Aromatic Side Chains In Proteins Research Articles

Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding.

Simple SummaryProteins are composed of compact domains, often of known three-dimensional structure, and natively unstructured polypeptide regions. The abundant cold-shock domain is among the set of canonical nucleic acid-binding domains and conserved from bacteria to man. Proteins containing cold-shock domains serve a large variety of biological functions, which are mostly linked to DNA or RNA binding. These functions include the regulation of transcription, RNA splicing, translation, stability and sequestration. Cold-shock domains have a simple architecture with a conserved surface ideally suited to bind single-stranded nucleic acids. Because the binding is mostly by non-specific molecular interactions which do not involve the sugar-phosphate backbone, cold-shock domains are not strictly sequence-specific and do not discriminate reliably between DNA and RNA. Many, but not all functions of cold shock-domain proteins in health and disease can be understood based of the physical and structural properties of their cold-shock domains.The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains’ ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration.

Aromatic 19 F-13 C TROSY-[19 F, 13 C]-Pyrimidine Labeling for NMR Spectroscopy of RNA.

We present the access to [5‐19F, 5‐13C]‐uridine and ‐cytidine phosphoramidites for the production of site‐specifically modified RNAs up to 65 nucleotides (nts). The amidites were used to introduce [5‐19F, 5‐13C]‐pyrimidine labels into five RNAs—the 30 nt human immunodeficiency virus trans activation response (HIV TAR) 2 RNA, the 61 nt human hepatitis B virus ϵ (hHBV ϵ) RNA, the 49 nt SAM VI riboswitch aptamer domain from B. angulatum, the 29 nt apical stem loop of the pre‐microRNA (miRNA) 21 and the 59 nt full length pre‐miRNA 21. The main stimulus to introduce the aromatic 19F–13C‐spin topology into RNA comes from a work of Boeszoermenyi et al., in which the dipole‐dipole interaction and the chemical shift anisotropy relaxation mechanisms cancel each other leading to advantageous TROSY properties shown for aromatic protein sidechains. This aromatic 13C–19F labeling scheme is now transferred to RNA. We provide a protocol for the resonance assignment by solid phase synthesis based on diluted [5‐19F, 5‐13C]/[5‐19F] pyrimidine labeling. For the 61 nt hHBV ϵ we find a beneficial 19F–13C TROSY enhancement, which should be even more pronounced in larger RNAs and will facilitate the NMR studies of larger RNAs. The [19F, 13C]‐labeling of the SAM VI aptamer domain and the pre‐miRNA 21 further opens the possibility to use the biorthogonal stable isotope reporter nuclei in in vivo NMR to observe ligand binding and microRNA processing in a biological relevant setting.

Site-selective 1H/2H labeling enables artifact-free 1H CPMG relaxation dispersion experiments in aromatic side chains

Aromatic side chains are often key residues in enzyme active sites and protein binding sites, making them attractive probes of protein dynamics on the millisecond timescale. Such dynamic processes can be studied by aromatic 13C or 1H CPMG relaxation dispersion experiments. Aromatic 1H CPMG relaxation dispersion experiments in phenylalanine, tyrosine and the six-ring moiety of tryptophan, however, are affected by 3J 1H–1H couplings which are causing anomalous relaxation dispersion profiles. Here we show that this problem can be addressed by site-selective 1H/2H labeling of the aromatic side chains and that artifact-free relaxation dispersion profiles can be acquired. The method has been further validated by measuring folding–unfolding kinetics of the small protein GB1. The determined rate constants and populations agree well with previous results from 13C CPMG relaxation dispersion experiments. Furthermore, the CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained directly from the spectra. In summary, site-selective 1H/2H labeling enables artifact-free aromatic 1H CPMG relaxation dispersion experiments in phenylalanine and the six-ring moiety of tryptophan, thereby extending the available methods for studying millisecond dynamics in aromatic protein side chains.

Optimal Isotope Labeling of Aromatic Amino Acid Side Chains for NMR Studies of Protein Dynamics.

Aromatic side chains in proteins are often directly evolved in stabilizing the hydrophobic core, protein binding, or enzymatic activity. They are also responsible for specific local dynamic processes, such as histidine tautomerization or ring flips. Despite their importance, they are often not targeted directly by NMR spectroscopy, because of spectroscopic complications and challenges. This chapter addresses state-of-the-art site-selective 13C-labeling methods for aromatic side chains, and describes how they solve several of the spectroscopic issues. A special emphasis is put on thereby enabled protein dynamics experiments of aromatic side chains.

Correction: Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations.

Correction for 'Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations' by Piotr Paluch et al., Phys. Chem. Chem. Phys., 2015, 17, 28789-28801.

Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations.

We report a new multidimensional magic angle spinning NMR methodology, which provides an accurate and detailed probe of molecular motions occurring on timescales of nano- to microseconds, in sidechains of proteins. The approach is based on a 3D CPVC-RFDR correlation experiment recorded under fast MAS conditions (ν(R) = 62 kHz), where (13)C-(1)H CPVC dipolar lineshapes are recorded in a chemical shift resolved manner. The power of the technique is demonstrated in model tripeptide Tyr-(d)Ala-Phe and two nanocrystalline proteins, GB1 and LC8. We demonstrate that, through numerical simulations of dipolar lineshapes of aromatic sidechains, their detailed dynamic profile, i.e., the motional modes, is obtained. In GB1 and LC8 the results unequivocally indicate that a number of aromatic residues are dynamic, and using quantum mechanical calculations, we correlate the molecular motions of aromatic groups to their local environment in the crystal lattice. The approach presented here is general and can be readily extended to other biological systems.

Aromatic-proline interactions: electronically tunable CH/π interactions.

Proline residues have unique roles in protein folding, structure, and function. Proline and the aromatic amino acids comprise the encoded cyclic protein residues. Aromatic protein side chains are defined by their negatively charged π faces, while the faces of the proline ring are partially positively charged. This polarity results from their two-point connection of the side chain to the electron-withdrawing protein backbone, and the lower electronegativity of hydrogen compared to carbon, nitrogen, and oxygen. The hydrogens adjacent to the carbonyl and amide nitrogen, Hα and Hδ, respectively, are the most partially positive. Proline's side chain is also conformationally restricted, allowing for interaction with aromatic residues with minimal entropic or steric penalty. Proline and aromatic residues can interact favorably with each other, due to both the hydrophobic effect and the interaction between the π aromatic face and the polarized C-H bonds, called a CH/π interaction. Aromatic-proline interactions can occur locally, for example, to stabilize cis-amide bonds, and over larger distances, in the tertiary structures of proteins, and intermolecularly in protein-protein interactions. In peptides and proteins, aromatic-proline sequences more readily adopt cis-prolyl amide bonds, where the aromatic ring interacts with the proline ring in the cis conformation. In aromatic-proline sequences, Trp and Tyr are more likely to induce cis-amide bonds than Phe, suggesting an aromatic electronic effect. This result would be expected for a CH/π interaction, in which a more electron-rich aromatic would have a stronger (more cis-stabilizing) interaction with partial positive charges on prolyl hydrogens. In this Account, we describe our investigations into the nature of local aromatic-proline interactions, using peptide models. We synthesized a series of 26 peptides, TXPN, varying X from electron-rich to electron poor aromatic amino acids, and found that the population of cis-amide bond (Ktrans/cis) is tunable by aromatic electronics. With 4-substituted phenylalanines, we observed a Hammett correlation between aromatic electronics and Ktrans/cis, with cis-trans isomerism electronically controllable by 1.0 kcal/mol. All aromatic residues exhibit a higher cis population than Ala or cyclohexylalanine, with Trp showing the strongest aromatic-proline interaction. In addition, proline stereoelectronic effects can modulate cis-trans isomerism by an additional 1.0 kcal/mol. The aromatic-proline interaction is enthalpic, consistent with its description as a CH/π interaction. Proline-aromatic sequences can also promote cis-prolyl bonds, either through interactions of the aromatic ring with the preceding cis-proline or with the Hα prior to cis-proline. Within proline-rich peptides, sequences commonly found in natively disordered proteins, aromatic residues promote multiple cis-amide bonds due to multiple favorable aromatic-proline interactions. Collectively, we found aromatic-proline interactions to be significantly CH/π in nature, tunable by aromatic electronics. We discuss these data in the context of aromatic-proline and aromatic-glycine interactions in local structure, in tertiary structure, in protein-protein interactions, and in protein assemblies.

UV Raman Markers for Structural Analysis of Aromatic Side Chains in Proteins

UV Raman spectroscopy is a powerful tool for investigating the structures and interactions of the aromatic side chains of Phe, Tyr, Trp, and His in proteins. This is because Raman bands of aromatic ring vibrations are selectively enhanced with UV excitation, and intensities and wavenumbers of Raman bands sensitively reflect structures and interactions. Interpretation of protein Raman spectra is greatly assisted by using empirical correlations between spectra and structure. Many Raman bands of aromatic side chains have been proposed to be useful as markers of structures and interactions on the basis of empirical correlations. This article reviews the usefulness and limitations of the Raman markers for protonation/deprotonation, conformation, metal coordination, environmental polarity, hydrogen bonding, hydrophobic interaction, and cation-π interaction of the aromatic side chains. The utility of Raman markers is demonstrated through an application to the structural analysis of a membrane-bound proton channel protein.

Peptide Structure Stabilization: A Study Of Aromatic-aromatic Interaction And pH Effect On A β-hairpin Stability

Aromatic side chains in proteins are often involved in aromatic pairs, most of which form interacting networks of three or more aromatic side chains. (Petsko et al., Science, 1985, 229, 23-28) Analysis of neighboring aromatic groups can lead to improved understanding of protein folding mechanisms and stability. We have used the β-hairpin forming peptide Trpzip2 (Cochran et al., PNAS, 2001, 98, 5578-5583) as a template to study the effect of aromatic-aromatic interaction on peptide stability. Optical spectra (ECD, FTIR) and NMR of the original TZ2 peptide and its Tyr and Val-substituted mutants were measured to characterize their conformation and thermal stability. Compared to the strongly interacting Trp-Trp edge-to-face geometry, Tyr-Tyr shows much weaker aromatic-aromatic interaction. These aromatic-aromatic interactions were also compared to simple hydrophobic interaction by substituting Val for two interacting Trp residues in this peptide. Aromatic interaction showed a stronger effect than hydrophobic interaction for stabilization of this peptide. The thermal unfolding process of three Val mutants was studied under both neutral and acidic conditions by IR and ECD. We see more random coil content at acidic pH than those at neutral pH from analysis of the IR amide I’ band, which reflects peptide secondary structure, and the transition temperatures obtained using both IR and CD are lower at acidic pH than at neutral pH, which suggests that this peptide is less stable at acidic pH.

Biosynthetic 13C Labeling of Aromatic Side Chains in Proteins for NMR Relaxation Measurements

Site-specific 13C labeling offers a desirable means of eliminating unwanted relaxation pathways and coherent magnetization transfer in NMR relaxation experiments. Here we use [1-13C]-glucose as the sole carbon source in the growth media for protein overexpression in Escherichia coli. The approach results in specific incorporation of 13C at isolated positions in the side chains of aromatic amino acids, which greatly simplifies the measurements and interpretation of 13C relaxation rates in these spin systems. The method is well suited for characterization of chemical exchange by CPMG or spin-lock relaxation methods. We validated the method by acquiring 13C rotating-frame relaxation dispersion data on the E140Q mutant of the C-terminal domain of calmodulin, which reveal conformational exchange dynamics with a time constant of 71 mus for Y138.

Biomolecular NMR using a microcoil NMR probe--new technique for the chemical shift assignment of aromatic side chains in proteins.

A specially designed microcoil probe for use in biomolecular NMR spectroscopy is presented. The microcoil probe shows a mass-based sensitivity increase of a minimal factor of 7.5, allowing for the first time routine biomolecular NMR spectroscopy with microgram amounts of proteins. In addition, the exceptional radio frequency capabilities of this probe allowed us to record an aliphatic-aromatic HCCH-TOCSY spectrum for the first time. Using this spectrum, the side chains of aliphatic and aromatic amino acids can be completely assigned using only a single experiment. Using the conserved hypothetical protein TM0979 from Thermotoga maritima, we demonstrate the capabilities of this microcoil NMR probe to completely pursue the sequence specific backbone assignment with less than 500 microg of (13)C,(15)N labeled protein.

Crystal structures of two complexes of the rare-earth-DOTA-binding antibody 2D12.5: ligand generality from a chiral system.

We report the crystal structures of antibody 2D12.5 Fab bound to an yttrium-DOTA analogue and separately to a gadolinium-DOTA analogue. The rare earth elements have many useful properties as probes, and 2D12.5 binds the DOTA (1,4,7,10-tetraazacyclododecane-N,N',N' ',N' "-tetraacetic acid) complexes of all of them (Corneillie et al. J. Am. Chem. Soc. 2003, 125, 3436-3437). The structures show that there are no direct protein-metal interactions: a bridging water acts as a link between the protein and metal, with the chelate present as the M isomer in each case. DOTA forms an amphipathic cylinder with the charged carboxylate groups toward the face of the chelate near the metal ion, while nonpolar methylene groups from the macrocycle and the carboxymethyl groups occupy the rear and sides of the molecule. The orientation of the metal-DOTA in the 2D12.5 complex places most of the methylene carbon atoms of DOTA in hydrophobic contact with aromatic protein side chains. Other binding interactions between the metal complex and the antibody include a bidentate salt bridge, four direct H-bonds, and four to five water-mediated H-bonds. We find that 2D12.5 exhibits enantiomeric binding generality, binding yttrium chelates in both Lambda(deltadeltadeltadelta) and Delta(lambdalambdalambdalambda) configurations with modestly different affinities. This develops from the symmetrical nature of the DOTA chelate, which places heteroatoms and hydrophobic atoms in approximately the same relative positions regardless of the helicity of DOTA.

The "cap-binding slot" of an mRNA cap-binding protein: quantitative effects of aromatic side chain choice in the double-stacking sandwich with cap.

The N7-methylguanine portion of the mRNA cap structure interacts with cap-binding proteins via an unusual double-stacking arrangement in which the positively charged cap is sandwiched between two parallel-oriented aromatic protein side chains. Three-dimensional costructures of cap with two mRNA cap-binding proteins, namely, translational initiation factor eIF4E and VP39 (the vaccinia virus-encoded mRNA cap-specific 2'-O-methyltransferase), have heretofore been reported. Despite striking similarities between the two proteins in the double stack with the cap, the stack differs most notably in the species of stacked side chain donated by the protein. Whereas eIF4E employs two tryptophans, VP39 uses a tyrosine and a phenylalanine. Here, we have generated tryptophan substitutions in VP39. Tryptophan substitution was shown, crystallographically, not to disrupt the maintenance of a bona fide parallel stack. However, the single-tryptophan and double-tryptophan substitutions were associated with increased affinity for cap nucleoside by factors of 10 and 50, respectively. VP39 interacted more strongly with a true substrate (containing portions of RNA downstream of the cap in addition to the cap itself) than with isolated cap nucleoside, by several orders of magnitude. VP39 mutants with tryptophan substitution at position 180 exhibited apparent defects in substrate catalytic rate during the first turnover cycle, indicating the possibility of an exquisite sensitivity of the catalytic center to subtle changes in substrate position brought about by alterations in the cap-binding slot. The X-ray structure of VP39 with a genuine nucleobase analogue of N7-methylguanosine, namely, N7,9-dimethylguanine, indicated that the N7-methylguanosine rotational orientation within the stack is a property of the cap nucleobase itself.

Suppression of diagonal peaks in three-dimensional protein NMR TROSY-type HCCH correlation experiments.

A novel method for suppression of (13)C-(13)C diagonal peaks without sensitivity loss in three-dimensional HCCH TROSY-type NMR correlation experiments involving aromatic side chains in proteins (Pervushin et al., J. Am. Chem. Soc. 120, 6394-6400 (1998)) is presented. The key element is a spin-state-selective filter in the (13)C-(13)C mixing sequence with the dual effect of selecting the TROSY resonance in the preceding evolution period and interchanging TROSY and anti-TROSY resonances. The cross peaks are invariant to this filter but diagonal peak coherence gets concentrated on the anti-TROSY transition so that it can be eliminated by a (13)C --> (1)H TROSY transfer element. The new method is demonstrated using a (13)C,(15)N-labeled protein sample, RAP 18-112 (N-terminal domain of alpha(2)-macroglobulin receptor associated protein), at 750 MHz.

Distribution of solvent and ligand molecules around aromatic side chains in proteins and its implication on carbonic anhydrase catalytic mechanism

Interactions between aromatic phenylalanine, tyrosine and tryptophan residues and water as well as ligand molecules were analyzed by a computer search of a large number of high resolution structures in the protein data bank. Water molecules and oxygen ligands have a preference for the edges of the aromatic residues, but the distribution of carbon ligands around the aromatic rings is different. The more hydrophilic tyrosine, followed by tryptophan, has the highest frequency of water contacts. However the situation is reversed for ligand interactions where phenylalanine is the most active of the three aromatic residues. The results indicate that hydrogen bonding by water molecules to aromatic π-electron does not occur in protein structures. The role of the conserved Trp 209 in the catalytic mechanism of carbonic anhydrase is discussed in consideration of the results from the data base search. Normally not considered as a catalytic residue, this tryptophan is proposed to participate in the physiologically important enzymatic interconversion of carbon dioxide and bicarbonate by stabilizing substrate coordination through van der Waals' interactions.

Novel Spinning Cell System for UVRR Measurements of Powder and Small-Volume Solution Samples in Back-Scattering Geometry: Application to Solid Tryptophan and Mutant Hemoglobin Solution

It has been shown in the last decade that ultraviolet (UV) resonance Raman (RR) spectroscopy is a powerful tool for studying protein structures and their dynamics. Changes in intensities and frequencies of UV Raman bands arising from aromatic side chains of proteins have been correlated with their structural or environmental changes, particularly for tyrosine (Tyr) and tryptophan (Trp) residues, in the same way as that for visible excitations. However, in comparison with visible excitation, UV excitation contains a high possibility of causing photochemical degradation of samples; accordingly, special illumination systems of samples, such as a wire-guided flow system, have been devised for individual experiments. Flow cell systems generally require a large volume of samples, and therefore it has been difficult to apply the UVRR technique to uncommon samples like mutant proteins for which a large number of samples are not available. The other technical problem is difficulty in measuring the spectra of solid samples since powder or crystalline samples are easily degraded by irradiation of the UV laser because of their strong UV absorption. The higher background in these measurements also brings about large noise in the spectra.

Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin

The crystal structure of the RNA-binding domain of the small nuclear ribonucleoprotein U1A bound to a 21-nucleotide RNA hairpin has been determined at 1.92 A resolution. The ten-nucleotide RNA loop binds to the surface of the beta-sheet as an open structure, and the AUUGCAC sequence of the loop interacts extensively with the conserved RNP1 and RNP2 motifs and the C-terminal extension of the RNP domain. These interactions include stacking of RNA bases with aromatic side chains of proteins and many direct and water-mediated hydrogen bonds. The structure reveals the stereochemical basis for sequence-specific RNA recognition by the RNP domain.

Planar Stacking Interactions of Arginine and Aromatic Side-Chains in Proteins

A parallel stacking arrangement of the guanidinium groups of arginines directly over the center of the rings of aromatic side-chains is observed much more frequently in proteins than would be expected by chance. This type of interaction, which is often found in locations critical to the function, apparently serves to orient the arginine side-chain without interfering with its ability to form hydrogen bonds elsewhere. It is distinct from the interactions which involve the side-chains of asparagine or glutamine, which do frequently assume a nearly planar relationship to the ring, but at a position at or beyond the ring edge.

Aromatic-aromatic interaction: a mechanism of protein structure stabilization.

Analysis of neighboring aromatic groups in four biphenyl peptides or peptide analogs and 34 proteins reveals a specific aromatic-aromatic interaction. Aromatic pairs (less than 7 A between phenyl ring centroids) were analyzed for the frequency of pair type, their interaction geometry (separation and dihedral angle), their nonbonded interaction energy, the secondary structural locations of interacting residues, their environment, and their conservation in related molecules. The results indicate that on average about 60 percent of aromatic side chains in proteins are involved in aromatic pairs, 80 percent of which form networks of three or more interacting aromatic side chains. Phenyl ring centroids are separated by a preferential distance of between 4.5 and 7 A, and dihedral angles approaching 90 degrees are most common. Nonbonded potential energy calculations indicate that a typical aromatic-aromatic interaction has energy of between -1 and -2 kilocalories per mole. The free energy contribution of the interaction depends on the environment of the aromatic pair. Buried or partially buried pairs constitute 80 percent of the surveyed sample and contribute a free energy of between -0.6 and -1.3 kilocalories per mole to the stability of the protein's structure at physiologic temperature. Of the proteins surveyed, 80 percent of these energetically favorable interactions stabilize tertiary structure, and 20 percent stabilize quaternary structure. Conservation of the interaction in related molecules is particularly striking.

Restriction of motion of protein side chains during the photocycle of bacteriorhodopsin.

Linear dichroism was measured during the photocycle of bacteriorhodopsin. The anisotropy of the sample was produced by the photoselection method. The measurements on purple membrane fragments embedded in agar gel were performed at room temperature with 200 microseconds time resolution at several wavelengths in the 240- to 550-nm spectral region. The induced anisotropy of the retinal chromophore remained constant after the formation of the photocycle intermediate M. The anisotropy was also time independent at the characteristic peaks of the UV absorption change. These experimental data suggest that the direction of the retinal transition dipole moment remains unchanged. Moreover, the affected aromatic protein side chains also do not show any rotational motion when they are in the perturbed or ground states during the photocycle. Our data render it possible to calculate the restricted range of sudden chromophore rotations that might be coupled to the appearance and decay of the M intermediate.