Strong electrostatic loop-helix interactions in bundle motif protein structures

Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding

Although not being classified as the most fundamental protein structural elements like α-helices and β-strands, the loop segment may play considerable roles for protein stability, flexibility, and dynamic activity. Meanwhile, the protein loop is also quite elusive; i.e. its interactions with the other parts of protein as well as its own shape-maintaining forces have still remained as a puzzle or at least not quite clear yet. Here, we report a molecular force, the so-called polar hydrogen-π interaction (Hp-π), which may play an important role in supporting the backbones of protein loops. By conducting the potential energy surface scanning calculations on the quasi π-plane of peptide bond unit, we have observed the following intriguing phenomena: (1) when the polar hydrogen atom of a peptide unit is perpendicularly pointing to the π-plane of other peptide bond units, a remarkable Hp-π interaction occurs; (2) the interaction is distance and orientation dependent, acting in a broad space, and belonging to the 'point-to-plane' one. The molecular force reported here may provide useful interaction concepts and insights into better understanding the loop's unique stability and flexibility feature, as well as the driving force of the protein global folding.

Ligand-induced dimer formation of calmodulin

Calmodulin (CaM) can bind to numerous proteins in several interaction modes. Recently a new mode of interaction was discovered, in which two CaM molecules form an X-shaped dimer and two binding sites to trap the CaM-binding domain (CBD) of calcineurin subunit A. However, the X-shaped CaM dimer alone without ligand has not been observed. We performed molecular dynamics (MD) simulations and used MM_PBSA approach to investigate the properties of this new binding mode using ligand-bound and -free dimer systems. MD trajectories show that two peptides of CBD play a critical role in stabilizing the X-shaped conformation of the CaM dimer which would otherwise be unstable, leading to dimer disassembly in the absence of the ligands. Furthermore, we have analyzed the interaction free energy of the complex by MM-PBSA method and provide further evidence to demonstrate that the CBD peptide ligands are responsible for the stabilization of the dimer. Comparing this new binding mode with the classical one represented by CaM in complex with smooth muscle myosin light chain kinase, we conclude that this new binding mode is induced by the CBD of calcineurin subunit A. Our results explain the fact that the X-shaped CaM dimer structure has never been observed in the absence of ligands.

Amino acid composition of parallel helix-helix interfaces

Amino acids at helix-helix parallel interfaces influence arrangement of helices and interhelical angles. Parallel interfaces in 79 proteins were considered. Location of amino acids at the positions analogous to a and d in GCN4 leucine zipper nomenclature shows that certain combinations of amino acids characteristic for parallel packing occur more often than could be expected by chance. Repeating sequence combinations occur at a and d positions of parallel helix-helix interfaces with similar values of interhelical angles not only in homologous proteins but also within the same protein and in nonhomologous proteins. Within each group of observed combinations correlation exists between the size of amino acid and magnitude of the interhelical angle.

Comparison of solution and crystal structures of maize nonspecific lipid transfer protein: a model for a potential in vivo lipid carrier protein

The three-dimensional solution structure of maize nonspecific lipid transfer protein (nsLTP) obtained by nuclear magnetic resonance (NMR) is compared to the X-ray structure. Although both structures are very similar, some local structural differences are observed in the first and the fourth helices and in several side-chain conformations. These discrepancies arise partly from intermolecular contacts in the crystal lattice. The main characteristic of nsLTP structures is the presence of an internal hydrophobic cavity whose volume was found to vary from 237 to 513 A3 without major variations in the 15 solution structures. Comparison of crystal and NMR structures shows the existence of another small hollow at the periphery of the protein containing a water molecule in the X-ray structure, which could play an important structural role. A model of the complexed form of maize nsLTP by alpha-lysopalmitoylphosphatidylcholine was built by docking the lipid inside the protein cavity of the NMR structure. The main structural feature is a hydrogen bond found also in the X-ray structure of the complex maize nsLTP/palmitate between the hydroxyl of Tyr81 and the carbonyl of the lipid. Comparison of 12 primary sequences of nsLTPs emphasizes that all residues delineating the cavities calculated on solution and X-ray structures are conserved, which suggests that this large cavity is a common feature of all compared plant nsLTPs. Furthermore several conserved basic residues seem to be involved in the stabilization of the protein architecture.

Association of somatotropin (BST) gene polymorphism at the 5th exon with selection for milk yield in Holstein cows

A selection project produced control cows from continuous matings with breed average bulls for predicted transmitting ability for milk (PTA-milk) in 1964 and select cows from matings to four of the highest PTA-milk bulls each year since 1964. Blood samples were collected in 1992 when milk yield difference of select and control line cows exceeded 3,800 kg of milk/305-day lactation. Genomic DNA from control (n = 49) and select (n = 101) cows was analyzed for the presence of variants associated with amino acid position 127 (leucine, AluI[+]; valine, AluI[-]) of bovine somatotropin (bST). Amplification of a 428 base-pair fragment of the bST gene from individual cows, subsequent restriction enzyme (AluI) digestion, and separation resulting fragments indicated three genotypes AluI(+/+), AluI(+/-), and AluI(-/-) in 110, 39, and 1 animal(s), respectively. Gene frequencies of leucine127 and valine 127 alleles were similar for control (0.867m 0.133) and select (0.861, 0.139) animals. United States Department of Agriculture-PTA values were compared between the two genotypes, AluI(+/+) and AluI(+/-). Estimated breeding value for milk (EBV-milk) and average yield deviation for milk (AYD-milk) were not associated with genotype for control animals. However, presence of the valine allele was correlated with decreased EBV-milk (P = 0.03) and AYD-milk (P = 0.16) in select animals and accounted for a decrease of approximately 170 kg of EBV-milk and 240 kg of AYD-milk.

Analysis of the loop-helix interaction in bundle motif protein structures

Molecular dynamics simulations and energy analysis have been carried out to study the structural mobility and stability of the four alpha-helix bundle motifs. The simulation results as well as the X-ray data show that the atomic RMS fluctuation is larger at the loop region for four representative proteins investigated: methemerythrin, cytochrome b-562, cytochrome c', and bovine somatotropin. The loop-loop, helix-helix, and loop-helix interactions are computed for the unfolded and folded proteins. In the folded and solvated protein structures the loop-helix interaction is stronger than the helix-helix interaction, especially in the electrostatic component. But the stabilization energies of both the loop-helix and the helix-helix interactions relative to those of an unfolded structure are of the same order of magnitude. The stabilization due to protein-solvent interaction is greater in the helix region than in the loop region. The percentage of hydrophilic solvent accessible area for the four proteins studied was calculated with the method of Eisenberg and McLachlan. The percentage of the hydrophilic area is greater in the loops than in the helices. A Poisson-Boltzmann calculation shows that the potential from the loops acting on a helix is generally more negative than that from other helices.

Seven-helix bundles: molecular modeling via restrained molecular dynamics

Simulated annealing via restrained molecular dynamics (SA/MD) has been used to model compact bundles of seven approximately (anti)parallel alpha-helices. Seven such helix bundles occur, e.g., in bacteriorhodopsin, in rhodopsin, and in the channel-forming N-terminal domain of Bacillus thuringiensis delta-endotoxin. Two classes of model are considered: (a) those consisting of seven Ala20 peptide chains; and (b) those containing a single polypeptide chain, made up of seven Ala20 helices linked by GlyN interhelix loops (where N = 5 or 10). Three different starting C alpha templates for SA/MD are used, in which the seven helices are arranged (a) on a left-handed circular template, (b) on a bacteriorhodopsin-like template, or (c) on a zig-zag template. The ensembles of models generated by SA/MD are analyzed in terms of their geometry and energetics, and the most stable structures from each ensemble are examined in greater detail. Structures resembling bacteriorhodopsin and structures resembling delta-endotoxin are both represented among the most stable structures. delta-Endotoxin-like structures arise from both circular and bacteriorhodopsin-like C alpha templates. A third helix-packing mode occurs several times among the stable structures, regardless of the C alpha template and of the presence or absence of interhelix loops. It is characterized by a "4 + 1" core, in which four helices form a distorted left-handed supercoil around a central, buried helix. The remaining two helices pack onto the outside of the core. This packing mode is comparable with that proposed for rhodopsin on the basis of two-dimensional electron crystallographic and sequence analysis studies.