Role of stabilization centers in 4 helix bundle proteins

Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design

Inter-residue interactions in protein structures provide valuable insights into protein folding and stability. Understanding these interactions can be helpful in many crucial applications, including rational design of therapeutic small molecules and biologics, locating functional protein sites, and predicting protein-protein and protein-ligand interactions. The process of developing machine learning models incorporating inter-residue interactions has been improved recently. This review highlights the theoretical models incorporating inter-residue interactions in predicting folding and unfolding rates of proteins. Utilizing contact maps to depict inter-residue interactions aids researchers in developing computer models for detecting remote homologs and interface residues within protein-protein complexes which, in turn, enhances our knowledge of the relationship between sequence and structure of proteins. Further, the application of contact maps derived from inter-residue interactions is highlighted in the field of drug discovery. Overall, this review presents an extensive assessment of the significant models that use inter-residue interactions to investigate folding rates, unfolding rates, remote homology, and drug development, providing potential future advancements in constructing efficient computational models in structural biology.

The crystal structures of Sau3AI with and without bound DNA suggest a self-activation-based DNA cleavage mechanism

The type II restriction endonuclease Sau3AI cleaves the sequence 5'-GATC-3' in double-strand DNA producing two sticky ends. Sau3AI cuts both DNA strands regardless of methylation status. Here, we report the crystal structures of the active site mutant Sau3AI-E64A and the C-terminal domain Sau3AI-C with a bound GATC substrate. Interestingly, the catalytic site of the N-terminal domain (Sau3AI-N) is spatially blocked by the C-terminal domain, suggesting a potential self-inhibition of the enzyme. Interruption of Sau3AI-C binding to substrate DNA disrupts Sau3AI function, suggesting a functional linkage between the N- and C-terminal domains. We propose that Sau3AI-C behaves as an allosteric effector binding one GATC substrate, which triggers a conformational change to open the N-terminal catalytic site, resulting in the subsequent GATC recognition by Sau3AI-N and cleavage of the second GATC site. Our data indicate that Sau3AI and UbaLAI might represent a new subclass of type IIE restriction enzymes.

Cation-π interactions in β-lactamases: the role in structural stability

β-lactam group of antibiotics is the most widely used therapeutic molecules for treating bacterial infections. The main mode of bacterial resistance to β-lactams is by β-lactamases. In the present study, we report our results on the role of cation-π interactions in β-lactamases and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while tyrosine is comparatively higher than phenylalanine and tryptophan in the π group. Our results indicate that cation-π interactions might play an important role in the global conformational stability of β-lactamases.

Influence of C-H...O interactions on the structural stability of β-lactamases

β-Lactamases produced by pathogenic bacteria cleave β-lactam antibiotics and render them ineffective. Understanding the principles that govern the structural stability of β-lactamases requires elucidation of the nature of the interactions that are involved in stabilization. In the present study, we systematically analyze the influence of CH...O interactions on determining the specificity and stability of β-lactamases in relation to environmental preferences. It is interesting to note that all the residues located in the active site of β-lactamases are involved in CH...O interactions. A significant percentage of CH...O interactions have a higher conservation score and short-range interactions are the predominant type of interactions in β-lactamases. These results will be useful in understanding the stability patterns of β-lactamases.

Probing dimer interface stabilization within a four-helix bundle of the GrpE protein from Escherichia coli via internal deletion mutants: conversion of a dimer to monomer

Insight into protein stability and folding remains an important area for protein research, in particular protein-protein interactions and the self-assembly of homodimers. The GrpE protein from Escherichia coli is a homodimer with a four-helix bundle at the dimer interface. Each monomer contributes a helix-loop-helix to the bundle. To probe the interface stabilization requirements, in terms of the amount of buried residues in the bundle necessary for dimer formation, internal deletion mutants (IDMs) were created that sequentially truncate each of the two helices in the helix-loop-helix region. Circular dichroism (CD) spectroscopy showed that all IDM's still contained a significant amount of α-helical secondary structure. IDM's that contained 11 or fewer of 22 residues originally present in the helices, or those that lost at least 50% of residues with less than 20% the solvent accessible surfaces (that is, hydrophobic residues) were unable to form a significant amount of dimer species as shown by chemical cross-linking. Gel filtration studies of IDM3.0 (one that retains 10 residues in each helix) show this variant to be mainly monomeric.

Crystal structure of Helicobacter pylori MinE, a cell division topological specificity factor

In Gram-negative bacteria, proper placement of the FtsZ ring, mediated by nucleoid occlusion and the activities of the dynamic oscillating Min proteins MinC, MinD and MinE, is required for correct positioning of the cell division septum. MinE is a topological specificity factor that counters the activity of MinCD division inhibitor at the mid-cell division site. Its structure consists of an anti-MinCD domain and a topology specificity domain (TSD). Previous NMR analysis of truncated Escherichia coli MinE showed that the TSD domain contains a long alpha-helix and two anti-parallel beta-strands, which mediate formation of a homodimeric alpha/beta structure. Here we report the crystal structure of full-length Helicobacter pylori MinE and redefine its TSD based on that structure. The N-terminal region of the TSD (residues 19-26), previously defined as part of the anti-MinCD domain, forms a beta-strand (betaA) and participates in TSD folding. In addition, H. pylori MinE forms a dimer through the interaction of anti-parallel betaA-strands. Moreover, we observed serial dimer-dimer interactions within the crystal packing, resulting in the formation of a multimeric structure. We therefore redefine the functional domain of MinE and propose that a multimeric filamentous structure is formed through anti-parallel beta-strand interactions.

Functionally and structurally relevant residues of enzymes: are they segregated or overlapping?

There is a delicate balance between stability and flexibility needed for enzyme function. To avoid undesirable alteration of the functional properties during the evolutionary optimization of the structural stability under certain circumstances, and vice versa, to avoid unwanted changes of stability during the optimization of the functional properties of proteins, common sense would suggest that parts of the protein structure responsible for stability and parts responsible for function developed and evolved separately. This study shows that nature did not follow this anthropomorphic logic: the set of residues involved in function and those involved in structural stabilization of enzymes are rather overlapping than segregated.

Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation

In nature, 1 out of every 10 proteins has an (alpha/beta)(8) (TIM)-barrel fold, and in most cases, pairwise comparisons show no sequence similarity between them. Hence, delineating the key residues that induce very different sequences to share a common fold is important for understanding the folding and stability of TIM-barrel domains. In this work, we propose a new consensus approach for locating these stabilizing residues based on long-range interactions, hydrophobicity, and conservation of amino acid residues. We have identified 957 stabilizing residues in 63 proteins from a nonredundant set of 71 TIM-barrel domains. Most of these residues are located in the 8-stranded beta-sheet, with nearly one half of them oriented toward the interior of the barrel and the other half oriented toward the surrounding alpha-helices. Several stabilizing residues are found in the N- and C-terminal loops, whereas very few appear in the alpha-helices that surround the internal beta-sheet. Further, these 957 residues are placed in 434 stabilizing segments of various sizes, and each domain contains 1-10 of these segments. We found that 8 segments per domain is the most abundant one, and two thirds of the proteins have 7-9 stabilizing segments. Finally, we verified the identified residues with experimental temperature factors and found that these residues are among the ones with less mobility in the considered proteins. We suggest that our new protocol serves as a powerful tool to identify the stabilizing residues in TIM-barrel domains, which can be used as potential candidates for studying protein folding and stability by means of protein engineering experiments.

Noncovalent Cross-links in Context with Other Structural and Functional Elements of Proteins

Proteins are heteropolymers with evolutionary selected native sequences of residues. These native sequences code for unique and stable 3D structures indispensable for biochemical activity and for proteolysis resistance, the latter which guarantees an appropriate lifetime for the protein in the protease rich cellular environment. Cross-links between residues close in space but far in the primary structure are required to maintain the folded structure of proteins. Some of these cross-links are covalent, most frequently disulfide bonds, but the majority of the cross-links are sets of cooperative noncovalent long-range interactions. In this paper we focus on special clusters of noncovalent long-range interactions: the Stabilization Centers (SCs). The relation between the SCs and secondary structural elements as well as the relation between SCs and functionally important regions of proteins are presented to show a detailed picture of these clusters, which are believed to be primarily responsible for major aspects of protein stability.

Servers for sequence-structure relationship analysis and prediction

We describe several algorithms and public servers that were developed to analyze and predict various features of protein structures. These servers provide information about the covalent state of cysteine (CYSREDOX), as well as about residues involved in non-covalent cross links that play an important role in the structural stability of proteins (SCIDE and SCPRED). We also discuss methods and servers developed to identify helical transmembrane proteins from large databases and rough genomic data, including two of the most popular transmembrane prediction methods, DAS and HMMTOP. Several biologically interesting applications of these servers are also presented. The servers are available through http://www.enzim.hu/servers.html.