Stereochemistry of the interaction between methionine sulfur and the protein core

Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine-Residue Low Complexity Peptide, as Probed by 2 H Solid-State NMR

Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid-state NMR to assess rotameric inter-conversions and other dynamic modes of the methionine in the context of a nine-residue random-coil peptide (RC9) with the low-complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine-containing systems, characterized previously. Namely, the M35 of hydrated amyloid-β1-40 in the three-fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)-methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.

Chalcogen bonds formed by protein sulfur atoms in proteins. A survey of high-resolution structures deposited in the protein data bank

The presence of chalcogen bonds in native proteins was investigated on a non-redundant and high-resolution (≤ 1 Angstrom) set of protein crystal structures deposited in the Protein Data Bank. It was observed that about one half of the sulfur atoms of methionines and disulfide bridges from chalcogen bonds with nucleophiles (oxygen and sulfur atoms, and aromatic rings). This suggests that chalcogen bonds are a non-bonding interaction important for protein stability. Quite numerous chalcogen bonds involve water molecules. Interestingly, in the case of disulfide bridges, chalcogen bonds have a marked tendency to occur along the S-S bond extension rather than along the C-S bond extension. Additionally, it has been observed that closer residues have a higher probability of being connected by a chalcogen bonds, while the secondary structure of the two residues connected by a chalcogen bond do not correlate with its formation.Communicated by Ramaswamy H. Sarma.

Interplay between hydrogen and chalcogen bonds in cysteine

Protein structures are stabilized by several types of chemical interactions between amino acids, which can compete with each other. This is the case of chalcogen and hydrogen bonds formed by the thiol group of cysteine, which can form three hydrogen bonds with one hydrogen acceptor and two hydrogen donors and a chalcogen bond with a nucleophile along the extension of the CS bond. A survey of the Protein Data Bank shows that hydrogen bonds are about 40-50 more common than chalcogen bonds, suggesting that they are stronger and, consequently, prevail, though not always. It is also observed that frequently a thiol group that forms a chalcogen bond is also involved, as a hydrogen donor, in a hydrogen bond.

Chalcogen Bonds Involving Selenium in Protein Structures

Chalcogen bonds are the specific interactions involving group 16 elements as electrophilic sites. The role of chalcogen atoms as sticky sites in biomolecules is underappreciated, and the few available studies have mostly focused on S. Here, we carried out a statistical analysis over 3562 protein structures in the Protein Data Bank (PDB) containing 18 266 selenomethionines and found that Se···O chalcogen bonds are commonplace. These findings may help the future design of functional peptides and contribute to understanding the role of Se in nature.

Participation of S and Se in hydrogen and chalcogen bonds

The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.

S···O and S···N Sulfur Bonding Interactions in Protein-Ligand Complexes: Empirical Considerations and Scoring Function

Sulfur bonding interactions between organosulfur compounds and proteins were examined using crystal structures deposited to-date in the PDB. The data was analyzed as a function of sulfur-σ-hole-bonding (i.e., sulfur bonds) to main chain Lewis bases, viz. oxygen and nitrogen atoms of the backbone amide linkages. The analyses also included an examination of sulfur bonding to side chain Lewis bases (O, N, and S) and to the "non-classical" Lewis bases present in electron-rich aromatic amino acids as-well-as to donor-acceptor bond angle distributions. The interactions analyzed included those restricted to the sum of van der Waals radii of the respective atoms or to a distance of 4 Å. The surveyed data revealed that sulfur bonding tendencies (C-S-C bond angles) were impacted not only by steric effects but perhaps also by enthalpic features present in both the donor and acceptor participants. This knowledge is not only of fundamental interest but is also important in terms of materials and drug-design involving moieties incorporating the sulfur atom. Additionally, a new empirical scoring function was developed to address the anisotropy of sulfur in protein-ligand interactions. This newly developed scoring function is incorporated into AutoDock Vina molecular docking program and is valuable for modeling and drug design.

Hypervalent nonbonded interactions of a divalent sulfur atom. Implications in protein architecture and the functions

In organic molecules a divalent sulfur atom sometimes adopts weak coordination to a proximate heteroatom (X). Such hypervalent nonbonded S···X interactions can control the molecular structure and chemical reactivity of organic molecules, as well as their assembly and packing in the solid state. In the last decade, similar hypervalent interactions have been demonstrated by statistical database analysis to be present in protein structures. In this review, weak interactions between a divalent sulfur atom and an oxygen or nitrogen atom in proteins are highlighted with several examples. S···O interactions in proteins showed obviously different structural features from those in organic molecules (i.e., π(o) → σ(s)* versus n(o) → σ(s)* directionality). The difference was ascribed to the HOMO of the amide group, which expands in the vertical direction (π(o)) rather than in the plane (n(o)). S···X interactions in four model proteins, phospholipase A₂ (PLA₂), ribonuclease A (RNase A), insulin, and lysozyme, have also been analyzed. The results suggested that S···X interactions would be important factors that control not only the three-dimensional structure of proteins but also their functions to some extent. Thus, S···X interactions will be useful tools for protein engineering and the ligand design.

Geometry of nonbonded interactions involving planar groups in proteins

Although hydrophobic interaction is the main contributing factor to the stability of the protein fold, the specificity of the folding process depends on many directional interactions. An analysis has been carried out on the geometry of interaction between planar moieties of ten side chains (Phe, Tyr, Trp, His, Arg, Pro, Asp, Glu, Asn and Gln), the aromatic residues and the sulfide planes (of Met and cystine), and the aromatic residues and the peptide planes within the protein tertiary structures available in the Protein Data Bank. The occurrence of hydrogen bonds and other nonconventional interactions such as C-H...pi, C-H...O, electrophile-nucleophile interactions involving the planar moieties has been elucidated. The specific nature of the interactions constraints many of the residue pairs to occur with a fixed sequence difference, maintaining a sequential order, when located in secondary structural elements, such as alpha-helices and beta-turns. The importance of many of these interactions (for example, aromatic residues interacting with Pro or cystine sulfur atom) is revealed by the higher degree of conservation observed for them in protein structures and binding regions. The planar residues are well represented in the active sites, and the geometry of their interactions does not deviate from the general distribution. The geometrical relationship between interacting residues provides valuable insights into the process of protein folding and would be useful for the design of protein molecules and modulation of their binding properties.

Possible roles of S···O and S···N interactions in the functions and evolution of phospholipase A2

To investigate possible roles of S···X (X= O, N, S) interactions in the functions and evolution of a protein, two types of database analyses were carried out for a vertebrate phospholipase A₂ (PLA₂) family. A comprehensive search for close S···X contacts in the structures retrieved from protein data bank (PDB) revealed that there are four common S···O interactions and one common S···N interaction for the PLA₂ domain group (PLA₂-DG), while an additional three S···O interactions were found for the snake PLA₂ domain group (sPLA₂-DG). On the other hand, a phylogenetic analysis on the conservation of the observed S···O and S···N interactions over various amino acid sequences of sPLA₂-DG demonstrated probable clustering of the interactions on the dendrogram. Most of the interactions characterized for PLA₂ were found to reside in the vicinity of the active site and to be able to tolerate the conformational changes due to the substrate binding. These observations suggested that the S···X interactions play some role in the functions and evolution of the PLA₂ family.

Statistical and theoretical investigations on the directionality of nonbonded S...O interactions. Implications for molecular design and protein engineering

Weak nonbonded interactions between a divalent sulfur (S) atom and a main-chain carbonyl oxygen (O) atom have recently been characterized in proteins. However, they have shown distinctly different directional propensities around the O atom from the S...O interactions in small organic compounds, although the linearity of the C-S...O or S-S...O atomic alignment was commonly observed. To elucidate the observed discrepancy, a comprehensive search for nonbonded S.O interactions in the Cambridge Structural Database (CSD) and MP2 calculations on the model complexes between dimethyl disulfide (CH(3)SSCH(3)) and various carbonyl compounds were performed. It was found that the O atom showed a strong intrinsic tendency to approach the S atom from the backside of the S-C or S-S bond (in the sigma(S) direction). On the other hand, the S atom had both possibilities of approach to the carbonyl O atom within the same plane (in the n(O) direction) and out of the plane (in the pi(O) direction). In the case of S...O(amide) interactions, the pi(O) direction was significantly preferred as observed in proteins. Thus, structural features of S...O interactions depend on the type of carbonyl groups involved. The results suggested that S.O interactions may control protein structures to some extent and that the unique directional properties of S...O interactions could be applied to molecular design.

Non-hydrogen bond interactions involving the methionine sulfur atom

Of all the nonbonded interactions, hydrogen bond, because of its geometry involving polar atoms, is the most easily recognizable. Here we characterize two interactions involving the divalent sulfur of methionine (Met) residues that do not need any participation of proton. In one an oxygen atom of the main-chain carbonyl group or a carboxylate side chain is used. In another an aromatic atom interacting along the face of the ring is utilized. In these, the divalent sulfur behaves as an electrophile and the other electron-rich atom, a nucleophile. The stereochemistry of the interaction is such that the nucleophile tends to approach approximately along the extension of one of the covalent bonds to S. The nitrogen atom of histidine side chain is extensively used in these nonbonded contacts. There is no particular geometric pattern in the interaction of S with the edge of an aromatic ring, except when an N-H group in involved, which is found within 40 degrees from the perpendicular to the sulfide plane, thus defining the geometry of hydrogen bond interaction involving the sulfur atom. As most of the Met residues which partake in such stereospecific interactions are buried, these would be important for the stability of the protein core, and their incorporation in the binding site would be useful for molecular recognition and optimization of the site's affinity for partners (especially containing aromatic and heteroaromatic groups). Mutational studies aimed at replacing Met by other residues would benefit from the delineation of these interactions.