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J Biol Chem, Vol. 274, Issue 35, 24906-24913, August 27, 1999

Trench-shaped Binding Sites Promote Multiple Classes of Interactions between Collagen and the Adherence Receptors, ₁₁ Integrin and Staphylococcus aureus Cna MSCRAMM^*

Rebecca L. Rich^§, Champion C. S. Deivanayagam^¶, Rick T. Owens, Michael Carson^¶, Agneta Höök, Dwight Moore^¶, Vivian W.-C. Yang, Sthanam, V. L. Narayana^¶, and Magnus Höök

From the  Center for Extracellular Matrix Biology, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas 77030 and the ^¶ Center for Macromolecular Crystallography, University of Alabama at Birmingham, Birmingham, Alabama 35294

	ABSTRACT

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS DISCUSSION REFERENCES

Most mammalian cells and some pathogenic bacteria are capable of adhering to collagenous substrates in processes mediated by specific cell surface adherence molecules. Crystal structures of collagen-binding regions of the human integrin ₂₁ and a Staphylococcus aureus adhesin reveal a "trench" on the surface of both of these proteins. This trench can accommodate a collagen triple-helical structure and presumably represents the ligand-binding site (Emsley, J., King, S. L., Bergelson, J. M., and Liddington, R. C. (1997) J. Biol. Chem. 272, 28512-28517; Symersky, J., Patti, J. M., Carson, M., House-Pompeo, K., Teale, M., Moore, D., Jin, L., Schneider, A., DeLucas, L. J., Höök, M., and Narayana, S. V. L. (1997) Nat. Struct. Biol. 4, 833-838). We report here the crystal structure of the  subunit I domain from the ₁₁ integrin. This collagen-binding protein also contains a trench on one face in which the collagen triple helix may be docked. Furthermore, we compare the collagen-binding mechanisms of the human ₁ integrin I domain and the A domain from the S. aureus collagen adhesin, Cna. Although the S. aureus and human proteins have unrelated amino acid sequences, secondary structure composition, and cation requirements for effective ligand binding, both proteins bind at multiple sites within one collagen molecule, with the sites in collagen varying in their affinity for the adherence molecule. We propose that (i) these evolutionarily dissimilar adherence proteins recognize collagen via similar mechanisms, (ii) the multisite, multiclass protein/ligand interactions observed in these two systems result from a binding-site trench, and (iii) this unusual binding mechanism may be thematic for proteins binding extended, rigid ligands that contain repeating structural motifs.

	INTRODUCTION

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS DISCUSSION REFERENCES

Collagen polypeptides are largely composed of repeats of the GPX tripeptide and associate to form triple-helical monomers. These monomers combine into macroscopic fibers. Prokaryotic and eukaryotic cells bind collagen via receptors on their cell surfaces (1-6). We now hypothesize that to accommodate such an unusually shaped ligand, the collagen-binding surface proteins of these cells must adopt an atypical binding-site structure.

Bacterial pathogens utilize this interaction as a means of adherence to collagenous host tissues. Some Staphylococcus aureus strains express an adhesin, Cna,¹ of the MSCRAMM class that binds collagen (1, 7-13). Cna from S. aureus FDA 574 is depicted in Fig. 1a: it contains two major domains, A and B, in addition to features characteristic of cell-surface proteins on Gram-positive bacteria (11). The collagen-binding site has been localized within the Cna A domain (12). Binding analyses demonstrate that (i) a synthetic peptide mimicking a short sequence of the A domain can inhibit collagen binding to S. aureus (8); (ii) the A domain/collagen interaction involves more than one affinity class and multiple sites of contact within a single collagen molecule (8, 10); and (iii) the B domain does not alter the collagen binding ability of the A domain (13).

View larger version (11K): [in this window] [in a new window]   Fig. 1.   a, schematic of the S. aureus FDA 574 collagen-binding MSCRAMM, Cna. The putative signal peptide (S), collagen-binding domain (A), domain of three repeat units (B1, B2, and B3), cell wall domain (W), membrane-spanning domain (M), and charged C-terminal domain (C) are indicated. b, recombinant protein used in this study that mimics the A domain of the MSCRAMM, with the inclusive residues indicated. The structure of a recombinant protein that encompasses the central region (residues 151-318) of the Cna A domain has been solved crystallographically (7). c, schematic of the human 1 integrin subunit. The putative signal peptide (S), collagen-binding inserted domain (I), membrane-spanning domain (M), and cytoplasmic C-terminal domain (C) are indicated. The numbering of residues corresponds to that published by Briesewitz et al. (23). d, recombinant protein used in this study that mimics the 1 integrin I domain, with the inclusive residues indicated.

The crystal structure of a truncated form of the Cna A domain reveals a binding-site "trench" on one face of the protein. In molecular modeling studies, this trench was found to accommodate a triple-helical peptide that mimics the collagen structure. Symersky et al. (7) noted that this trench complemented well the structure of a collagen triple helix and binding studies of site-specific mutants of the S. aureus Cna truncate revealed that (i) no single residue or area within the trench was responsible for collagen binding, but rather, a number of contacts contributed to the protein/collagen interaction and (ii) this binding-domain truncate bound to multiple sites along a collagen molecule. The affinity of Cna for an individual site within collagen may be the consequence of the number of "good" and "bad" contacts within the binding trench.

Binding of eukaryotic cells to collagen serves not only as a mechanism of tissue adherence, but also may induce a complex signaling cascade in the cell. Attachment of eukaryotic cells to the extracellular matrix is primarily mediated by integrins. The integrins are transmembrane heterodimeric proteins that direct cell-cell and cell-matrix interactions and are found on most mammalian cells. To date, several integrins, including ₁₁, ₂₁, ₃₁, ₉₁, ₁₀₁, and _M2, have been reported to mediate cellular adherence to collagen (14-18). Of these, ₁₁ and ₂₁ are apparently the primary collagen-binding integrins. The ₁, ₂, and ₁₀ subunits each contain an "inserted" (I) domain near the N terminus (Fig. 1c). The I domains have been shown to contain a ligand-binding site and a MIDAS motif, which needs to be occupied by an appropriate cation for effective ligand binding by the integrin. Recombinant proteins duplicating these small (approximately 200 amino acids) I domain polypeptide segments effectively bind collagen, presumably it is these regions that are responsible for the integrins' binding to collagens.

A binding site-trench in the I domain of the human ₂₁ integrin was also suggested by the crystal structure of the ₂ integrin I domain. Molecular modeling of this protein complexed with a collagen triple-helical peptide (19) demonstrated favorable ligand docking encompassing about 10 residues of the collagen sequence within a trench spanning the MIDAS motif. From this work Liddington and co-workers (19) suggested that the divalent cation is involved in direct ligand binding via coordination of an amino acid residue (most probably, glutamate) within the collagen molecule.

Our previous work has shown that the full-length A domain of the S. aureus Cna protein binds collagen more efficiently than the binding-domain truncate does (7, 8, 10, 12). The causes of this behavior have not been investigated to date. In addition, detailed analysis of collagen-binding activity of the human ₁ integrin I domain, which binds Type I collagen more efficiently than the ₂ integrin I domain does (14), has not been performed. The questions we seek to answer here include: (a) can the gross structure of I domains and the detailed topology of their MIDAS-centered binding site be determined from modeling experiments based on known structures? (b) Is a trench similar to that found on Cna the binding-site motif employed by the ₁₁ integrin? (c) Does the ₁ integrin I domain bind to a single or multiple class(es) of sites within a collagen macromolecule? To address these questions, we compare the structures and collagen-binding characteristics of the S. aureus Cna A and the human ₁ integrin I domains.

	EXPERIMENTAL PROCEDURES

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS DISCUSSION REFERENCES

Construction of Expression Plasmids-- The expression plasmid pQE-₁I was constructed based on the vector pQE-30 (Qiagen Inc., Chatsworth, CA) using standard molecular biology protocols (20, 21). cDNA encoding the I domain of the human ₁ integrin was obtained by polymerase chain reaction using a human hepatoma cDNA library as a template and the oligonucleotide primers, 5'-CGGATCCCCCACATTTCAAGTCGTGAAT-3' and 5'-GCTGCAGTCATATTCTTTCTCCCAGAGTTTT-3'. The amplified gene fragment was digested with the BamHI and the PstI restriction endonucleases, purified by agarose gel electrophoresis (Geneclean kit, ISC BioExpress), and ligated into the vector pQE-30 (previously linearized by digestion with the same endonucleases). Ligation mixtures were subsequently transformed into Escherichia coli strain JM101.

Plasmids from isolated transformants were analyzed by restriction digestions and automated DNA sequencing analysis (Molecular Genetics Core Facility, University of Texas Medical School, Houston, TX) to confirm the expected open reading frame. The ₁ integrin I domain sequence examined here corresponds to the sequence published by Briesewitz et al. (22) except for nucleotide substitutions resulting in Lys¹⁷⁴  Glu and Thr²³⁰  Ile.

The ₁ integrin I domain cDNA was also cloned into the glutathione S-transferase expression vector pGEX-KG (23). Recombinant GST-₁I fusion proteins were purified by chromatography over glutathione-agarose and cleaved by digestion with thrombin as described in Ref. 23.

The construction of a plasmid for the expression of the Cna A domain has been previously described and consists of the gene segment encoding the S. aureus collagen MSCRAMM amino acids Ala³⁰-Glu⁵³¹ cloned between the BamHI and SalI restriction sites of the pQE-30 expression vector (13).

Expression and Purification of Recombinant Proteins-- Large-scale preparations of recombinant protein were prepared and purified as follows. Overnight cultures (40 ml) of stationary-phase bacteria were used to inoculate 1 liter of Luria broth and the cells were allowed to grow for 2.5 h at 37 °C (OD_{600 nm} ~ 0.6). Protein expression was induced by addition of isopropyl--D-thiogalactopyranoside to a final concentration of 0.2 mM and the culture was incubated for an additional 3 h at 37 °C. Bacteria were then collected by centrifugation and resuspended in a minimal volume of 4 mM Tris, 100 mM NaCl, pH 7.9, before being frozen at 80 °C.

Induced bacteria were thawed and passed through a French press (11,000 p.s.i) twice to lyse the cells. Insoluble debris was removed by centrifugation at 14,000 rpm for 20 min and the supernatant was filtered through a 0.45 µM membrane. Imidazole was added to a final concentration of 6.67 mM and the lysates were applied to a 10 × 100-mm column of Ni²⁺-charged iminodiacetic acid/Sepharose. The column was washed with 50 ml of 4 mM Tris, 100 mM NaCl, 5 mM imidazole, pH 7.9, and bound protein eluted with a 200-ml linear gradient of 0-200 mM imidazole in 4 mM Tris, 100 mM NaCl, pH 7.9. Fractions containing the desired protein, as determined by SDS-PAGE, were pooled and concentrated using an Amicon ultrafiltration system. The isolated proteins were essentially pure and appeared as single bands on an overloaded SDS-PAGE gel. The isolated recombinant proteins were dialyzed against 3 × 1-liter changes of 1 mM EDTA, 50 mM HEPES, 150 mM NaCl, pH 7.4, to remove all cations, and then dialyzed against 3 × 1-liter changes of 50 mM HEPES, 150 mM NaCl, pH 7.4, to remove EDTA. All buffers for the ₁ integrin I domain protein also contained 5 mM -mercaptoethanol; the justification for adding a reducing agent to this sample solution is discussed below.

During our initial analyses of the recombinant His₆ tag ₁ integrin I domain protein, we observed gradual precipitation of the protein within several days post-purification when the solution was kept at 4 °C. The presence of dimeric and higher-order multimers of the recombinant ₁ integrin I domain protein in the solution was apparent by SDS-PAGE (data not shown). Addition of 5 mM -mercaptoethanol delayed the protein precipitation for several weeks. All studies discussed here are the analyses of recombinant ₁ integrin I domain within 2 weeks of expression and purification and in buffer containing 5 mM -mercaptoethanol, unless noted otherwise. The far-UV CD spectra of freshly purified ₁ integrin I domain in the presence and absence of 5 mM -mercaptoethanol were identical (data not shown). Also, the SPR sensorgrams of freshly purified ₁ integrin I domain flowed over immobilized collagen in the presence and absence of 5 mM -mercaptoethanol are identical (data not shown). The sensorgrams measured over a period of days for the ₁ integrin I domain protein flowed over collagen in buffer containing the reducing agent remain unchanged; repeating this experiment in the absence of the reducing agent, however, revealed the gradual increase in association and decrease in dissociation of the protein-collagen complex over time. After approximately 2 weeks, the sensorgrams for the ₁ integrin I domain in the absence of -mercaptoethanol duplicated those published previously (24). The increase in apparent affinity of the ₁ integrin I domain protein after storage for collagen may be due to the contribution of multiple I domain elements in the protein aggregate binding at one location within the collagen macromolecule. The addition of the reducing agent is therefore necessary to preserve the monomeric state of the recombinant protein and does not alter its structure or function.

Surface Plasmon Resonance Spectroscopy (SPR)-- Analyses were performed using the BIAcore system as described in Ref. 13, with 5 mM -mercaptoethanol and 0.25% octyl--D-glucopyranoside included in the buffer for ₁ integrin I domain analyses. No mass transport effects were observed in these measurements. The data for the construction of the Scatchard plots was obtained from the equilibrium portion of the SPR sensorgrams and analyzed as described.²

Enzyme-linked Immunosorbent Assays-- Assays were performed as described in Ref. 13. For wells in which the buffer included MgCl₂, all washes and incubations were performed in the presence of 1 mM MgCl₂.

Equilibrium Dialysis-- The equilibrium dialysis experiments were carried out in a double acrylic microdialysis module (Hoffer, San Francisco, CA) as described by Yang et al. (26). Aliquots of 150 µl of thrombin-cleaved ₁ integrin I domain protein in 10 mM Tris-HCl, 150 mM NaCl, pH 7.0, were added to the inner compartments. The same volume of 0-5 mM ultrapure MgCl₂ (Sigma) in 10 mM Tris-HCl, 150 mM NaCl, pH 7.0, was added to the outer compartments. After incubation, the concentration of Mg²⁺ in the outer compartments was determined using a Mg²⁺ detection kit (Sigma). An aliquot of 10 µl from each outer compartment and 100 µl of each kit component were mixed. The reaction was immediate and sample absorbance was measured at 525 nm using a Molecular Devices plate-reading visible spectrophotometer. Calculation of the Mg²⁺-complexed ₁ integrin I domain fraction was performed as described in Ref. 27.

Crystallization Conditions-- Recombinant His₆ tag ₁ integrin I domain protein in 10 mM HEPES, 200 mM NaCl, 5 mM -mercaptoethanol, pH 7.0, was further purified using a 300 × 7.5 Bio-sil-TSK125 gel-filtration column. The protein solution was then concentrated to 20 mg/ml using an Amicon ultrafiltration system and dialyzed against 10 mM HEPES, 200 mM NaCl, 5 mM MgCl₂, 5 mM -mercaptoethanol, pH 7.0. Crystallization trials were set up using the hanging-drop vapor-diffusion method. High quality crystals were obtained from a droplet made by mixing 2 µl of protein solution and 2 µl of 31% PEG2000, 50 mM HEPES, 200 mM NaCl, 5 mM MgCl₂, 5 mM -mercaptoethanol, pH 7.5 (solution A), and equilibrating it against 1 ml of solution A. Crystals were prism-shaped, with the largest having dimensions of 0.3 × 0.2 × 0.1 mm.

Diffraction Data Collection-- Crystals were soaked in a synthetic mother liquor containing 15% glycerol as cryoprotectant and subsequently cryo-cooled using the Oxford cryosystem (Oxford Cryosystems, Oxford, United Kingdom). X-ray diffraction data were collected to 2.0-Å resolution using a RAXIS IV imaging plate system mounted on a RIGAKU RU-HBR rotating-anode generator (50 kV, 100 mA). A complete native data set was collected over 99 frames (oscillation of 2°, exposure time of 20 min, and crystal-to-image plate distance of 150 mm). The frames were indexed and scaled using DENZO and SCALEPACK (28). The scaled data had 99% completeness, where 71.5% of the data in the last shell was above 3 level with an R_sym value of 6.1%. The calculated Matthews coefficient, V_m, was 1.9 Å³ Da¹, suggesting two molecules exist in the asymmetric unit with an estimated solvent content of 35%. Data collection details are presented in Table I.

Structure Determination-- The crystal structure of the recombinant His₆ tag ₁ integrin I domain was determined by the molecular replacement method using the CCP4 integrated version of AmoRe (29, 30). We used the molecular model of the human complement factor B middle domain as the initial molecular replacement unit (31). The C-terminal helix and all the connecting loops were removed from the starting molecular replacement search model, which had 109 residues. Repeated rounds of rigid-body refinement and checking for acceptable crystal packing helped us to identify two solutions having high correlation factors and the lowest R-factors (0.62 and 41%, respectively, for 8.0-4.5-Å resolution data). The two molecules in the asymmetric unit were not related by an exact 2-fold non-crystallographic axis. Next, the side chains of the correctly positioned model were replaced with the corresponding homologous side chains of the ₁ integrin I domain. Rigid body refinement to 3.0-Å resolution, where the individual secondary structural elements were treated as independent units in XPLOR (32), resulted in an R-factor of 39% and R_free (calculated on 10% of the reflections) of 44%. Several rounds of manual refitting to 2F_o  F_c maps using the graphics program "O" (33) and positional refinement in XPLOR were done while extending the resolution to 2.5 Å in small increments. At this stage, the R-factor was 31%, R_free value was 41%, and a 2F_o  F_c map calculated had visible density for the missing C-terminal helix and for most of the deleted loop regions. At this juncture, the resolution was extended to the final 2.0 Å and two rounds of simulated annealing and model rebuilding led to the tracing of the complete C-terminal end. After one refinement cycle of individual B-factors (r = 26% and R_free = 30%), water molecules were added to the model by picking the peaks above 3 level in a calculated (F_o  F_c) difference map. Two of these water molecules were identified as metal ions based on their bonding geometry. The OOPS program (34) was used throughout the cycles of rebuilding for quality checks. The cross-validated maximum likelihood refinements were performed with CNS-0.4 (35). Bulk solvent corrections were applied in the last few cycles of refinement. The final refinement yielded 229 water molecules, two Mg²⁺ ions, 3008 non-hydrogen atoms, and four cis-prolines. For 24,537 reflections (out of 24,807 reflections) between 100.0 and 2.0-Å resolution, the final R-factor was 20.6% and R_free was 24.3%. The final structure was checked using PROCHECK (36, 37) and WHAT_CHECK (38). The complete refinement statistics are presented in Table I. The ₁ integrin I domain structure was aligned with other integrin I domains and von Willebrand factor A3 domain crystal structures taken from the protein data bank (1AO3 for von Willebrand factor, 1AOX for the ₂ integrin, 1JLM for the _M integrin, and 1ZON for the _L integrin) using the program MODELER (39).

Non-crystallographic constraints were removed when refining the models at 2.0-Å resolution. The two molecules present in the asymmetric unit were refined independently and the root mean square deviation between molecules A and B for main chain atoms was 0.23 Å. The C-terminal ends were identical, while two extra residues could be traced at the N-terminal end of molecule A. Both molecules were almost identical, especially around the metal-binding site. Solvent molecules around the MIDAS site were conserved between the two non-crystallographically related ₁ integrin I domain molecules in the asymmetric unit.

Docking Search-- The collagen peptide mimic used in the docking simulations was similar to the one used in the studies of S. aureus Cna (7). It was obtained from the Protein Data Bank crystal structure entry 1cag (40) and shortened to the C-terminal [(G-P-P*)₄]₃. The docking target was the molecule B in the refined crystal structure of the ₁ integrin I domain, as molecule B had the lower average temperature factors of the two molecules present in the asymmetric unit. Docking was performed as a full six-dimensional search using the matching cubes algorithm (41) implemented in the program SoftDock.³ Of the eight best-fit solutions, four showed the collagen triple-helical peptide bound in the trench on the MIDAS face. The other four solutions were eliminated because the peptide mimic bound at the face opposite the MIDAS, where the I domain is proposed to interface with the ₁ integrin repeat units (42). The four solutions selected were superimposable, except that each was translated along the triple helical axis by one (GPP*) unit. The one solution that extended symmetrically across the MIDAS was selected for energy-minimization in XPLOR.

	RESULTS

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS DISCUSSION REFERENCES

Recombinant ₁ Integrin I Domain Protein Adopts a Dinucleotide-binding Fold and Contains an Active MIDAS Motif-- Resolution of the crystallographic data of the ₁ integrin I domain revealed that this protein adopts a dinucleotide-binding (Rossman) fold, in which a central core of five parallel -strands and one smaller anti-parallel -strand are encased in seven -helices (Fig. 2a). This general structural organization has been observed in the crystal structures of I domains from other integrin -subunits and I domain-like segments of von Willebrand factor and complement factor B (43-50). The order of the -strands, beginning at the N terminus, is ₁-₆. Five (₁-₃-₄-₆-₇) helices are parallel to one another and anti-parallel to the neighboring -strands. The ₂ helix is parallel to the ₂ strand where its N-terminal end is connected to the C-terminal end of the ₁-strand through the short anti-parallel ₃-strand. The short, two-turn ₅ helix protrudes above the molecule in the carboxyl end of the central -sheet.

View larger version (43K): [in this window] [in a new window]   Fig. 2.   a, ribbon diagram of the human 1 integrin I domain. -Sheets are shown in green, -helices in cyan, 310-helices in navy, and loops in orange; the Mg2+ ion is depicted as a orange sphere. b, structure of the MIDAS and coordination of Mg2+. The numbering of residues follows that given for the 1 integrin I domain in Ref. 19. The backbone of the molecule is shown in gray, with specific carbon atoms in green and oxygen atoms in red. The cation (M) is shown in orange and the ion-coordinated water (W) molecules are depicted as magenta spheres. c, space-filled depiction of a collagen triple-helical mimic docked in the MIDAS-centered trench of the 1 integrin I domain.

A MIDAS motif composed of Asp¹⁵⁴, Ser¹⁵⁶, Ser¹⁵⁸, Thr²²⁴, and Asp²⁵⁷ (the numbering of residues in the mature protein follows that given by Emsley et al. (19)) exists in the ₁ integrin I domain (Fig. 2b). The crystal structure of the ₁ integrin I domain protein in the presence of 5 mM MgCl₂ revealed that Mg²⁺ is octahedrally coordinated to Ser¹⁵⁶, Ser¹⁵⁸, and Asp²⁵⁷, and three water molecules with distances of 2.1 ± 0.1 Å. Asp¹⁵⁴ and Thr²²⁴ of the ₁ integrin I domain are hydrogen-bonded to the Mg²⁺ through one of the coordinated water molecules. The MIDAS residues are conserved between the ₁ and ₂ integrin I domains.

A Binding Site Trench in the ₁ Integrin I Domain Accommodates a Triple-helical Collagen Peptide Mimic-- The ₁ integrin I domain contains a structural feature found in the ₂ integrin I domain but not observed in the other I domains: the short, two-turn ₅ helix (denoted as the C-helix in the ₂ integrin I domain (19)), which defines one side of the putative ligand-binding surface. In the ₁ integrin I domain, this helix is composed of residues 287-291 (GSYNR) and protrudes out from the main body of the I domain. This ₅ helix is a major determinant in the formation of a MIDAS-centered trench of the ₁ integrin I domain (Fig. 2c). Molecular surface calculations of the ₁ integrin I domain using GRASP (51) and RIBBONS (52) yielded trench dimensions of approximately 8 Å deep, 30-35 Å long, and 18 Å wide. Such a trench also exists on the surface of the ₂ integrin I domain (19). This trench is reported to be 25 Å long and 20 Å wide and is also centered around the cation.

The trench in the ₁ integrin I domain protein is composed largely of polar residues (Ser¹⁵⁶, Asn¹⁵⁷, Ser¹⁵⁸, Tyr¹⁶⁰, Ser¹⁶⁴, Gln²²³, Thr²²⁴, Asn²⁶³, Ser²⁸⁸, and Tyr²⁸⁹), with a few hydrophobic (Leu²⁹⁴), acidic (Asp²⁵⁷ and Glu²⁵⁹), and basic (Arg²²², His²⁶¹, His²⁶⁴, Arg²⁹¹, and Lys²⁹⁸) residues possibly participating in ligand binding (Fig. 3a). The Mg²⁺ ion is located in the deep central trench pocket, which is lined with all four types of residues. From Fig. 3a, it is apparent that the cation contributes a small percentage of the surface area of the trench and is potentially involved in ligand capture. Similar results were reported for the cation in the ₂ integrin I domain trench (19).

View larger version (127K): [in this window] [in a new window]   Fig. 3.   Comparison of residues that line the collagen-binding trench. a, the 1 integrin I domain (Mg2+ shown in navy); and b, Cna 151-318. Docking of a triple-helical collagen peptide mimic in the trench of (c) 1 integrin I domain and (d) Cna 151-318. Hydrophobic residues are depicted in green, acidic in red, basic in blue, and polar in purple. The cation is drawn larger than its proportional atomic radius for clarity of the figure.

Complex Protein/Collagen Interactions May Result from Ligand Binding in the Trenches of the ₁ Integrin I Domain and S. aureus Cna-- A bacterial adhesin, Cna from S. aureus, also binds collagen (1, 7-13). In crystallographic studies, collagen docked well in a trench-shaped binding site on one face of its minimal binding domain, Cna 151-318 (7). The trench in Cna 151-318 is 5 Å deep, 25 Å long, and 15 Å wide (7), and encompasses three collagen GPX repeats, as do the trenches in the I domains of the ₁ and ₂ integrin I domains, but its topology and residue distribution are unlike that of the I domains. The trench in Cna 151-318 is dominated by polar residues, with very few acidic, basic, and hydrophobic residues possibly participating in collagen binding (Fig. 3b). This trench contains two polar pockets and one hydrophobic/polar pocket that may be amenable to the binding of bulky collagen side chains (Fig. 3d).

Divalent Cations Enhance the Collagen Binding of Human ₁ Integrin I Domain, but Not That of the S. aureus Cna A Domain-- SPR changes were used to analyze the binding of recombinant forms of the ₁ integrin I and S. aureus A domains to immobilized Type I collagen. In both panels of Fig. 4, the protein/collagen association occurred between 140 and 375 s, with the dissociation beginning at 375 s. For both the ₁ integrin I domain/Mg²⁺ and S. aureus Cna A domain, the association and dissociation with collagen was rapid and apparently quite similar.

View larger version (17K): [in this window] [in a new window]   Fig. 4.   Representative profiles of the relative SPR responses for the binding of 25 µM recombinant Cna A and 1 integrin I domains to immobilized Type I collagen. a, human 1 integrin I domain in the presence () or absence (- - -) of 1 mM Mg2+. b, S. aureus Cna A in the presence () or absence (- - -) of 1 mM Mg2+. In the analyses shown here, the 4-min injection (begun at 140 s) employed a flow rate of 5 µl/min.

The sensorgrams shown in Fig. 4a demonstrate that the presence of 1 mM Mg²⁺ in the milieu increased the ₁ integrin I domain's collagen-binding capacity dramatically. A Scatchard analysis of equilibrium dialysis determination of the ₁ integrin I domain's affinity for Mg²⁺ was linear and showed a single Mg²⁺-binding site in the I domain having a K_D of approximately 10 µM (data not shown). This results in >99% of the ₁ I domain being cation-complexed in 1 mM Mg²⁺ (27).

In contrast, addition of 1 mM Mg²⁺ to the analysis buffer had little observable effect on the collagen binding capacity of the Cna A domain in the SPR measurements (Fig. 4b). The collagen binding by the recombinant A domain truncate, Cna 151-318 (of which the crystal structure is known), was also cation-independent (data not shown). These results were not surprising considering the absence of MIDAS, EF-hand, or other cation-binding motifs in the Cna protein sequence.

Multiple Binding Classes Exist for the Interaction of Collagen with Human ₁ Integrin I and S. aureus Cna A Domains-- In an attempt to obtain kinetic and equilibrium constants for these protein/collagen interactions, we examined the SPR profiles over a range of concentrations of ₁ integrin I and Cna A domains flowed over immobilized collagen. Fig. 5a illustrates the SPR profiles expected for a simple 1:1 immobilized ligand/mobile protein system (or 1:P, where all protein macromolecules, P, bind the immobilized ligand noncooperatively and with equal affinity) over a range of mobile protein concentrations (53).⁴ As the protein concentration exceeds the dissociation constant, saturation of sites within the immobilized ligand occurs earlier in the sensorgram, with the equilibrium plateau becoming more apparent. Fig. 5, b and c, are the profiles of the mobile Cna A and ₁ integrin I domains flowed over immobilized Type I collagen. From these panels it is apparent that neither the Cna A nor the ₁ integrin I domain recombinant proteins obey pseudo first-order binding kinetics; but rather, both proteins' interactions with collagen are more complex.

View larger version (23K): [in this window] [in a new window]   Fig. 5.   Comparison of sensorgrams over a range of protein concentrations. a, a theoretical system that obeys pseudo first-order binding kinetics, as described by Schuck (52); b, Cna A domain; and c, 1 integrin I domain (+1 mM Mg2+). The range of concentrations shown in each panel span 0.1 KD  10 KD, where KD is the dissociation constant estimated from enzyme-linked immunosorbent assays. Half-maximal binding of recombinant Cna A to Type I collagen was determined to be 1.3 ± 0.2 µM. Half-maximal binding of recombinant 1 integrin I domain was determined to be 0.6 ± 0.1 µM in the presence of 1 mM Mg2+. The affinity reported here for the 1 integrin I domain/collagen interaction is much poorer than that reported in Footnote 2. The explanation for this difference is detailed under "Experimental Procedures." In the enzyme-linked immunosorbent assays, bovine serum albumin bound Type I collagen and the recombinant proteins bound bovine serum albumin at undetectable levels (data not shown).

To examine these interactions further, we determined the binding of each recombinant to collagen using SPR across an even wider concentration range and calculated the populations of collagen-bound and -free recombinant protein. These measurements produced the Scatchard plots shown in Fig. 6. The hypothetical one-simple-binding-class data from Fig. 5a would yield a linear Scatchard plot. The Scatchard plots of the Cna A and ₁ integrin I domain recombinant proteins shown in Fig. 6 are dramatically concave upward, however. Similar concave Scatchard plots were obtained: 1) by flowing these proteins over Type II collagen; 2) by replacing Mg²⁺ with Mn²⁺ in the ₁ integrin I domain analysis buffer; and 3) for recombinant Cna proteins spanning residues 151-318 and 30-721 (data not shown). The nonlinear Scatchard plots of Fig. 6 are not merely experimental artifacts, for under similar experimental conditions we obtained a linear plot for the binding of collagen by an Enterococcus faecalis MSCRAMM, Ace.

View larger version (13K): [in this window] [in a new window]   Fig. 6.   Scatchard plots of Cna A domain and 1 integrin I domain binding to immobilized Type I collagen as measured by SPR. a, S. aureus Cna A. KD1 = 0.21 ± 0.02 µM, n1 = 1.3 ± 0.1; KD2 = 35 ± 9 µM, n2 = 19 ± 3. b, human 1 integrin I domain in buffer containing 1 mM Mg2+. KD1 = 0.09 ± 0.06 µM, n1 = 2.5 ± 0.5; KD2 = 7 ± 4 µM, n2 = 18 ± 6. [P] is the concentration of unbound protein. Indistinguishable results were obtained for the His6 tag and thrombin-cleaved 1 integrin I domain recombinant proteins. Fitted lines, binding constants (KDi values), and number of binding interactions (n1) reported here represent the lowest and highest affinities observed, with intermediate binding classes not resolved. Analysis of each protein was performed over multiple flow cells immobilized with varying amounts of collagen.

Not only do the Scatchard plots in Fig. 6 demonstrate the multiple binding classes of these proteins' interactions with collagen, but the plots also reveal that the recombinant ₁ integrin I and Cna A domains bind at a host of sites along the collagen strand. The highest affinity interactions of the ₁ integrin I or Cna A domain with collagen occur at the fewest number of sites, with an increasing number of sites, n, occupied as the proteins' affinities for collagen decreases. The n_i obtained from the linear extrapolations in Fig. 6 represent those matching the "highest" and "lowest" affinities described above. Clearly, intermediate n_i also exist, as may higher-order n_i that correlate with the very low affinity protein/collagen interactions.

	DISCUSSION

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS DISCUSSION REFERENCES

As different as the MSCRAMM and cation-bound integrin recombinant proteins appear initially by sequence and structure comparisons, their collagen-binding mechanisms appear quite similar. The ₁ integrin I (Mg²⁺) and Cna A domains exhibited comparable net affinities (Fig. 5, legend) and k_a and k_d (Fig. 4) in their interactions with Type I collagen. (Fitting the kinetic data for each protein to one (or even two) on- and off-rates did not yield statistically acceptable results, indicating the presence of more than two on- and off-rates.) In addition, the sensorgrams of neither the ₁ integrin I (Mg²⁺) nor Cna A domain flowed over immobilized Type I collagen approximated that of a system having one or very few binding classes (Fig. 5) and the Scatchard plots of both these proteins binding to collagen were not easily resolved into standard fitting curves (Fig. 6). We interpreted these data to be the result of multiple classes of interactions occurring between the protein and collagen (with each class, i, have a corresponding number of interactions, n_i). We have considered several of the typical binding mechanism scenarios (most significantly, the possibilities of binding cooperativity (54) and overlapping adhesin-binding sites in collagen (55)), but have found that none fit the data in Fig. 6 well, for each lacks a factor to account for the microscopic heterogeneity in collagen and consequently, the possibility of multiple nonidentical adhesin-binding sites (56). From the linear regressions of the Scatchard plots in Fig. 6, we report here 1) the lowest and relative highest number of interactions and 2) the class of highest affinity, the class of lowest observed affinity, and noted that intermediate classes of undetermined affinities exist (as well as classes of progressively weaker affinities beyond the detection limits of this assay system).

This atypical ligand-binding behavior may result from collagen binding in the trench of the ₁ integrin I or the Cna A domains. Many segments of collagen may fit within the trench, but the protein's affinity for a particular segments may be determined by the specific interactions (e.g. hydrophobic, ionic, hydrogen-bonding) between particular residues in collagen and those lining the binding-site trench. The microstructure of collagen (particularly the presence of a particular amino acid in the third position of the repeat sequence, GPX) will determine which segment is most amenable to docking in the protein's trench. From Fig. 3 it is apparent that the topologies of the ₁ integrin I and the Cna A domains' trenches are quite different, suggesting that these two adherence receptors preferentially bind different collagen segments. It is also possible that the differences in these trenches provide for the integrin and bacterial protein to differ in their affinities for various collagen types.

A collagen triple-helical peptide composed of three GPX repeats also docked well within the ₂ integrin I domain trench (19). Superposition of the accessible surface areas within the trenches of the ₁ and ₂ integrin I domains revealed that the ₂ integrin I domain trench is: 1) much less flexible and 2) more restricted in the number of collagen triple-helical conformations it is amenable to docking than the trench of the ₁ integrin I domain (data not shown). The most significant difference between the trench topologies of the ₁ and ₂ integrin I domain trenches is the positioning of a tyrosine residue. Tyr²⁸⁵ of the ₂ integrin I domain was found to be pointing into the trench, but the comparable tyrosine of the ₁ integrin I domain (Tyr²⁸⁹) is shifted to the bottom of the trench and held in place by enhanced hydrophobic interactions due to the substitution of Phe²⁹⁹ for the Leu²⁹⁶ present in the ₂ integrin I domain. In addition, the hydroxyl group of Tyr²⁸⁹ is buried and hydrogen-bonded to a backbone nitrogen and the carboxylate side chain of Glu²⁵⁹. In addition, there appear to be significant differences in the contours and charge/hydrophobocity distributions within the trenches of the ₁ and ₂ integrin I domains, which indicates that these two proteins may bind dissimilar segments of collagen (or differ in their affinities for various collagen types).

Each of these adhesive proteins binds at multiple sites in collagen, with perhaps the most efficient interaction occurring at only one (or a very few) site. If the recombinant Cna or integrin protein recognizes various peptide sequences in the collagen macromolecule (which may contain a few required key residues and other variable residues that determine binding efficiency), the protein population may well bind at multiple locations along the collagen strand, with each binding event having a unique K_D (Fig. 7). There may be indeed a particular amino acid sequence or conformation in the collagen strand that is most amenable for binding to a trench of a particular adherence molecule, but this site in the collagen strand is not dramatically more suitable than many others. Such behavior would explain the collagen-binding results we observe for the MSCRAMM and integrin ligand-binding domains: multiple protein molecules bound, with varying affinity, to a single collagen moiety, with equilibrium and site saturation not easily achieved. The sum of all these interactions could produce the spectrum of affinities that we observe in the binding analyses of these recombinants and collagen.

View larger version (14K): [in this window] [in a new window]   Fig. 7.   Cartoon depiction of the interaction between triple-helical collagen and human 1 integrin I domain or S. aureus Cna A domain, demonstrating the promiscuity of these adhesive proteins for binding sites in collagen. The protein population is uniform; degree of shading of the circle depicts that protein's affinity for a particular site in the microscopically heterogeneous collagen. The relative sizes of collagen and the protein are not proportionate.

The high degree of amino acid sequence homology between the ₁ and ₂ integrin I domains would indicate that the 2-fold similarly. Hence, it is no surprise that ribbon diagrams of the two proteins appear almost identical, with a root mean square deviation of 1.45 Å for the main chain atoms. In fact, modeling the ₁ integrin I domain sequence using the structural coordinates of the ₂ integrin I domain suggested that the ₁ integrin I domain would adopt a Rossman folding motif. This modeling, however, did not provide adequate resolution to refine the trench microstructure. Only upon solving the crystallographic structure of the ₁ integrin I domain were we able to characterize its trench topology and propose which residues interact with collagen. We suggest that modeling of other I domains for which the structures have not been solved experimentally will reveal whether or not they adopt the expected Rossman fold, but the characterization of the ligand-binding site (particularly the putative trench of the collagen-binding ₁₀ integrin I domain (17)) needs to be experimentally determined, however.

The trench-as-binding-site motif has also been reported for collagen-binding proteins that are not cell-surface proteins. These include the fiddler crab and human fibroblast collagenases. Fletterick and co-workers (57) reported that the fiddler crab collagenase-binding site is a negatively-charged, elongated, cylindrical pocket wide enough to accommodate the collagen triple helix. The human fibroblast collagenase resembles the integrin I domains in that a cation (Zn²⁺) resides in the center of the trench and is crucial for efficient catalysis (58). Lovejoy et al. (58) identified multiple interactions between residues within the collagenase trench and the inhibitor: 1) the zinc ion presumably coordinates a inhibitor carboxylate group; 2) eight hydrogen bonds exist between the two species; and 3) inhibitor hydrophobic residues fit in complementary pockets within the trench.

We suggest that the trench observed in the crystal structures of Cna 151-318 and ₁ integrin I domain may resemble that of the major histocompatibility complex class II molecule (the classical example of the trench-as-binding-site model (25)), in which approximately 13 amino acids fit within the binding trench, with the ligands additional flanking polypeptide at the N and C termini remaining unbound. Stern et al. (25) determined that peptide binding in a particular major histocompatibility complex class II molecule's trench occurred when residues at positions 1, 4, 6, 7, and 9 were conserved among a subclass of amino acids. These residues were shown to fit within one major hydrophobic and four minor trench pockets. Conservation of other residues in the peptide was not required for efficient binding, presumably because the trench could accommodate a variety of residues in these positions. In many respects, the trenches of the ₁ and ₂ integrin I domains and the Cna A domain may be analogous to the trench of the major histocompatibility complex class II molecule: for a few collagen residues within an approximately 25-35-Å long segment may be critical for binding to occur and additional residues within the segment determine the strength of the protein/ligand interaction.

In summary, we propose that the atypical binding profiles observed for the both the S. aureus MSCRAMM and the human ₁ integrin I domain complexes with Type I collagen may be representative of a class of collagen/protein interactions in general: the triple-helical peptide of collagen fits within a long trench on a face of the cell surface protein and no one contact determines the binding efficacy, but rather, a sum of multiple, weak interactions provide sufficient contact for efficient binding. We have demonstrated that there is not a unique motif within collagen, but rather, binding occurs at several sites.

	FOOTNOTES

^* This work was supported by the Arthritis Foundation (to R. L. R.) and National Institutes of Health Grant AR44415 (to M. H. and S. V. L. N.).The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The atomic coordinates and structure factors (code 1QC5) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^§ To whom correspondence should be addressed. Tel.: 713-677-7557; Fax: 713-677-7576; E-mail: rrich@ibt.tamu.edu.

² Rich, R. L., Kreikemeyer, B., Owens, R. T., LaBrenz, S., Narayana, S. V. L., Murray, B., Weinstock, G. M., and Höök, M. (1999) J. Biol. Chem., in press.

³ M. Carson, unpublished data.

⁴ Fig. 5a is derived from the figures and discussion found in Ref. 53.

	ABBREVIATIONS

The abbreviations used are: Cna, Staphylococcus aureus collagen adhesin; MSCRAMM, microorganism surface component recognizing adhesive matrix molecules; MIDAS, metal ion-dependent adhesion site; PAGE, polyacrylamide gel electrophoresis; SPR, surface plasmon resonance spectroscopy.

	REFERENCES

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS DISCUSSION REFERENCES