We find reasonable qualitative ag...

متن کامل

MP2 study on the variation of stacking interactions in aniline and some para substituted aniline systems

The use of appropriate level of theories for studying weak van der Waal interactions such as 8-8stacking interactions of aromatic molecules has been an important aspect, since the high levelmethods have limitations for application to large molecules. The differences in the stacking energiesof various aromatic molecular structures are found significant. It is also very important for identifyingt...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • Journal of chemical information and modeling

دوره 51 7  شماره 

صفحات  -

تاریخ انتشار 2011