A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution

Analysis of proteins commonly requires the partition of their structure into regions such as the surface, interior, or interface. Despite the frequent use of such categorization, no consensus definition seems to exist. This study thus aims at providing a definition that is general, is simple to implement, and yields new biological insights. This analysis relies on 397, 196, and 701 protein structures from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens, respectively, and the conclusions are consistent across all three species. A threshold of 25% relative accessible surface area best segregates amino acids at the interior and at the surface. This value is further used to extend the core-rim model of protein-protein interfaces and to introduce a third region called support. Interface core, rim, and support regions contain similar numbers of residues on average, but core residues contribute over two-thirds of the contact surface. The amino acid composition of each region remains similar across different organisms and interface types. The interface core composition is intermediate between the surface and the interior, but the compositions of the support and the rim are virtually identical with those of the interior and the surface, respectively. The support and rim could thus “preexist” in proteins, and evolving a new interaction could require mutations to form an interface core only. Using the interface regions defined, it is shown through simulations that only two substitutions are necessary to shift the average composition of a  1000-Ų surface patch involving ∼ 28 residues to that of an equivalent interface. This analysis and conclusions will help understand the notion of promiscuity in protein-protein interaction networks.     

Membrane protein assembly patterns reflect selection for non-proliferative structures

Membrane proteins that regulate solute movement are often built from multiple copies of an identical polypeptide chain. These complexes represent striking examples of self-assembling systems that recruit monomers only until a prescribed level for function is reached. Here we report that three modes of assembly - distinguished by sequence and stoichiometry - describe all helical membrane protein complexes currently solved to high resolution. Using the 13 presently available non-redundant homo-oligomeric structures, we show that two of these types segregate with protein function: one produces energy-dependent transporters, while the other builds channels for passive diffusion. Given such limited routes to functional complexes, membrane proteins that self-assemble exist on the edge of aggregation, susceptible to mutations that may underlie human diseases.     

Dissociation of Abeta(16-22) amyloid fibrils probed by molecular dynamics

The mechanisms of deposition and dissociation are implicated in the assembly of amyloid fibrils. To investigate the kinetics of unbinding of Abeta(16-22) monomers from preformed fibrils, we use molecular dynamics (MD) simulations and the structures for Abeta(16-22) amyloid fibrils. Consistent with experimental studies, the dissociation of Abeta(16-22) peptides involves two main stages, locked and docked, after which peptides unbind. The lifetime of the locked state, in which a peptide retains fibril-like structure and interactions, extends up to 0.5 micros under normal physiological conditions. Upon cooperative rupture of all fibril-like hydrogen bonds (HBs) with the fibril, a peptide enters a docked state. This state is populated by disordered random coil conformations and its lifetime ranges from approximately 10 to 200 ns. The docked state is stabilized by hydrophobic side chain interactions, while the contribution from HBs is small. Our simulations also suggest that the peptides located on fibril edges may form stable beta-strand conformations distinct from the fibril "bulk". We propose that such edge peptides can act as fibril caps, which impede fibril elongation. Our results indicate that the interactions between unbinding peptides constitute the molecular basis for cooperativity of peptide dissociation. The kinetics of fibril growth is reconstructed from unbinding assuming the reversibility of deposition/dissociation pathways. The relation of in silica dissociation kinetics to experimental observations is discussed.     

Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: contribution of cross-domain polar networks to thermostability

A novel LAGLIDADG-type homing endonuclease (HEase), I-Tsp061I, from the hyperthermophilic archaeon Thermoproteus sp. IC-061 16 S rRNA gene (rDNA) intron was characterized with respect to its structure, catalytic properties and thermostability. It was found that I-Tsp061I is a HEase isoschizomer of the previously described I-PogI and exhibits the highest thermostability among the known LAGLIDADG-type HEases. Determination of the crystal structure of I-Tsp061I at 2.1 A resolution using the multiple isomorphous replacement and anomalous scattering method revealed that the overall fold is similar to that of other known LAGLIDADG-type HEases, despite little sequence similarity between I-Tsp061I and those HEases. However, I-Tsp061I contains important cross-domain polar networks, unlike its mesophilic counterparts. Notably, the polar network Tyr6-Asp104-His180-107O-HOH12-104O-Asn177 exists across the two packed alpha-helices containing both the LAGLIDADG catalytic motif and the GxxxG hydrophobic helix bundle motif. Another important structural feature is the salt-bridge network Asp29-Arg31-Glu182 across N and C-terminal domain interface, which appears to contribute to the stability of the domain/domain packing. On the basis of these structural analyses and extensive mutational studies, we conclude that such cross-domain polar networks play key roles in stabilizing the catalytic center and domain packing, and underlie the hyperthermostability of I-Tsp061I.     

Molecular modeling of human serum transferrin for rationalizing the changes in its physicochemical properties induced by iron binding. Implication of the mechanism of binding to its receptor

In order to rationalize the physicochemical properties of human serum-transferrin (STf) and the STf-receptor (TfR) recognition process, we have tried to predict the 3D structures of apo- and iron-loaded STf using a homology modeling technique to study the changes in the structural characteristics that take place upon the uptake of iron by STf in solution. The crystal structures of both forms for ovotransferrin were used as templates for the STf modeling. The modeled structure of STf gave a satisfactory interpretation for the typical physicochemical properties such that (1) STf has a negative electrophoretic mobility and its value increases with iron uptake, and (2) the radius of gyration R_g of Tf decreases with iron uptake. It was found that upon iron binding, interdomain closures take place with large movements of the NII and CII subdomains comprising the N- and C-lobes in STf through a hinge-bending motion, accompanied by the opening of the bridge region with a displacement of more than 15 Å. Moreover, in view of the findings from our capillary electrophoresis experiments that the electrostatic interactions significantly contribute to a specific binding of Fe₂-STf with TfR, it is inferred that the connecting (bridge) and its neighboring region associated with a surface exposure of negative charge play an important role in the STf-receptor recognition process.     

An empirical relationship between rotational correlation time and solvent accessible surface area

Structure–dynamics interrelationships are important in understanding protein function. We have explored the empirical relationship between rotational correlation times (_c and the solvent accessible surface areas (SASA) of 75 proteins with known structures. The theoretical correlation between SASA and _c through the equation SASA = K_rc ^(2/3) is also considered. SASA was determined from the structure, _c ^calc was determined from diffusion tensor calculations, and _c ^expt was determined from NMR backbone¹³ C or ¹⁵N relaxation rate measurements. The theoretical and experimental values of _c correlate with SASA with regression analyses values of K_r as 1696 and 1896 m²s^-(2/3), respectively, and with corresponding correlation coefficients of 0.92 and 0.70.