Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity

This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.

An "up" oriented methionine-aromatic structural motif in SUMO is critical for its stability and activity

Protein structural bioinformatic analyses suggest preferential associations between methionine and aromatic amino acid residues in proteins. Ab initio energy calculations highlight a conformation-dependent stabilizing interaction between the interacting sulfur-aromatic molecular pair. However, the relevance of buried methionine-aromatic motifs to protein folding and function is relatively unexplored. The Small Ubiquitin-Like Modifier (SUMO) is a β-grasp fold protein and a common posttranslational modifier that affects diverse cellular processes, including transcriptional regulation, chromatin remodeling, metabolic regulation, mitosis, and meiosis. SUMO is a member of the Ubiquitin-Like (UBL) protein family. Herein, we report that a highly conserved and buried methionine-phenylalanine motif is a unique signature of SUMO proteins but absent in other homologous UBL proteins. We also detect that a specific "up" conformation between the methionine-phenylalanine pair of interacting residues in SUMO is critical to its β-grasp fold. The noncovalent interactions of SUMO with its ligands are dependent on the methionine-phenylalanine pair. MD simulations, NMR, and biophysical and biochemical studies suggest that perturbation of the methionine-aromatic motif disrupts native contacts, modulates noncovalent interactions, and attenuates SUMOylation activity. Our results highlight the importance of conserved orientations of Met-aromatic structural motifs inside a protein core for its structure and function.

Contributions of methionine to recognition of trimethyllysine in aromatic cage of PHD domains: implications of polarizability, hydrophobicity, and charge on binding

Recognition of trimethyllysine (Kme3) by reader proteins is an important regulator of gene expression. This recognition event is mediated by an aromatic cage made up of 2-4 aromatic residues in the reader proteins that bind Kme3 via cation-π interactions. A small subset of reader proteins contain a methionine (Met) residue in place of an aromatic sidechain in the binding pocket. The unique role of sulfur in molecular recognition has been demonstrated in a number of noncovalent interactions recently, including interactions of thiols, thioethers, and sulfoxides with aromatic rings. However, the interaction of a thioether with an ammonium ion has not previously been investigated and the role of Met in binding Kme3 has not yet been explored. Herein, we systematically vary the Met in two reader proteins, DIDO1 and TAF3, and the ligand, Kme3 or its neutral analog tert-butyl norleucine (tBuNle), to determine the role of Met in the recognition of the cationic Kme3. Our studies demonstrate that Met contributes to binding via dispersion forces, with about an equal contribution to binding Kme3 and tBuNle, indicating that electrostatic interactions do not play a role. During the course of these studies, we also discovered that DIDO1 exhibits equivalent binding to tBuNle and Kme3 through a change in the mechanism of binding.

Modeling Protein S-Aromatic Motifs Reveals Their Structural and Redox Flexibility

S-aromatic motifs are important noncovalent forces for protein stability and function but remain poorly understood. Hence, we performed quantum calculations at the MP2(full)/6-311++G(d,p) level on complexes between Cys (H₂S, MeSH) and Met (Me₂S) models with models of Phe (benzene, toluene), Trp (indole, 3-methylindole), Tyr (phenol, 4-methylphenol), and His (imidazole, 4-methylimidazole). The most stable gas-phase conformers exhibit binding energies of -2 to -6 kcal/mol, and the S atom lies perpendicular to the ring plane. This reveals preferential interaction with the ring π-system, except in the imidazoles where S binds edge-on to an N atom. Complexation tunes the gas-phase vertical ionization potentials of the ligands over as much as 1 eV, and strong σ- or π-type H-bonding supports charge transfer to the H-bond donor, rendering it more oxidizable. When the S atom acts as an H-bond acceptor (N/O-H_ar···S), calibration of the CHARMM36 force field (by optimizing pair-specific Lennard-Jones parameters) is required. Implementing the optimized parameters in molecular dynamics simulations in bulk water, we find stable S-aromatic complexes with binding free energies of -0.6 to -1.1 kcal/mol at ligand separations up to 8 Å. The aqueous S-aromatics exhibit flexible binding conformations, but edge-on conformers are less stable in water. Reflecting this, only 0.3 to 10% of the S-indole, S-phenol, and S-imidazole structures are stabilized by N/O-H_ar···S or S-H···O_ar/N_ar σ-type H-bonding. The wide range of energies and geometries found for S-aromatic interactions and their tunable redox properties expose the versatility and variability of the S-aromatic motif in proteins and allow us to predict a number of their reported properties.

Oxidation increases the strength of the methionine-aromatic interaction

Oxidation of methionine disrupts the structure and function of a range of proteins, but little is understood about the chemistry that underlies these perturbations. Using quantum mechanical calculations, we found that oxidation increased the strength of the methionine-aromatic interaction motif, a driving force for protein folding and protein-protein interaction, by 0.5-1.4 kcal/mol. We found that non-hydrogen-bonded interactions between dimethyl sulfoxide (a methionine analog) and aromatic groups were enriched in both the Protein Data Bank and Cambridge Structural Database. Thermal denaturation and NMR spectroscopy experiments on model peptides demonstrated that oxidation of methionine stabilized the interaction by 0.5-0.6 kcal/mol. We confirmed the biological relevance of these findings through a combination of cell biology, electron paramagnetic resonance spectroscopy and molecular dynamics simulations on (i) calmodulin structure and dynamics, and (ii) lymphotoxin-α binding toTNFR1. Thus, the methionine-aromatic motif was a determinant of protein structural and functional sensitivity to oxidative stress.

Analysis of the interactions of sulfur-containing amino acids in membrane proteins

The interactions of Met and Cys with other amino acid side chains have received little attention, in contrast to aromatic-aromatic, aromatic-aliphatic or/and aliphatic-aliphatic interactions. Precisely, these are the only amino acids that contain a sulfur atom, which is highly polarizable and, thus, likely to participate in strong Van der Waals interactions. Analysis of the interactions present in membrane protein crystal structures, together with the characterization of their strength in small-molecule model systems at the ab-initio level, predicts that Met-Met interactions are stronger than Met-Cys ≈ Met-Phe ≈ Cys-Phe interactions, stronger than Phe-Phe ≈ Phe-Leu interactions, stronger than the Met-Leu interaction, and stronger than Leu-Leu ≈ Cys-Leu interactions. These results show that sulfur-containing amino acids form stronger interactions than aromatic or aliphatic amino acids. Thus, these amino acids may provide additional driving forces for maintaining the 3D structure of membrane proteins and may provide functional specificity.

Ligand selectivity of estrogen receptors by a molecular dynamics study

Estrogen receptors α (ERα) and β (ERβ) have different physiological functions and expression levels in different tissues. ERα and ERβ are highly homologous and have only two residue substitutions in the binding pocket. This high similarity at the active site stimulates the interests for discovering subtype selective ligands. In this study, molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method have been carried out to analyze the basis of selectivity of three ligands (659, 818 and 041). The calculated binding free energies show that all the ligands bind more tightly to ERβ than to ERα. The dominant free energy components of selectivity for 659 are similar to that for 041, but different from that for 818. The decompositions of free energy contributions and structural analysis imply that there are eight residues primarily contributing to the selectivity for 659, five residues for 041, as well as two residues for 818. The structural analysis implies that two residue substitutions in binding packet cause the position of 659 in ERβ-659 complex to shift relative to that in ERα-659 complex and also cause the conformational changes of other residues in the binding pocket. The higher selectivity for 041 is mainly caused by three residues, Ile373 (Met421), His475 (His524) and Leu476 (Leu525).

Sulfur-containing amino acids in 7TMRs: molecular gears for pharmacology and function

Seven-transmembrane receptors (7TMRs) mediate the majority of physiological responses to hormones and neurotransmitters in higher organisms. Tertiary structure stability and activation of these versatile membrane proteins require formation or disruption of complex networks of well-recognized interactions (such as H-bonds, ionic, or aromatic-aromatic) but also of other type of interactions which have been less studied. In this review, we compile evidence from crystal structure, biophysical, and site-directed mutagenesis data that indicate or support the importance of interactions involving Met and Cys in 7TMRs in terms of pharmacology and function. We show examples of Met/Cys-aromatic and Met-Met interactions participating in ligand binding, in tuning the orientation of functionally important aromatic residues during activation or even in modulating the type of signaling response. Collectively, data presented enlarge the repertoire of interactions governing 7TMR functioning.

Cis-trans amide bond rotamers in β-peptoids and peptoids: evaluation of stereoelectronic effects in backbone and side chains

Non-natural peptide analogs have significant potential for the development of new materials and pharmacologically active ligands. One such architecture, the β-peptoids (N-alkyl-β-alanines), has found use in a variety of biologically active compounds but has been sparsely studied with respect to folding propensity. Thus, we here report an investigation of the effect of structural variations on the cis-trans amide bond rotamer equilibria in a selection of monomer model systems. In addition to various side chain effects, which correlated well with previous studies of α-peptoids, we present the synthesis and investigation of cis-trans isomerism in the first examples of peptoids and β-peptoids containing thioamide bonds as well as trifluoroacetylated peptoids and β-peptoids. These systems revealed an increase in the preference for cis-amides as compared to their parent compounds and thus provide novel strategies for affecting the folding of peptoid constructs. By using NMR spectroscopy, X-ray crystallographic analysis, and density functional theory calculations, we present evidence for the presence of thioamide-aromatic interactions through C(sp(2))-H···S(amide) hydrogen bonding, which stabilize certain peptoid conformations.

Evidence for a strong selenium-aromatic interaction derived from crystallographic data and ab initio quantum chemical calculations

Increasing attention is being paid to the role of selenium, both as an essential component required for the activity of many enzymes and in the context of selenium-based pharmaceutical agents. A wide range of therapeutics that include selenium are on the market and under development, such as antihypertensive, anticancerogenic, antiviral, and immunosuppressive agents. Computer-aided drug design (CADD) has proven to be an important tool for the development of new drugs. Many CADD techniques, including docking, molecular dynamics simulation, and other receptor-based approaches, require an accurate understanding of the nature of the intermolecular forces that act to stabilize protein-ligand complexes; moreover, a quantitative assessment of these interactions furthers our efforts to rationalize the drug design process. In this paper, we consider one class of interaction involving selenium, that between Se and aromatic rings. Prior work has shown that interactions between divalent sulfur and aromatic rings are observed much more frequently than would be expected on the basis of chance, both in protein structures and the crystal structures of organic compounds that include these moieties. Recent studies on the optimization of inhibitor-protein binding also suggest that sulfur-aromatic interactions are important in stabilizing these complexes and may be crucial focal point for CADD. Given that selenium and sulfur have similar chemistry, and that selenium is significantly more polarizable, we propose that Se-aromatic interactions may also play an important stabilizing role in the structure of folded proteins and in drug-protein complexes. We have tested this hypothesis against data from the Cambridge Crystallographic Database and ab initio quantum chemical calculations. We have found evidence that selenium does interact strongly with aromatic rings and may play a role analogous to sulfur in stabilizing protein folds. In addition, selenium should be considered along with sulfur in rational drug design strategies that seek to improve binding to target protein sites that include aromatic rings.

Propensities of polar and aromatic amino acids in noncanonical interactions: nonbonded contacts analysis of protein-ligand complexes in crystal structures

The nonbonded contacts analysis of 14 polar and aromatic amino acid side chains was carried out for protein-ligand complexes derived from the crystal structures in the Protein Data Bank. Through the exhaustive analysis, several unusual contacts were observed as well as the well-known interactions. CH-S interactions were frequently found in Met-related contacts, which have not yet been the subject of systematic investigations. We have also described the propensity of each amino acid for nonbonded interactions. All amino acids studied in this work showed high frequencies for the canonical hydrogen-bonding NH-O, OH-N, and OH-O interactions, while the preferences in noncanonical interactions such as CH- pi interactions were not always consistent among the side chains with similar characteristics. Understanding such amino acid side chain propensities is important for improving the accuracy of structure-based drug design, and this study will open new possibilities for developing unique compounds with high binding affinity.

Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions

The X-ray crystal structures of mannose trimming enzyme drosophila Golgi alpha-mannosidase II (dGMII) complexed with the inhibitors mannostatin A (1) and an N-benzyl analogue (2) have been determined. Molecular dynamics simulations and NMR studies have shown that the five-membered ring of mannostatin A is rather flexible occupying pseudorotational itineraries between 2T3 and 5E, and 2T3 and 4E. In the bound state, mannostatin A adopts a 2T1 twist envelope conformation, which is not significantly populated in solution. Possible conformations of the mannosyl oxacarbenium ion and an enzyme-linked intermediate have been compared to the conformation of mannostatin A in the cocrystal structure with dGMII. It has been found that mannostatin A best mimics the covalent linked mannosyl intermediate, which adopts a 1S5 skew boat conformation. The thiomethyl group, which is critical for high affinity, superimposes with the C-6 hydroxyl of the covalent linked intermediate. This functionality is able to make a number of additional polar and nonpolar interactions increasing the affinity for dGMII. Furthermore, the X-ray structures show that the environment surrounding the thiomethyl group of 1 is remarkably similar to the arrangements around the methionine residues in the protein. Collectively, our studies contradict the long held view that potent inhibitors of glycosidases must mimic an oxacarbenium ion like transition state.

Understanding the selectivity of genistein for human estrogen receptor-beta using X-ray crystallography and computational methods

We present X-ray crystallographic and molecular modeling studies of estrogen receptors-alpha and -beta complexed with the estrogen receptor-beta-selective phytoestrogen genistein, and coactivator-derived NR box peptides containing an LXXLL motif. We demonstrate that the ligand binding mode is essentially identical when genistein is bound to both isoforms, despite the considerably weaker affinity of this ligand for estrogen receptor-alpha. In addition, we examine subtle differences between binding site residues, providing an explanation for why genistein is modestly selective for the beta isoform. To this end, we also present the results of quantum chemical studies and thermodynamic arguments that yield insight to the nature of the interactions leading to estrogen receptor-beta selectivity. The importance of our analysis to structure-based drug design is discussed.

Estimates of the ab Initio Limit for Sulfur−π Interactions: The H2S−Benzene Dimer

The interaction between aromatic rings and sulfur atoms in the side chains of amino acids is a factor in the formation and stabilization of alpha-helices in proteins. We studied the H(2)S-benzene dimer as the simplest possible prototype of sulfur-pi interactions. High-quality potential energy curves were obtained using coupled-cluster theory with single, double, and perturbative triple substitutions (CCSD(T)) and a large, augmented quadruple-zeta basis set (aug-cc-pVQZ). The equilibrium intermonomer distance for the hydrogens-down C(2)(v) configuration is 3.8 A with an interaction energy of -2.74 kcal mol(-1). Extrapolating the binding energy to the complete basis set limit gives -2.81 kcal mol(-1). This binding energy is comparable to that of H(2)O-benzene or of the benzene dimer, and the equilibrium distance is in close agreement with experiment. Other orientations of the dimer were also considered at less complete levels of theory. A considerable reduction in binding for the sulfur-down configuration, together with an energy decomposition analysis, indicates that the attraction in H(2)S-benzene is best thought of as arising from a favorable electrostatic interaction between partially positive hydrogens in H(2)S with the negatively charged pi-cloud of the benzene.

Cation-pi interactions of a thiocarbonyl group and a carbonyl group with a pyridinium nucleus

Attractive interactions between a thiocarbonyl group and a pyridinium nucleus, and between a carbonyl group and a pyridinium nucleus have been proven by (1)H and (13)C NMR studies, UV-vis spectral analyses, and X-ray crystallographic analyses of nicotinic amides 1 and 3, and pyridinium salts 2 and 4. Comparison of the Deltadelta values, which are the differences in the chemical shifts with reference compounds 5 or 6, showed that the absolute Deltadelta values of 2 and 4 are much larger than those of 1 and 3. In the UV-vis spectra, the n-->pi absorption of the C=S group of 2a exhibited a significant blue shift in CHCl(3). X-ray crystallographic analysis of 1-4 clearly showed that the C=S group of 2a and the C=O group of 4 are very close to the pyridinium moiety compared to the case of 1 and 3. In addition, the X-ray crystal packing structure of 2a showed the C=S group is sandwiched between two pyridinium rings. These experimental results strongly suggested the existence of attractive (C=S)...Py(+) and (C=O)...Py(+) interactions in solution and in crystal. The optimized geometries of 1 and 2 calculated at the HF/6-311G level are in good agreement with their X-ray geometries. MP2/6-311G calculations for the model systems of pyridinium salts 2 and 4 predicted that the electrostatic and induction energies are the major source of the attractive interactions. Since the larger contribution of electrostatic and induction interactions are characteristic features of cation-pi interactions, the (C=S)...Py(+) and (C=O)...Py(+) interactions would be classified as a cation-pi interaction.

Evidence for a strong sulfur-aromatic interaction derived from crystallographic data

We have uncovered new evidence for a significant interaction between divalent sulfur atoms and aromatic rings. Our study involves a statistical analysis of interatomic distances and other geometric descriptors derived from entries in the Cambridge Crystallographic Database (F. H. Allen and O. Kennard, Chem. Design Auto. News, 1993, Vol. 8, pp. 1 and 31-37). A set of descriptors was defined sufficient in number and type so as to elucidate completely the preferred geometry of interaction between six-membered aromatic carbon rings and divalent sulfurs for all crystal structures of nonmetal-bearing organic compounds present in the database. In order to test statistical significance, analogous probability distributions for the interaction of the moiety X-CH(2)-X with aromatic rings were computed, and taken a priori to correspond to the null hypothesis of no significant interaction. Tests of significance were carried our pairwise between probability distributions of sulfur-aromatic interaction descriptors and their CH(2)-aromatic analogues using the Smirnov-Kolmogorov nonparametric test (W. W. Daniel, Applied Nonparametric Statistics, Houghton-Mifflin: Boston, New York, 1978, pp. 276-286), and in all cases significance at the 99% confidence level or better was observed. Local maxima of the probability distributions were used to define a preferred geometry of interaction between the divalent sulfur moiety and the aromatic ring. Molecular mechanics studies were performed in an effort to better understand the physical basis of the interaction. This study confirms observations based on statistics of interaction of amino acids in protein crystal structures (R. S. Morgan, C. E. Tatsch, R. H. Gushard, J. M. McAdon, and P. K. Warme, International Journal of Peptide Protein Research, 1978, Vol. 11, pp. 209-217; R. S. Morgan and J. M. McAdon, International Journal of Peptide Protein Research, 1980, Vol. 15, pp. 177-180; K. S. C. Reid, P. F. Lindley, and J. M. Thornton, FEBS Letters, 1985, Vol. 190, pp. 209-213), as well as studies involving molecular mechanics (G. Nemethy and H. A. Scheraga, Biochemistry and Biophysics Research Communications, 1981, Vol. 98, pp. 482-487) and quantum chemical calculations (B. V. Cheney, M. W. Schulz, and J. Cheney, Biochimica Biophysica Acta, 1989, Vol. 996, pp.116-124; J. Pranata, Bioorganic Chemistry, 1997, Vol. 25, pp. 213-219)-all of which point to the possible importance of the sulfur-aromatic interaction. However, the preferred geometry of the interaction, as determined from our analysis of the small-molecule crystal data, differs significantly from that found by other approaches.