Conformational Transition of Glycoprotein Iba Mutants in Flow Molecular Dynamics Simulation

Transkript

1 Cellular and Molecular Bioengineering, Vol., No., September (Ó ) pp. 9 DOI:./s9--- Conformational Transition of Glycoprotein Iba Mutants in Flow Molecular Dynamics Simulation QINGSHENG HUANG,, JIZHONG LOU,, JIANHUA WU, and CHENG ZHU,, School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA; Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA; Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA; Laboratory of Non-coding RNAs, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; and Institute of Biomechanics and Department of Biomedical Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China (Received November ; accepted April ; published online May ) Associate Editor David Sept oversaw the review of this article. Abstract Glycoprotein Iba (GPIba) interacts with von Willebrand factor (VWF) inducing the tethering of platelets to injured vessel walls and subsequent hemostasis process. We have previously shown that the conformation of the b-switch region of GPIbaN can be regulated by flow. Flow induces a loop-to-b-hairpin conformational change in this region, which is a suggested mechanism for the flowenhanced binding of GPIba to VWF-A. To further evaluate the mechanism and obtain more complete evidences, here we performed flow molecular dynamics simulations of wild type and a number of mutants of the b-switch. The results demonstrate that the gain-of-function mutations GV, DV, and KV promote the conformational transition toward b-hairpin, while the loss-of-function mutation QV impedes the transition. The promotion is caused mainly by the improved polarity similarity of the paired residues on the b-hairpin, and also by the decreased flexibility of one strand of the b-switch. The gain-of-function mutations exert the influence locally, affecting only hydrogen bonds near the mutated residues. The impediment of the loss-of-function mutant may be non-essential hydrophobic interactions blocking the conformational change. Keywords Flow molecular dynamics, Conformational change, Glycoprotein Iba, von Willebrand factor, Platelettype von Willebrand disease. INTRODUCTION Glycoprotein Iba (GPIba) is a platelet adhesion receptor, the major component of the glycoprotein Ib IX V complex. The interaction of GPIba with Address correspondence to Jizhong Lou, Laboratory of Noncoding RNAs, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. Electronic mail: jlou@ibp.ac.cn 9 von Willebrand factor (VWF) induces the tethering of platelets to injured vessel walls and initiates hemostasis. This interaction is regulated by blood flow, with shear stress paradoxically enhancing the binding of wild type () GPIba to VWF. Malfunction of the regulation results in disorders of hemostasis, such as platelet-type von Willebrand disease (VWD),, which is associated with gain-of-function (GOF) mutations in GPIba b-switch region. These GOF mutations increase the binding affinity of GPIba to VWF and decrease the shear stress requirement, resulting in rapid clearance of the highest molecular weight multimers of VWF 9 from blood plasma. Thus, patients with platelet-type VWD have abnormalities of hemostasis, such as prolonged bleeding time and intermittent thrombocytopenia. Loss-of-function (LOF) mutants of GPIba have also been engineered, 9 with decreased binding affinities to VWF 9,9 and increased shear stress requirements. A structural mechanism of the flow-enhanced GPIba/VWF-A interaction was recently proposed, based on flow molecular dynamics (flow MD), of GPIba and two mutants, a GOF mutant M9V and a LOF mutant AV. The flow MD, showed that flow induced a loop-to-b-hairpin conformational change (Fig. a) on the b-switch region,, which is a binding site at the concave face of GPIba, and stabilized its b-hairpin conformation. The b-hairpin conformation is different from loop conformations in the absence of flow,,,, and it can be adopted, also after GPIba is bound to VWF-A, when this b-switch region aligns with the central b-sheet of A. Compared with, mutation M9V reduces the flow requirement for the conformational change, whereas AV increases it. -//9-9/ Ó Biomedical Engineering Society

2 9 HUANG et al. Thus, the GPIba b-switch is a prototype of peptide chains whose conformation is sensitive to both the sequence and the environment,, : it switches between ordered b-hairpin and disordered loop. As a type of secondary structure, a b-hairpin (Fig. b) consists of a linking reverse turn and two b-strands with a hydrogen bond (H-bond) pattern like an antiparallel b-sheet. The other secondary structure loop is structureless, without any significant H-bond pattern. The flow-induced loop-to-b-hairpin transition on the GPIba b-switch suggests that this sequence controls the GPIba/VWF-A interaction in a flow-regulated way. It has been pointed out that side chains of the b-switch were pushed by the flow. Zou et al. s theoretical analysis suggested that the conformational transition should involve a shift of balance between entropy and enthalpy. Nevertheless, previous studies, were concerned about only mutations M9V and AV, neglecting effects derived from the difference of mutation sites, since the two tested mutations are near the proximal end of the formed b-hairpin. In this study, we performed systematic flow MD simulations to measure b-hairpin propensities of various GPIba b-switch mutants (Table ), including M9V and AV which have been studied earlier. Mutations QV (LOF) 9,9 and KV (GOF) 9,9 are on respective strands of the formed b-hairpin and near the turn, and GV (GOF),9, and DV (GOF) 9 are right on the turn (Fig. b). M9V and AV were examined again so that we could have their data handy to compare with other mutants. Our simulations cover most b-switch mutations (naturally occurring or engineered) with known phenotypes. Based on the simulation results, we discuss the mechanism of the conformational change affected by these mutations. MATERIALS AND METHODS Molecular Dynamics Simulations We performed flow MD simulations of isolated GPIba b-switch (residues ) of seven sequences (Table ) in loop conformations:, QV, GV, DV, KV, AV, and M9V. All simulation systems were prepared with VMD. The loop conformation structure of was taken from the standalone GPIba structure (Fig. a, PDB id: QYY) ; the mutant peptides were modeled by mutating the corresponding residues of. After patched with the neutral termini, acetylated N-terminus (ACE) and N-methylamide C-terminus (CT), each peptide was soaked into a 9 9 A water box with a certain number of chloride ions to neutralize the system (Table ). Five independent simulations for each mutant were carried out with NAMD package and CHARMM force fields.,, During (a) (b) FIGURE. Structure of GPIba b-switch. (a) Structure of unliganded GPIbaN domain with b-switch (highlighted in licorice representation) in a loop conformation (solid licorice, PDB id: QYY ) and in a b-hairpin conformation (translucent licorice, PDB id: SQ ). (b) The H-bond pattern of the b-hairpin. H-bonds indicated by solid lines between N atom and O atom are numbered from to according to their positions. Residues highlighted by circles are the mutation sites studied with flow MD in this study. TABLE. Phenotypes and sequences of peptides examined with flow MD. Name Phenotype Sequence Added ions Wild type VYVWKQGVDVKAMTSNV Cl QV LOF 9,9 VYVWKVGVDVKAMTSNV Cl GV GOF,9, VYVWKQVVDVKAMTSNV Cl DV GOF 9 VYVWKQGVVVKAMTSNV Cl KV GOF 9,9 VYVWKQGVDVVAMTSNV None AV LOF 9 VYVWKQGVDVKVMTSNV Cl M9V GOF 9,, VYVWKQGVDVKAVTSNV Cl

3 Flow MD Simulation of Glycoprotein Iba Mutants 9 all simulations, the a carbon (C a ) atoms of residues,,, and, as well as the CAY atom of ACE and the CAT atom of CT, were fixed so that the b-switch was anchored as if the other portion of GPIbaN domain was present. Each system was first subjected to -step minimization and then -ns equilibration. During the equilibration, the temperature of the system was maintained at K via Langevin thermostat with a damping coefficient c =ps. In addition, pressure control targeting. kpa was applied with Langevin piston method. After the equilibration, flow MD simulation was performed in an NVT ensemble for ns. Water flow was generated along x-axis, the direction in which the b-switch elongated, by applying a.9-pn force to the oxygen atom of every water molecule within the leftmost.-nm-thin layer. To keep the flow stable, all oxygen atoms of water were subjected to damping forces by Langevin dynamics with a damping coefficient c =. ps. A uniform constant flow with a velocity about nm/ns was achieved soon after the starting of the simulation (within ps). We saved trajectories of atoms in the system every fs, and analyzed the data using the same frequency. Data Analysis We characterized the conformational change of the b-switch in flow MD as root mean square deviation (RMSD) of C a atoms, as formation of the b-hairpin H-bonds, and as rotation of residues near the distal end. Differences between groups were verified by the Wilcoxon test or by the Kruskal Wallis test. RMSD was calculated using either the unstructured loop (PDB id: QYY) or the b-hairpin (PDB id: SQ) as the reference, after aligning C a atoms of residues,,, and. of an H-bond is defined as the ratio of time that the H-bond is formed to time that the peptide has been subjected to flow. Formation of an H-bond means that the distance of participated oxygen and nitrogen atoms is less than. A. We measured formation frequency of seven H-bonds (Figs. b, h). Rotation of a residue is reflected by its backbone dihedral angles u and w, two parameters denoted by coordinates of a point on a Ramachandran plot. On a Ramachandran plot (Fig. ), b-strand conformations lie in the upper left quadrant, a-helical in the lower left, and left-handed helical in the upper right. 9 To find out the favorite conformation of a residue during simulation, we counted points within each region on the plot. By doing so, we inspected conformations of residues,, and of GV, DV, and, so as to determine if these mutations increase the stability of the b-hairpin by promoting the turn formation. To compare transition tendencies toward the b-hairpin in simulations of QV and KV, we calculated formation frequency of b conformations as a fraction of time that each residue (,,,,, and ) formed a b conformation (as a point in region enclosed by dotted line in the upper left quadrant, in Fig. ) in ns flow MD. RESULTS Conformational Transition of the Backbone In our flow MD simulation for both and mutants, RMSD between the simulated b-switch and the reference loop conformation (starting point) increased, while RMSD between the simulated b-switch and the reference b-hairpin (destination) decreased (Figs. a g), suggesting the tendency of a loop-to-b-hairpin conformational change. The time course of RMSD can be divided into two stages. The first stage is short, within ns of the beginning of the flow MD, which perhaps reflects the stretching of the peptide by flow. In this stage, RMSD with respect to the reference b-hairpin drops to a moderate value, while RMSD with respect to the reference loop increase steeply. The second stage starts after the first stage and lasts until the end of simulation, which may correspond to fine-tuning of the conformation. In this stage, the time course of RMSD behaves as a plateau. To verify whether the RMSD remains the same after the first stage, we ran one of the simulations for another ns to a total of ns. The ns simulation confirms that RMSD, especially the one with respect to the b-hairpin, remains unchanged until the end of the simulation (Fig. S). According to the hypothesis that the conformation of peptide depends on an entropy enthalpy balance induced by flow, the second stage may be driven or disturbed by entropy, thus the transition is slow. RMSD between the simulated b-switch and the b-hairpin is suitable (Fig. i) for evaluating the b-hairpin propensity of a peptide in flow, because it decreased more significantly in GOF than in LOF. In some simulations of LOF, for example in those of QV (Fig. b), the RMSD even slightly increased in the second stage. Shown by the Kruskal Wallis test for the null hypothesis that, GOF, and LOF come from the same population (Fig. i), averaged RMSD of the entire flow MD discriminates (p =.) between these three groups. In contrast, RMSD with respect to the loop conformation seems to be sensitive to thermal fluctuation (Fig. h). It reaches large values in all simulations, but the differences among the three groups are not significant (p =.).

4 HUANG et al. (d) DV M9V AV (i) (h) GV (f) KV (g) (e) (c) QV p=. 9 LOF GOF Cα RMSD to hairpin (Å) (b) Cα RMSD to loop (Å) (a) 9 p=. LOF GOF FIGURE. Ca atoms RMSD in flow MD. (a g) RMSD plotted against time for the indicated mutants. RMSD with respect to loop conformation (gray line) are calculated using the standalone GPIba structure (PDB id: QYY) as the reference, and RMSD with respect to b-hairpin conformation (black line) are calculated using the GPIba in complex with VWF-A (PDB id: SQ). The plotted RMSD is an average of five independent runs for each mutant. (h, i) Box plots of RMSD averaged of the entire flow MD runs. Sample of LOF contains observations from QV and AV, sample of observations, and sample of GOF observations from GV, DV, KV, and M9V. On each box, the central line is the median of the group, the lower and upper edges are the th and th percentiles, and the whiskers extend to the minimum and maximum. Above the boxes is the p-value of the Kruskal Wallis test for the null hypothesis that samples of three groups come from the same population. Among all GOF mutants, KV displayed the smallest RMSD with respect to the b-hairpin (Fig. ), implying its least flow requirement for conformational transition.9 Other GOF mutants displayed RMSDs between and KV, in which DV was the largest, very close to. Although the difference is not significant (p =. of the Kruskal Wallis test), such divergence is the same as observed9 in experiments of ristocetin-induced VWF binding, where KV mutant seemed to bind more VWF than other GOF mutants.9 Formation of Backbone H-Bonds In most of our flow MD simulations, formation frequency of backbone H-bonds monotonically increased with time (Fig. ), no matter what phenotype the peptide corresponds. Similar to what have been reported,, formation frequency of distal H-bonds (near residues and ) were smaller than the proximal ones (near residues and ), indicating H-bonds were formed sequentially from the proximal end to the distal end for all cases. Sequential formation of H-bonds indicates also the stepwise conformational change, as observed in the RMSD measurement. We compare the formation frequencies of H-bonds among all systems simulated (Fig. ). Under the same conditions, GOF mutants formed more H-bonds and formed them earlier (Figs. c e, g) than did (Fig. a). As a result, formation frequencies of H-bonds in GOF at the end of simulation were generally larger than that in. LOF mutants were opposite to GOF (Figs. b, f), which formed less H-bonds and formed them at later time under the same conditions. These results extend our previous finding, on M9V and AV to most mutants that have been studied experimentally, suggesting that the phenotype changes in these mutations may come from the same mechanism, that is, their modified behavior in the loop-to-b-hairpin conformational change induced by flow. To verify the enhancement of H-bond formation, we perform the Wilcoxon test (Table ). In KV simulations, the averaged formation frequencies of H-bonds HN:O, HN:O, and

5 Flow MD Simulation of Glycoprotein Iba Mutants 99 HN:O (H-bonds,, and in Fig. h and Table ) were larger than that of the other mutations. Similarly, M9V enhanced H-bonds 9HN:O and HN:9O (H-bonds and in Fig. h and Table ). C α RMSD to hairpin (Å) p=. DV GV M9V KV FIGURE. C a atoms RMSD averaged over the entire flow MD snapshots of and four GOF mutants. On each box, the central line is the median of the mutant, the lower and upper edges are the th and th percentiles, and the whiskers extend to the minimum and maximum. Above the boxes is the p-value of the Kruskal Wallis test for the null hypothesis that samples of the four GOF mutants come from the same population. H-bonds near the distal end were relatively hard to form in most simulations. The formation frequency of H-bond HN:O (H-bond in Fig. h) was almost zero in, while it was slightly larger in LOF mutants QV and AV, suggesting that this H-bond might not play an important role in determining the phenotype, in agree with the observation that this H-bond is absent in a few solved crystal structures (PDB id: SQ, M and UN),, where the b-hairpin is bound to VWF-A. In some crystal structures (PDB id: SQ and M),, residue forms an H-bond with residue instead of,,, through the carbonyl oxygen of residue and the amide of residue (H-bond HN:O). In our simulation, this H-bond (H-bond in Fig. h, inset) was formed more frequently in GOF than in or LOF. During the flow MD, its formation frequency was maintained at a relatively constant value, which did not increase with time (Fig. ), suggesting that flow does not accelerate the formation of this H-bond. It seems that this H-bond is important in maintaining the c-turn of the b-hairpin. If so, this observation supports (a).... (d). DV... (g).... M9V (b) QV.... (e). KV... (h).... 9HN:O HN:9O HN:O (c).. GV.. (f). AV... HN:O Hydrogen bond.. HN:O HN:O QV AV GV DV KV M9V HN:O FIGURE. of interstrand H-bonds of the b-hairpin in flow MD. (a g) plotted against time for the indicated mutants. The frequency is calculated as a running fraction of time during which the H-bond is formed and is averaged over five runs. Numbering of the H-bonds, from to, is indicated near the right margin of the graph, while for the H-bond it is indicated midway for the sake of clarity. Only the formation of proximal H-bonds is obvious. (h) H-bond formation frequency at ns. Each bar represents mean SEM of five independent runs. The donor/acceptor pairs of H-bonds are shown in the bottom. (h, inset) of H-bond at ns in flow MD.

6 TABLE. HUANG et al. The p-values of the Wilcoxon tests for the changes in formation frequency of H-bonds after introducing mutations. H-bond 9HN:O HN:9O HN:O HN:O HN:O HN:O HN:O QV fl. fl. fl. fl. fl. fl.9 fl. AV fl. fl. fl..9 fl. fl. fl. GV.. fl. fl. fl... DV fl.9 fl.9. fl. fl. fl.99.9 KV fl. fl.9 M9V Each arrow denotes that formation frequency of an H-bond in a mutant is larger ( ) or smaller (fl) than the average of the other six peptides (including ). The p-value results from the Wilcoxon test for the comparison between each mutant and the other six peptides. Underlines highlight the p-values supporting the inference that mutations enhance H-bonds nearby. the hypothesis that binding of VWF-A favors GPIba with a preformed b-hairpin. Formation of the Turn in GOF Mutants GV and DV In the complexes of GPIba/VWF-A, where GPIba b-switch assumes the b-hairpin conformations, residues,, and form a classic c-turn (PDB id: M) or an inverse c-turn (PDB id: SQ). Both turn conformations are different from the loop conformation, which was the starting point of these residues in our simulation. Thus, conformational transition of these residues, mainly residues and, was expected in flow MD. Indeed, such transition was observed in simulations of GV and DV, but not. In the simulations of, residues and mainly maintained b conformations (Fig. a) similar to their conformations at the beginning of the simulations. On the other hand, in one simulation of GV (Fig. b) and two simulations of DV (Fig. c), residues and yielded turn conformations similar to those observed in the complexes,, of GPIba/VWF-A: the classic c-turn and the inverse c-turn (Figs. a c, arrows with dashed lines). These two GOF mutations speeded up the conformational transition toward the turn. Influence of GV onto the Backbone Flexibility Backbone flexibility may affect the conformation of a peptide chain. When a glycine residue is mutated into valine, the flexibility decreases. 9, Thus, the glycineto-valine mutation of residue may change the conformational propensity of the b-switch. At the beginning of our flow MD, residue in and GV assumed almost the same left-helix conformation (in, u., w. ; in GV, u 9.9, w. ). In the subsequent simulation, the rotation of Gly in was active but with little hairpin-forming tendency, because of the flexibility of glycine and also the thermal fluctuation. In two simulations of, the conformation of the residue started deviating from left-handed helix after -ns flow MD, changed to a conformation later, and kept the conformation until the end (Fig. d). In the other three simulations, the conformation was fluctuating around left-handed helix all through the course. In contrast to, the valine residue in GV adjusted its torsion angles during the transition so as to fulfill the b conformation, since residue belongs to one of the b-strands in the formed b-hairpin. Though significant conformational change happened as late as.9 ns in flow MD (maybe due to the bulky side chain of Val), b conformations were accomplished at last in two simulations, where Val was packed with Val via hydrophobic interactions. To evaluate further the effect of mutation GV, we compare root mean square fluctuations (RMSF) of C a of residue in all peptides (Fig. a). RMSF in GV is smaller than the other peptides where residue is glycine. The Wilcoxon test (Fig. b; Fig. S) gives a small p-value (p =.9) for the null hypothesis that GV and the other peptides are the same. Effects of Mutations QV and KV In the formed b-hairpin, residues and are adjacent, (Fig. b), but their corresponding mutants to valine show different phenotypes 9,9 : QV is LOF, while KV is GOF. To figure out the difference during flow MD, we detailed the preference for b conformations of residues,,,,, and, since these residues are most possible to be spatially affected by the mutations. Although most residues adopted b conformations in flow MD (Fig. ), residues and largely excluded such conformations. Rotation of residue seems to be a bottleneck of the formation of b-hairpin, for its formation frequency of b conformations was very low in all three peptides. The bottleneck was dominant in simulation of LOF QV, where the formation frequency was 9 (Fig., inset), but it was less

7 (a) Flow MD Simulation of Glycoprotein Iba Mutants (b) SQ SQ ψ M UN ψ M UN - - GV - - φ φ (c) (d) SQ ψ M UN ψ GV - DV - φ - - φ FIGURE. Ramachandran plots for residues,, and at ns in flow MD of, GV, and DV. In each plot, solid lines enclose regions in which amino acid of a protein is allowed to enter, while dotted lines enclose regions in which amino acid with a small side chain is allowed to enter., (a c) Ramachandran plots for residues and in, GV, and DV. Arrow goes from residue to residue. Arrows with solid lines show our simulation data, and arrows with dashed lines show experimental values of three crystal structures of the GPIba/VWF-A complex (PDB id: M, SQ, and UN). One simulation of GV and two of DV (indicated by ticks) resemble the conformations of residues and in crystal structures. (d) Ramachandran plot for residue in and GV. Two points within the dotted polygon in the upper left quadrant indicate residue Val participates in a b-strand in two simulations of GV. (a) (b) C α RMSF (Å) C α RMSF (Å) p=.9 QV AV GV DV KV M9V GV Others FIGURE. C a atoms RMSF of residue in flow MD. (a) RMSF calculated using the entire ns flow MD. Each bar represents mean SEM of five independent runs. (b) Box plot of RMSF displaying the difference of GV and other six peptides. Sample of GV contains observations and sample of other peptides contains observations. On each box, the central line is the median of a group, the lower and upper edges are the th and th percentiles, and the whiskers extend to the minimum and maximum. Below the boxes is the p-value of the Wilcoxon test for the null hypothesis that GV is the same as other peptides. significant in simulation of GOF KV, where the frequency was higher, about.. Rotation of residue might be another but less important bottleneck (Fig. ), which could be due to its role of the counterpart of residue in forming H-bonds. Residues,,, and had high formation frequencies of b conformations, differences in which might not essential in evaluating the b-hairpin propensity. We performed on the frequency of these residues the Kruskal Wallis test for the null hypothesis that three peptides come from the same population (Fig. ), and the p-values show that the difference of residue in three peptides is the only significant one (p =.). DISCUSSION Secondary structure of protein is defined by its H-bond pattern and torsion and curvature of the backbone. Our flow MD simulations of GPIba

8 HUANG et al. Frequency Residue QV KV FIGURE. of b conformations of residue,,,,, and, in flow MD of QV,, and KV. is a fraction of time that each residue formed b conformations in ns flow MD, and is shown as a bar representing mean SEM of five independent runs. Values of residue are very low and shown in the inset as a histogram on a logarithmic scale. Above each cluster of bars is the p-value of the Kruskal Wallis test for the null hypothesis that three samples of the cluster are the same. b-switch show its b-hairpin propensity concerning the H-bond pattern and the torsion angles of its backbone. Though no simulation resulted in a perfect b-hairpin, RMSD between the simulated peptide and the b-hairpin decreased monotonically in and all GOF mutants. As a measurement of b-hairpin propensity of various peptides, RMSD correlates with the phenotype observed in experiments,,9,9, suggesting the relative benefits of mutations to their interactions with VWF- A. Besides the reported discrimination, between LOF,, and GOF, we notice a correlation between RMSD and VWF binding characteristics of the four GOF mutants (DV, GV, M9V, and KV in Fig. ). Dong et al. identified 9 these four as GOF mutants based on their VWF binding characteristics, and found KV seemed to bind even more VWF than the others in ristocetin of low concentrations. Considering the heightened response to ristocetin in Dong et al. s experiments, together with the acceleration of conformational transition in our simulations, we may conclude that GOF mutations enhance the VWF binding by lowering the energy barrier of the transition toward b-hairpin in GPIba b-switch. In GOF mutants, the introduced valine should compel the conformational transition by hydrophobic packing, because interactions of C b -branched residues (such as valine) stabilize b-hairpin., The effect of hydrophobic packing is entropy-driven, and it operates when two hydrophobic side chains are able to get close. From the observations of KV and M9V (Fig. h; Table ), we infer that, via hydrophobic packing, a mutation enhances only the assumed H-bonds nearby. Reduction of peptide s flexibility in some proper site may help b-hairpin maintain the straight shape. For example, flexibility of residue has a negative impact on the b-hairpin, and mutation of glycine into other residues may accelerate the formation of b-hairpin. This possibility relates our simulations of GV to a previous clinical observation on another GOF mutant GS, where the serine residue is not hydrophobic. However, the role of residue in the conformational transition is opposite to residue, mutation of which to glycine (VG) is GOF, improving the flexibility but decreasing the flow requirement., This opposition shows the location of the mutation site is crucial: residue locates on one of the strands of the b-hairpin, but residue is on the turn. The conformational transition takes a series of steps,, thus not only formation of H-bonds but also rotation of the backbone is important. Zou et al. reported that a partial formed b-hairpin containing only two to four H-bonds is common in simulation of for a long time in -m/s flow and in -m/s flow. In our simulations, some differences between and GOF can only be recognized by rotation of the backbone, specifically the transition of the distal end of the peptide (Fig. ). Formation of H-bond seems to be a too stringent criterion to judge the conformational change, because it concerns the conformation of both strands and measures the behavior of a group of residues. When the relevant residues are on the turn, or when they change their conformation asynchronously, a peptide chain with a larger tendency toward b-hairpin may not be found by this criterion. For example, GOF GV and DV did not surpass in the formation of some H-bonds (for example, H-bond in Fig. h and Table ), although they should benefit from hydrophobic packing because respective counterparts of residues and in the formed b-hairpin are native valine residues (residues and ). The criterion of backbone rotation, which measures individual residues, is suitable in the situation, because in this study it detects some kind of sequences of turn-promoting, which increase the folding rate of a b-hairpin. The GOF phenotype of KV has been explained by the introduced valine residue stabilizing the b-hairpin, while the LOF phenotype of QV has

9 Flow MD Simulation of Glycoprotein Iba Mutants been explained in part by steric hindrance. The reason of the latter seems unclear. We observed in one of the simulations of QV that hydrophobic interaction of Val and Trp made the peptide stuck, blocking the rotation of Gly. The blockade appeared after two proximal H-bonds (9HN:O and HN:9O) were formed, and delayed the stepwise conformational change, thus formation frequencies of the next four H-bonds dramatically decreased (H-bonds,,, and in Fig. h). This hindrance accounts for the decreased association rate 9 of QV, while the increased dissociation rate observed in experiment should also account for its phenotype. In conclusion, the conformation of GPIba b-switch is regulated by flow, and mutation in this region changes its phenotype by introducing hydrophobic packing and tuning the peptide s flexibility. Mutation exerts the mechanisms locally, affecting formation of H-bonds and rotation of residues nearby. Such knowledge may help us in prediction and design of sequences of flow sensors. ELECTRONIC SUPPLEMENTARY MATERIAL The online version of this article (doi:./ s9---) contains supplementary material, which is available to authorized users. ACKNOWLEDGMENTS The computational resources for the MD simulations were provided by the Interactive High Performance Computing Laboratory of the College of Computing, Georgia Institute of Technology and by the NSF Teragrid LRAC grant (MCAX). This work was supported by NIH grant HL9 (to C.Z.), NSFC grant (to J.W.) and AHA Scientist Development Grant N (to J.L.). REFERENCES Ambroggio, X. I., and B. Kuhlman. Design of protein conformational switches. Curr. Opin. Struct. Biol. ():,. Arya, M., A. B. Kolomeisky, G. M. Romo, M. A. Cruz, J. A. Lopez, and B. Anvari. Dynamic force spectroscopy of glycoprotein Ib IX and von Willebrand factor. Biophys. J. ():9,. Awasthi, S. K., S. C. Shankaramma, S. Raghothama, and P. Balaram. 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