Distinct roles of conventional non-covalent and cation–π interactions in protein stability

The Changing Phases of Bromopentafluorobenzene

As part of a much larger study on non-covalent interactions in binary adducts, we have explored the solid-state structures of bromopentafluorobenzene (C6F5Br) using differential scanning calorimetry (DSC), variable-temperature powder X-ray diffraction (VT-PXRD), and single-crystal X-ray diffraction (SXD). DSC data initially indicated a single solid-state phase below the freezing point, but revealed additional weak transitions upon heating. The crystal structures of three solid-state phases have been solved. The SXD data showed that phases I and IV are centrosymmetric, whilst phase II is polar. However, the structure of phase III remains elusive due to the changing phase behaviour of C6F5Br that is determined as much as by kinetics as thermodynamics. The results underline the need for multiple analytical techniques to study non-covalent interactions and offer valuable data for refining computational models in crystal structure prediction and machine learning. A comparison with the iodinated counterpart is also made.

Protein Stability: Enhancement and Measurement

This article defines protein stability, emphasizes its importance and surveys the field of protein stabilization, with summary reference to a selection of 2009-2015 publications. One can enhance stability by, in particular, protein engineering strategies and by chemical modification (including conjugation) in solution. General protocols are set out on how to measure a given protein's (1) kinetic thermal stability, and (2) oxidative stability, and (3) how to undertake chemical modification of a protein in solution.

A thorough anion-π interaction study in biomolecules: on the importance of cooperativity effects

The importance of anion–π interactions in key biological processes is reported from a PDB analysis of anion–π interactions in biomolecules, also considering cooperativity effects by including other interactions.

Noncovalent interactions have a constitutive role in the science of intermolecular relationships, particularly those involving aromatic rings such as π–π and cation–π. In recent years, anion–π contact has also been recognized as a noncovalent bonding interaction with important implications in chemical processes. Yet, its involvement in biological processes has been scarcely reported. Herein we present a large-scale PDB analysis of the occurrence of anion–π interactions in proteins and nucleic acids. In addition we have gone a step further by considering the existence of cooperativity effects through the inclusion of a second noncovalent interaction, i.e. π-stacking, T-shaped, or cation–π interactions to form anion–π–π and anion–π–cation triads. The statistical analysis of the thousands of identified interactions reveals striking selectivities and subtle cooperativity effects among the anions, π-systems, and cations in a biological context. The reported results stress the importance of anion–π interactions and the cooperativity that arises from ternary contacts in key biological processes, such as protein folding and function and nucleic acids–protein and protein–protein recognition. We include examples of anion–π interactions and triads putatively involved in enzymatic catalysis, epigenetic gene regulation, antigen–antibody recognition, and protein dimerization.

Comparison of aromatic NH···π, OH···π, and CH···π interactions of alanine using MP2, CCSD, and DFT methods

A comparison of the performance of various density functional methods including long-range corrected and dispersion corrected methods [MPW1PW91, B3LYP, B3PW91, B97-D, B1B95, MPWB1K, M06-2X, SVWN5, ωB97XD, long-range correction (LC)-ωPBE, and CAM-B3LYP using 6-31+G(d,p) basis set] in the study of CH···π, OH···π, and NH···π interactions were done using weak complexes of neutral (A) and cationic (A(+)) forms of alanine with benzene by taking the Møller-Plesset (MP2)/6-31+G(d,p) results as the reference. Further, the binding energies of the neutral alanine-benzene complexes were assessed at coupled cluster (CCSD)/6-31G(d,p) method. Analysis of the molecular geometries and interaction energies at density functional theory (DFT), MP2, CCSD methods and CCSD(T) single point level reveal that MP2 is the best overall performer for noncovalent interactions giving accuracy close to CCSD method. MPWB1K fared better in interaction energy calculations than other DFT methods. In the case of M06-2X, SVWN5, and the dispersion corrected B97-D, the interaction energies are significantly overrated for neutral systems compared to other methods. However, for cationic systems, B97-D yields structures and interaction energies similar to MP2 and MPWB1K methods. Among the long-range corrected methods, LC-ωPBE and CAM-B3LYP methods show close agreement with MP2 values while ωB97XD energies are notably higher than MP2 values.

Engineering protein stability

This article defines protein stability, emphasizes its importance and surveys some notable recent publications (2004-2008) in the field of protein stability/stabilization. Knowledge of the factors stabilizing proteins has emerged from denaturation studies and from study of thermophilic (and other extremophilic) proteins. One can enhance stability by protein engineering strategies, the judicious use of solutes and additives, immobilization, and chemical modification in solution. General protocols are set out on how to measure the kinetic thermal stability of a given protein and how to undertake chemical modification of a protein in solution.

Nature of cation-pi interactions and their role in structural stability of immunoglobulin proteins

Cation-pi interactions are known to be important contributors to protein stability and ligand-protein interactions. In this study, we have analyzed the influence of cation-pi interactions in single chain immunoglobulin proteins. We observed 87 cation-pi interactions in a data set of 33 proteins. These interactions are mainly formed by long-range contacts, and there is preference of Arg over Lys in these interactions. Arg-Tyr interactions are predominant among the various pairs analyzed. Despite the scarcity of interactions involving Trp, the average energy for Trp-cation interactions is quite high. This information suggests that the cation-pi interactions involving Trp might be of high relevance to the proteins. Secondary structure analysis reveals that cation-pi interactions are formed preferably between residues in which at least one is in beta-strand. Proteins having beta-strand regions have the highest number of cation-pi interaction-forming residues.

Influence of cation-pi interactions to the structural stability of prokaryotic and eukaryotic translation elongation factors

We have investigated the role of cation-pi interactions on translation elongation factors. In our investigation, an average of four significant cation-pi interactions were found, that is, an average of one cation-pi interaction per 44 residues in the ten elongation factors were observed. The analysis on the influence of short (< + or - 4), medium (> + or - 4 to < + or - 20) and long (>20) range contacts showed that cation-pi interactions are mainly formed by medium and long-range contacts. Arg-Tyr pair was found largest in number but energetic contribution of Arg-Trp pair was found most. Preferred secondary structural conformation analysis of the residues involved in cation-pi interaction indicates that the cationic Arg prefers to be in helix and Lys having equal probability for helix and strand, whereas the aromatic Phe and Trp were found mostly in helix while Tyr in strand regions. The cation-pi interaction residues involved in these proteins were found highly conserved with 48.86% residues having conservation score of > or = 6. Analysis of secondary structure preference of the energetically significant cation-pi residues in different solvent accessible range indicates that most of the pi residues are found buried or partially buried whereas cationic residues were found mostly at the protein surface. The results presented in this study will be useful for structural stability studies in translation elongation factors.

Influence of cation-π interactions on RNA-binding proteins

The energy contribution due to cation-pi interactions has been computed for 37 RNA binding proteins. The contribution of these cation-pi interacting residues in sequential separation, secondary structure involvement, solvent accessibility, and stabilization centers has been evaluated. Sequential separation of the cation-pi involving residues show that, long range contacts predominates in all the proteins studied. Lys and Arg prefers to be in helical structures. Of the cation-pi interacting residues, Arg and Lys were in the exposed regions and the aromatic residues (Phe, Tyr and Trp) were in the buried and partially buried regions in the protein structures. Stabilization centers for these proteins showed that all the five residues found in cation-pi interactions are important in locating one or more of such centers. On the whole, the results presented in this work will be very useful for further investigations on the specificity and selectivity of RNA binding proteins and also for their structural studies.

Role of inter and intramolecular interactions in protein-DNA recognition

Protein-DNA recognition plays an essential role in the regulation of gene expression. Regulatory proteins are known to recognize specific DNA sequences directly through atomic contacts between protein and DNA, and/or indirectly through the conformational properties of the DNA. In this work, we have analyzed the specificity of intermolecular interactions by statistical analysis of base-amino acid interactions within protein-DNA complexes as well as the computer simulations of base-amino acid interactions. The specificity of the intramolecular interactions was studied by statistical analysis of the sequence-dependent DNA conformational parameters and the elastic properties of DNA. Systematic comparison of these specificities in a large number of protein-DNA complexes revealed that both intermolecular and intramolecular interactions contribute to the specificity of protein-DNA recognition, and their relative contributions vary depending upon the protein-DNA complex. We demonstrated that combination of the intermolecular and intramolecular energies leads to enhanced specificity and the combined energy could explain experimental data on binding affinity changes caused by base mutations. These results provided new insight into the relationship between specificity and structure in the process of protein-DNA recognition, which would lead to prediction of specific protein-DNA binding sites.

Structural analysis of residues involving cation-π interactions in different folding types of membrane proteins

Cation-pi interactions play an important role to the stability of protein structures. In our earlier work, we have analyzed the influence and energetic contribution of cation-pi interactions in three-dimensional structures of membrane proteins. In this work, we investigate the characteristic features of residues that are involved in cation-pi interactions. We have computed several parameters, such as surrounding hydrophobicity, number of long-range contacts, conservation score and normalized B-factor for all these residues and identified their location, whether in the membrane or at surface. We found that the cation-pi interactions are mainly formed by long-range interactions. The cationic residues involved in cation-pi interactions have higher surrounding hydrophobicity than their average values in the whole dataset and an opposite trend is observed for aromatic residues. In transmembrane helical proteins, except Phe, all other residues that are responsible for cation-pi interactions are highly conserved with other related protein sequences whereas in transmembrane strand proteins, an appreciable conservation is observed only for Arg. The analysis on the flexibility of residues reveals that the cation-pi interaction forming residues are more stable than other residues. The results obtained in the present study would be helpful to understand the role of cation-pi interactions in the structure and folding of membrane proteins.