Observation of a weak intra-residue C5 hydrogen-bond in a dipeptide containing Gly-Pro sequence

The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function

Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.

Sequence dependent folding motifs of the secondary structures of Gly-Pro and Pro-Gly containing oligopeptides

Folding motifs of the secondary structures of peptides and proteins are primarily based on the hydrogen bonding interactions in the backbone as well as the sequence of the amino acid residues present. For instance, the β-turn structure directed by the Pro-Gly sequence is the key to the β-hairpin structure of peptides/proteins as well as a selective site for the enzymatic hydroxylation of pro-collagen. Herein, we have investigated the sequence dependent folding motifs of end-protected Gly-Pro and Pro-Gly dipeptides using a combination of gas phase laser spectroscopy, quantum chemistry calculations, solution phase IR and NMR spectroscopy and single crystal X-Ray diffraction (XRD). All three observed conformers of the Gly-Pro peptide in the gas phase have been found to have extended β-strand or polyproline-II (PP-II) structures with C5-C7 hydrogen bonding interactions, which correlates well with the structure obtained from solution phase spectroscopy and XRD. On the other hand, we have found that the Pro-Gly peptide has a C10/β-turn structure in the solution phase in contrast to the C7-C7 (i.e. 2₇-ribbon) structure observed in the gas phase. Although the lowest energy structure in the gas phase is not C10, we find that C7-C7 is an abundantly found structural motif of Pro-Gly containing peptides in the Cambridge Structural Database, indicating that the gas phase conformers are not sampling any unusual forms. We surmise that the role of the solvent could be crucial in dictating the preferential stabilization of the C10 structure in the solution phase. The present investigation provides a comprehensive picture of the folding motifs of the Gly-Pro and Pro-Gly peptides observed in the gas phase and condensed phase weaving a fine interplay of the intrinsic conformational properties, solvation, and crystal packing of the peptides.

Newly identified C–H⋯O hydrogen bond in histidine

Histidine C–H bonds observed in protein structures include (clockwise from top left): myoglobin, β-lactamase, and photoactive yellow protein; calculations indicate that tautomeric/protonation state influences H-bonding ability (bottom left).

Tracking the Amide I and αCOO- Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study

The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue's amide I ν(C=O) and the αCOO- terminal ν(C=O) bands on the neighboring side chain, the length of the peptide fragment, and the extent of intramolecular hydrogen bonding in the structure are investigated here via the EGEDEA peptide. The hexapeptide is broken down into fragments increasing in size from dipeptides to hexapeptides, including EG, ED, EA, EGE, EDE, DEA, EGED, EDEA, EGEDE, GEDEA, and, finally, EGEDEA, which are investigated with experimental Raman spectroscopy and density functional theory (DFT) computations to model the zwitterionic crystalline solids (in vacuo). The molecular geometries and Boltzmann sum of the simulated Raman spectra for a set of energetic minima corresponding to each peptide fragment are computed with full geometry optimizations and corresponding harmonic vibrational frequency computations at the B3LYP/6-311++G(2df,2pd) level of theory. In absence of the crystal structure, geometry sampling is performed to approximate solid phase behavior. Natural bond order (NBO) analyses are performed on each energetic minimum to quantify the magnitude of the intramolecular hydrogen bonds. The extent of the intramolecular charge transfer is dependent on the overall polarity of the fragment considered, with larger and more polar fragments exhibiting the greatest extent of intramolecular charge transfer. A steady blue shift arises when considering the amide I band position moving linearly from ED to EDE to EDEA to GEDEA and, finally, to EGEDEA. However, little variation is observed in the αCOO- ν(C=O) band position in this family of fragments.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.