Biological Noncovalent Motif

The classic view of the central dogma of biology states that "the coded genetic information hard-wired into DNA is transcribed into individual transportable cassettes, composed of messenger RNA (mRNA); each mRNA cassette contains the program for synthesis of a particular protein sequence." With the progress in the field of biology at subcellular level in recent years, however, our notion about the complete pathway of the genetic information-flow is enlarged to cover biomolecular folding and recognition—that are fundamentally dominated by weak, reversible chemical forces, or called biological noncovalent interactions (BNIs). Here, we further extended the concept of BNI to biological noncovalent motif (BNM) as a description of the functional entity composed of one or several BNIs in biological context. In this dissertation, we define, analyze, and demonstrate a series of specific BNMs that are largely underappreciated in the sophisticated biochemical community. In addition, an in-house program called the 2D-GraLab is also described for automatically generating schematic representation of BNMs across the protein binding interfaces.(ⅰ) Sulfur-containing hydrogen bonds in proteins. Sulfur atoms have been known to participate in hydrogen bonds (H-bonds) and these sulfur-containing H-bonds (SCHBs) are suggested to play important roles in certain biological processes. This study aims to comprehensively characterize all the SCHBs in 500 high-resolution (<1.8 A) protein structures retrieved from the Top500 database. We categorize SCHBs into six types according to donor/acceptor behaviors and then employ explicit hydrogen approach to distinguish SCHBs from those of non-hydrogen bonding interactions. It is revealed that sulfur atom is a very poor H-bond acceptor, but a moderately good H-bond donor. In a-helix, considerable SCHBs are found between the sulphydryl group of cysteine residueⅰand the carbonyl oxygen of residueⅰ-4, and these SCHBs exert appreciable effect in stabilizing helices. Although for most SCHBs, they possess no specific secondary structure preference, their geometrical characteristics in proteins and in free small compounds are significantly distinct, indicating that protein SCHBs are geometrically distorted. Interestingly, sulfur atom in disulfide bond tends to form bifurcated H-bond whereas in cysteine-cysteine pairs prefer to form dual H-bond. These special H-bonds remarkably boost the interaction between H-bond donor and acceptor. By oxidation/reduction manner, the mutual transformation between the dual H-bonds and disulfide bonds for cysteine-cysteine pairs can accurately adjust the structural stability and biological function of proteins in different environments. Furthermore, few loose H-bonds are observed to form between the sulphydryl groups and aromatic rings, and in these cases the donor H is almost over against the rim rather than the center of the aromatic ring.(ⅱ) Fluorine bonds at protein-ligand interfaces. Although fluorination of pharmacologically active compounds has long been a common strategy to increase their metabolic stability and membrane permeation, the functionality of protein-ligand interactions involving fluorine atoms, that we named fluorine bonds, was only recently recognized in chemistry and biology communities. Here, the geometrical characteristics and energetic behaviors of fluorine bonds are systematically investigated by combining two quite disparate but complementary approaches:X-ray structural analysis and theoretical calculations. We find that the short contacts involving fluorine atoms between proteins and fluorinated ligands are very frequent and these contacts, compared to those of routine hydrogen/halogen bonds, are more similar to above-mentioned SCHBs. ONIOM-based QM/MM analysis further reveal that fluorine bonds do play an essential role in protein-ligand binding, albeit the strength of isolated fluorine bonding is quite modest. Furthermore, 14 quantum mechanics (QM) and molecular mechanics (MM) methods are performed to reproduce fluorine bond energies obtained at the rigorous MP2/aug-cc-pVDZ level of theory, and results show that most QM methods and very few MM methods perform well in the reproducibility; the MPWLYP functional and MMFF94 force field are recommended to study moderate and large fluorine bonding systems, respectively.(ⅲ) Halogen-water-hydrogen bridges in biomolecules. The importance of water in biological systems has long been recognized in the field of biology. Here, we describe a new manner by which water affects biomolecular behaviors, called halogen-water-hydrogen bridge (XWH bridge), that is, one H-bond in water-mediated H-bond bridge is replaced functionally by a halogen bond (X-bond). Although behaving similarly to water-mediated H-bond motif, the XWH bridge usually stands in multifurcated forms and possesses stronger directionality. QM analysis on several model and real systems reveals that the XWH bridges are more thermodynamically stable than other water-involved interactions, and this stability is further enhanced by the cooperation between X-bond and H-bond. Crystal structure survey clearly demonstrates the significance of XWH bridges in stabilization of biomolecular conformations and in mediation of protein-protein, protein-nucleic acid, and receptor-ligand recognition and binding.(ⅳ) Halogen-ionic bridges in biomolecules. If considering that the pronouncedly charged halide anions are ubiquitous in the biological world, then it is interesting to ask whether the halogen-ionic bridges—this term is named by us to describe the interaction motif of a nonbonded halogen ion with two or more electrophiles simultaneously—commonly exist in biomolecules and how they contribute to the stability and specificity of biomolecular folding and binding? To address these problems, we herein present a particularly systematic investigation on the geometrical profile and energy landscape of halogen ions interacting with and bridging between polar and charged molecular moieties in small model systems and real crystal structures, by means of ab initio calculation, database survey, continuum electrostatic analysis, and hybrid QM/MM examination. All of these unequivocally demonstrate that this putative halide motif is broadly distributed in biomolecular systems (>6000) and can confer a substantial stabilization for the architecture of proteins and their complexes with nucleic acids and small ligands. This stabilization energy is estimated to be generally more than 100 kcal·mol-1 for gas-phase state or about 20 kcal·mol-1 for solution condition, which is much greater than that found in sophisticated water-mediated bridge (<10 kcal·mol-1) and salt bridge (～3.66 kcal·mol-1).(ⅴ) Contribution of halide motifs to protein stability. Halide anions are traditionally recognized as the structure maker and breaker of water to indirectly influence the physicochemical and biological properties of biomacromolecules immersing in electrolyte solution, but here we are more interested in whether they can be structured in protein interior, forming that we named halide motifs, to stabilize the protein architecture through direct noncovalent interactions with their context? In the current work, we present a systematical investigation on the energy components in 782 high-quality protein halide motifs retrieved from the Protein Data Bank (PDB), by means of the continuum electrostatic analysis coupled with non-electrostatic considerations as well as hybrid QM/MM examination. We find that most halide motifs (91.6%) in our dataset are substantially stabilizing and their average stabilization energy is significantly larger than that previously obtained for sophisticated protein salt bridges (-15.16 vs.-3.66 kcal·mol-1). Strikingly, non-electrostatic factors, especially the dispersion potential, rather than the electrostatic aspect, dominate the energetic profile of the pronouncedly charged halide motifs, since the expensive cost for electrostatic desolvation penalty requires to be paid off using the income receiving from the favorable Coulomb interactions during the motif formation. In addition, all the energy terms involved in halide motifs, regardless of their electrostatic or non-electrostatic nature, show to highly depend on the degree of motif's burial in protein, and the buried halide motifs are generally associated with a high stability.(vi) 2D depiction of interfacial NBMs for protein complexes. A program called the 2D-GraLab is described for automatically generating schematic representation of diverse NBMs across the protein binding interfaces. The input file of this program takes the standard PDB format, and the outputs are two-dimensional PostScript diagrams giving intuitive and informative description of the protein-protein interactions and their energetics properties, including hydrogen bond, salt bridge, van der Waals interaction, hydrophobic contact, p-p stacking, disulfide bond, desolvation effect, and loss of conformational entropy. To ensure the accuracy and reliability of determined interaction information, methods and standalone programs employed in the 2D-GraLab are all widely used in the chemistry and biology communities. The generated diagrams allow intuitive visualization of the interaction mode and binding specificity between two subunits in protein complexes, and by providing information on nonbonding energetics and geometrical characteristics, the program offers the possibility of comparing different protein binding profiles in a detailed, objective, and quantitative manner.