Cα-H···O=C hydrogen bonds contribute to the specificity of RGD cell-adhesion interactions
© Bella and Humphries; licensee BioMed Central Ltd. 2005
Received: 18 August 2004
Accepted: 14 February 2005
Published: 14 February 2005
The Arg-Gly-Asp (RGD) cell adhesion sequence occurs in several extracellular matrix molecules known to interact with integrin cell-surface receptors. Recently published crystal structures of the extracellular regions of two integrins in complex with peptides containing or mimicking the RGD sequence have identified the Arg and Asp residues as key specificity determinants for integrin recognition, through hydrogen bonding and metal coordination interactions. The central Gly residue also appears to be in close contact with the integrin surface in these structures.
When hydrogen atoms are modelled on the central Gly residue with standard stereochemistry, the interaction between this residue and a carbonyl group in the integrin surface shows all the hallmarks of Cα-H···O=C hydrogen bonding, as seen in the collagen triple helix and in many crystal structures of small organic molecules. Moreover, molecular dynamic simulations of the docking of RGD-containing fragments on integrin surfaces support the occurrence of these interactions. There appears to be an array of four weak and conventional hydrogen bonds lining up the RGD residues with main chain carbonyl groups in the integrin surface.
The occurrence of weak Cα-H···O=C hydrogen bonds in the RGD-integrin interaction highlights the importance of the conserved Gly residue in the RGD motif and its contribution to integrin-ligand binding specificity. Our analysis shows how weak hydrogen bonds may also play important biological roles by contributing to the specificity of macromolecular recognition.
The Arg-Gly-Asp (RGD) sequence is one of the most easily recognised motifs in molecular biology . Discovered in fibronectin in 1984 , this tripeptide appears to be conserved in the cell attachment sites of many proteins from the extracellular matrix (ECM). The later discovery that RGD is recognised by members of the integrin family of cell surface receptors , confirmed the central role of RGD and suggested that its presence in a protein sequence might be indicative of cell-adhesion functionality . Integrins are ubiquitously expressed heterodimer cell surface molecules that act as receptors for ECM molecules and other cell-surface adhesins. Through these cell-matrix and cell-cell interactions integrins control diverse cell functions such as adhesion, shape, growth, differentiation and mobility, and therefore contribute to important physiological processes such as development, immune responses and cancer . Integrins are complex signalling engines: their extracellular domains interact with the ECM while their cytoplasmic tails interact with the cytoskeleton and other intracellular signalling molecules. Current hypotheses suggest that conformational changes resulting from these interactions enable integrins to transmit signals across the membrane in both directions. Recent advances in the structural biology of several integrin domains and their interactions with ligands have begun to define possible working scenarios for the signalling mechanisms [6–13].
At first glance, two interactions consistently seen in these crystal structures appear to be key in defining the specific molecular recognition between the RGD sequence in an integrin ligand and the surface of its integrin receptor: the Asp residue of the RGD triad completes the coordination of a divalent metal ion bound to the β subunit, while the Arg side chain extends in the opposite direction to form salt-bridge hydrogen bonds with one or two Asp residues in the α subunit. These two specific interactions or their equivalent are seen both in the c RGD-αVβ3 structure and in the structures of αIIbβ3 in complex with ligand-mimetics (Figure 1). There are no significant hydrophobic "pockets" or exosites contributing to the binding specificity. For example, a large fraction of the c RGD peptide does not make any contact with the αVβ3 integrin surface (Figure 1a). In the broader context of RGD-containing ligands and their integrin receptors, it would seem that these interactions are mainly electrostatic and that the two charged residues in the RGD sequence are necessary and sufficient for attachment .
So-called "weak" hydrogen bonds, such as those between carbon and oxygen atoms, have been traditionally neglected in descriptions of three-dimensional structures of macromolecules. Yet, C-H···O hydrogen bonds are ubiquitous in protein structures: virtually every conventional N-H···O=C hydrogen bond in every β-sheet in every determined protein structure carries a companion Cα-H···O=C interaction [16, 17]. This applies to both parallel and antiparallel β-sheets, and exactly the same topology is also observed in the collagen triple helix . For collagen and the β-sheet structures, the occurrence of Cα-H···O=C interactions is indicative of a very tight fit between the molecules involved, a close-packed structure in which all groups participate in some form of hydrogen bonding interaction.
How important are Cα-H···O=C and other weak hydrogen bonds in shaping the three-dimensional structure of proteins and macromolecular complexes? The subject has stimulated considerable debate (see  and  for reviews), although theoretical studies leave no doubt about the cohesive nature of these interactions [20–23]. With a strength approximately one-half of that from conventional hydrogen bonds, it seems reasonable to assume that the large numbers of weak hydrogen bonds detected in proteins may contribute to their stability. Furthermore, several biochemical functions have been linked to specific C-H···O hydrogen bonds, where position is more important that numbers. One example is the Gly-X-X-X-Gly motif, known to favour helix-helix interactions in membrane  and soluble proteins via position-specific Cα-H···O=C hydrogen bonds. Another is the proposed role of C-H···O hydrogen bonds from cytosine and thymine bases to amino acid side chains during DNA-protein recognition . Weak C-H···O hydrogen bonds have also been surveyed at protein-protein interfaces , and have been reported to play specific roles in catalysis , and in substrate and inhibitor recognition [29–32]. Recently, a server to identify weak hydrogen bonding interactions in protein structures has been made publicly available .
The functional occurrence of weak C-H···O hydrogen bonds in protein-ligand, protein-protein, and protein-DNA recognition suggests that their presence should be examined in detail in the structures of macromolecules with biomedical or biotechnological interest. Their potential should not be neglected in rational drug design approaches . With this in mind, we present here an analysis of possible Gly-Cα-H···O=C interactions between RGD motifs and the RGD-binding sites from the αVβ3 and αIIbβ3 crystal structures. We conclude that the mutual geometry of the interaction is consistent with Cα-H···O=C hydrogen bonding. We discuss the implications of these hydrogen bonds for the cell adhesion interactions between integrins and their RGD-containing ligands.
Results and discussion
Interatomic distances and angles for proposed and observed Gly-Cα-Hα···O hydrogen bonding interactions.
PDB structures *
CSD Average values †
An obvious caveat to this analysis comes from the moderate resolution of the c RGD-αVβ3 and EFB-αIIbβ3 crystal structures (3.2 Å and 2.9 Å respectively). Positional errors inevitable at that resolution may affect the precision of the fitting of the c RGD and EFB peptides and the accuracy of the hydrogen bonding geometries for both weak and strong hydrogen bonds. For example, a close look at the salt-bridge interactions between the Arg guanidinium group from the c RGD peptide and two Asp side chains on the αV integrin surface (Asp150 and Asp218), shows less than "ideal" hydrogen bonding orientation, especially for Asp150 (not shown). Yet, the accumulated knowledge of hydrogen bonding geometries in high-resolution crystal structures and their significant variability leaves no doubt about the existence of these strong hydrogen bonds and their contribution to the specificity of binding.
Gly-Cα-H···O=C contact distances (Å) for the lowest-energy model in each set of molecular docking simulations. Underlined distances correspond to Hα atoms in hydrogen bonding orientation (angle Cα-H···O=C > 90°).
How important are these weak C-H···O hydrogen bonds in stabilising the c RGD-αVβ3 and EFB-αIIbβ3 complexes? A quantitative analysis of C-H···O hydrogen bonding at protein-protein interfaces has shown that they have an important contribution to the association and stability of protein complexes, accounting for about one third of the total hydrogen bonding interaction energy . In fact, some of the hydrophobic or van der Waals interactions usually invoked to explain stabilising close contacts between molecules can be described better as weak C-H···O hydrogen bonds. These occupy a middle ground between the highly directional, conventional hydrogen bonds, and the directionless van der Waals interactions .
It is clear from the c RGD-αVβ3 and EFB-αIIbβ3 structures that any side chain other than Gly in the RGD triad would not allow it to fit snugly within the integrin binding site, with the resulting weakening of hydrogen bonding and van der Waals interactions. Furthermore the main chain conformation for the central Gly residue in the c RGD-αVβ3 structure falls in a region of the Ramachandran map that is not allowed to any L-amino acid residue. Thus, Gly residues at the centre of the RGD motif are essential for being small, for being able to adopt specific main chain conformations, and for being able to interact closely with the integrin surface via Cα-H···O=C hydrogen bonds. All three characteristics contribute to the integrin-binding specificity of Gly residues at the centre of RGD motifs.
Inasmuch as the c RGD-αVβ3 and EFB-αIIbβ3 structures remain valid models for the structural basis of integrin-RGD ligand-binding specificity, it is reasonable to assume that the weak Cα/β-H···O=C hydrogen bonds depicted in Figure 8 will also occur in RGD-based cell-adhesion interactions. A special feature of the integrin surface at the RGD-binding site is the presence of two main chain carbonyl groups exposed to the solvent in the β3 subunit: Asn215 and Arg216. In absence of ligands these groups will probably interact with water molecules through conventional hydrogen bonding interactions (as seen for example in the crystal structure of the cacodylate-bound form of αIIbβ3, PDB accession code 1TXV ). Upon ligand binding, the RGD residues will displace these waters and place one amide and two methylene groups in hydrogen bonding position to carbonyl groups, increasing the specificity of the RGD-integrin interaction through multipoint recognition (Figure 8). This strategy will obviously be exploited by many competitive inhibitors for the integrin RGD-binding site. For example it is possible to substitute the weaker Cα-H donors from the Gly residue by a conventional N-H group (Figure 7c). This strategy has been exploited already in the design of aza-peptide and azacarba-peptide RGD mimetics [37–39], several of them with nanomolar activity. Molecular modelling of the interaction of these peptides with αVβ3 and αVβ5 RGD binding sites predicts the hydrogen bonding topology shown in Figure 7c. It is interesting to notice that even in the absence of a conventional hydrogen bonding donor, the carbonyl group Arg216 in the β3 subunit still may be acceptor for weak hydrogen bonds. In the crystal structure of αIIbβ3 in complex with tirofiban , a non-peptidomimetic inhibitor derived from L-tyrosine, the Cδ1 atom from the substituted Tyr ring is some 3.01 Å away from the carbonyl oxygen of the very same Arg216. If a hydrogen atom is built with standard geometry on Cδ1, the calculated Hδ1···O distance is 2.01 Å and the Cδ1-Hδ1···O angle is 172°, again hydrogen bonding-like metrics. How should this Cδ1···O=C contact be called? We think that a description in terms of weak C-H···O hydrogen bonding is in this case more accurate than referring to this interaction as simply hydrophobic.
We have analysed in detail recently published structural data on the interaction between the extracellular regions of two integrins and peptides containing or mimicking the RGD sequence [8, 12]. From this analysis we conclude that Cα-H···O=C hydrogen bonds from the central Gly residue also contribute to the specificity of binding. Weak hydrogen bonds are traditionally overlooked when describing protein structures, although they probably contribute to their stability. We think that our analysis provides one of the most interesting examples of C-H···O hydrogen bonds playing an important biological role, and may contribute to reverse the current trend of neglect of these interactions. In a recent paper, Sarkhel and Desiraju suggest that Nature may take advantage of the weaker C-H···O hydrogen bonds to optimise the efficiency of protein-ligand interactions, with a larger number of interactions coming into play even at the expense of the strength of the individual interactions . By using more interactions, they suggest, specificity of recognition is increased, and because individual interactions are weaker, reversibility is possible. Our analysis of the interaction between the c RGD and EFB peptides and the αVβ3 and αIIbβ3 integrin surfaces would seem to corroborate this suggestion.
Integrin binding sites and hydrogen building
The following crystal structure coordinates were downloaded from the Protein Data Bank : αVβ3 integrin in complex with a cyclic RGD peptide (c RGD), PDB accession code 1L5G ; αIIbβ3 integrin structure at 2.7 Å resolution, PDB accession code 1TXV ; αIIbβ3 in complex with eptifibatide (EFB), PDB accession code 1TY6 ; αIIbβ3 in complex with tirofiban, PDB accession code 1TY5. Models for integrin RGD-binding sites on αVβ3 and αIIbβ3 were obtained by selecting coordinates from integrin residues within 10 Å from the bound peptides. For the αIIbβ3 binding site, coordinates of the corresponding residues in the 1TXV structure were used, as this crystal structure has a better resolution. Coordinates for metal ions and structural waters present in the RGD-binding sites but not interfering with the binding of c RGD or EFB were also maintained. Hydrogen atoms were built with standard stereochemistry for the c RGD and EFB peptides and for the integrin RGD-binding sites as defined above, using the program REDUCE . For the purpose of the analysis presented here all hydrogen atoms discussed in this paper could be positioned with satisfactory accuracy and predictable orientation.
Molecular docking calculations
For the molecular docking calculations, conformational models for RGD and VTGRGDSPAS peptides were obtained from the NMR structures of the adhesion domain in fibronectin . Ten conformational models were used for each peptide. Each model was first manually docked approximately into the coordinates of the binding sites of αVβ3 and αIIbβ3 integrins, using the c RGD-αVβ3 and EFB-αIIbβ3 structures for guidance. Then each docked model was pulled away to about 10 Å from the integrin surfaces, and was docked back into the integrin binding site via molecular dynamics (MD) simulations using the program CNS . Five simulations were run for each model, to a total of 50 MD simulations for each peptide-integrin pairing. A set of distance restraints was applied to the docking MD simulations, as observed on the c RGD-αVβ3 and EFB-αIIbβ3 structures. The side chain of the Asp residue group was restrained to coordinate the bound metal ion in the RGD-binding sites and to receive a hydrogen bond from the amide group of Asn215, in the β3 subunit. The side chain of the Arg residue was restrained to form hydrogen bonds with residues Asp150 and Asp218 on the αV subunit or residue Asp224 on the αIIb subunit. Additional restraints were imposed in the MD simulations with the VTGRGDSPAS peptide: the ring of Pro172 was restrained to hydrophobic contact with the side chain of Lys125, in the β3 subunit, and the Cα atoms of the N- and C-terminal residues in the peptide model were restrained not to separate more than 5 Å from each other. The coordinates of the integrin binding sites were kept fixed in all the simulations, and only the peptides were allowed to refine by restrained MD and energy minimisation. All molecular models were analysed with the program CHAIN  in a Silicon Graphics workstation.
Analysis of hydrogen bonding geometry in crystal structures of organic molecules
List of abbreviations
- c RGD:
cyclic pentapeptide with sequence Arg-Gly-Asp-D-Phe-N(Me)-Val
Protein Data Bank
Cambridge Structural Database
We acknowledge the authors of the original paper on the c RGD-αVβ3 structure, Jian-Ping Xiong, Thilo Stehle and M. Amin Arnaout for useful criticisms to an early version of this manuscript.
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