Complete integrin headpiece opening in eight steps

Carefully soaking crystals with Arg-Gly-Asp (RGD) peptides, we captured eight distinct RGD-bound conformations of the αIIbβ3 integrin headpiece. Starting from the closed βI domain conformation, we saw six intermediate βI conformations and finally the fully open βI with the hybrid domain swung out in the crystal lattice. The β1-α1 backbone that hydrogen bonds to the Asp side chain of RGD was the first element to move followed by adjacent to metal ion-dependent adhesion site Ca2+, α1 helix, α1’ helix, β6-α7 loop, α7 helix, and hybrid domain. We define in atomic detail how conformational change was transmitted over long distances in integrins, 40 Å from the ligand binding site to the opposite end of the βI domain and 80 Å to the far end of the hybrid domain. During these movements, RGD slid in its binding groove toward αIIb, and its Arg side chain became ordered. RGD concentration requirements in soaking suggested a >200-fold higher affinity after opening. The thermodynamic cycle shows how higher affinity pays the energetic cost of opening

Structural basis for distinctive recognition of fibrinogen γC peptide by the platelet integrin αIIbβ3

Hemostasis and thrombosis (blood clotting) involve fibrinogen binding to integrin αIIbβ3 on platelets, resulting in platelet aggregation. αvβ3 binds fibrinogen via an Arg-Asp-Gly (RGD) motif in fibrinogen's α subunit. αIIbβ3 also binds to fibrinogen; however, it does so via an unstructured RGD-lacking C-terminal region of the γ subunit (γC peptide). These distinct modes of fibrinogen binding enable αIIbβ3 and αvβ3 to function cooperatively in hemostasis. In this study, crystal structures reveal the integrin αIIbβ3–γC peptide interface, and, for comparison, integrin αIIbβ3 bound to a lamprey γC primordial RGD motif. Compared with RGD, the GAKQAGDV motif in γC adopts a different backbone configuration and binds over a more extended region. The integrin metal ion–dependent adhesion site (MIDAS) Mg2+ ion binds the γC Asp side chain. The adjacent to MIDAS (ADMIDAS) Ca2+ ion binds the γC C terminus, revealing a contribution for ADMIDAS in ligand binding. Structural data from this natively disordered γC peptide enhances our understanding of the involvement of γC peptide and integrin αIIbβ3 in hemostasis and thrombosis

A Distributed Approach to Efficient Model Predictive Control of Building HVAC Systems

Model based predictive control (MPC) is increasingly being seen as an attractive approach in controlling building HVAC systems. One advantage of the MPC approach is the ability to integrate weather forecast, occupancy information and utility price variations in determining the optimal HVAC operation. However, application to largescale building HVAC systems is limited by the large number of controllable variables to be optimized at every time instance. This paper explores techniques to reduce the computational complexity arising in applying MPC to the control of large-scale buildings. We formulate the task of optimal control as a distributed optimization problem within the MPC framework. A distributed optimization approach alleviates computational costs by simultaneously solving reduced dimensional optimization problems at the subsystem level and integrating the resulting solutions to obtain a global control law. Additional computational efficiency can be achieved by utilizing the occupancy and utility price profiles to restrict the control laws to a piecewise constant function. Alternatively, under certain assumptions, the optimal control laws can be found analytically using a dynamic programming based approach without resorting to numerical optimization routines leading to massive computational savings. Initial results of simulations on case studies are presented to compare the proposed algorithms

Structure of a Complete Integrin Ectodomain in a Physiologic Resting State and Activation and Deactivation by Applied Forces

The complete ectodomain of integrin αIIbβ3 reveals a bent, closed, low-affinity conformation, the β knee, and a mechanism for linking cytoskeleton attachment to high affinity for ligand. Ca and Mg ions in the recognition site, including the synergistic metal ion binding site (SyMBS), are loaded prior to ligand binding. Electrophilicity of the ligand-binding Mg ion is increased in the open conformation. The β3 knee passes between the β3-PSI and αIIb-knob to bury the lower β leg in a cleft, from which it is released for extension. Different integrin molecules in crystals and EM reveal breathing that appears on pathway to extension. Tensile force applied to the extended ligand-receptor complex stabilizes the closed, low-affinity conformation. By contrast, an additional lateral force applied to the β subunit to mimic attachment to moving actin filaments stabilizes the open, high-affinity conformation. This mechanism propagates allostery over long distances and couples cytoskeleton attachment of integrins to their high-affinity state. © 2008 Elsevier Inc. All rights reserved

Structural specializations of α4β7\alpha_4 \beta_7, an integrin that mediates rolling adhesion

The lymphocyte homing receptor integrin $\alpha_4 \beta_7$ is unusual for its ability to mediate both rolling and firm adhesion. $\alpha_4 \beta_1$ and $\alpha_4 \beta_7$ are targeted by therapeutics approved for multiple sclerosis and Crohn’s disease. Here, we show by electron microscopy and crystallography how two therapeutic Fabs, a small molecule (RO0505376), and mucosal adhesion molecule-1 (MAdCAM-1) bind α4β7. A long binding groove at the $\alpha_4 -\beta_7$interface for immunoglobulin superfamily domains differs in shape from integrin pockets that bind Arg-Gly-Asp motifs. RO0505376 mimics an Ile/Leu-Asp motif in $\alpha_4$ ligands, and orients differently from Arg-Gly-Asp mimics. A novel auxiliary residue at the metal ion–dependent adhesion site in $\alpha_4 \beta_7$ is essential for binding to MAdCAM-1 in $Mg^{2+}$ yet swings away when RO0505376 binds. A novel intermediate conformation of the $\alpha_4 \beta_7$ headpiece binds MAdCAM-1 and supports rolling adhesion. Lack of induction of the open headpiece conformation by ligand binding enables rolling adhesion to persist until integrin activation is signaled

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Structural study of a novel vitamin B6 biosynthetic pathway

Pyridoxal 5\u27-phosphate (PLP, vitamin B6), a cofactor in many enzymatic reactions, has two distinct biosynthetic routes, which do not coexist in any organism. Two proteins, known as PdxS and PdxT, together form a PLP synthase in plants, fungi, archaea, and some eubacteria. PLP synthase is a heteromeric glutamine amidotransferase in which PdxT produces ammonia from glutamine and PdxS combines ammonia with five- and three-carbon phosphosugars to form PLP. A 2.2-Å crystal structure of PdxS is reported in this thesis. PdxS monomer has a classic (β/α)8 barrel fold. However, PdxS monomers form a cylindrical dodecamer in the crystal. Two hexamer rings of PdxS are linked by sulfate ions between the rings with the active sites positioned on the inside of the cylinder. A novel phosphate-binding site is suggested by another bound sulfate. This sulfate, bound at the top of the barrel, and another bound molecule, methyl pentanedial (MPD), were used to model the substrate ribulose 5-phosphate, and to propose catalytic roles for residues in the active site. The aggregation states of PdxS, PdxT and PLP synthase were investigated by analytical ultracentrifugation (AUC). The hexamer and dodecamer forms of PdxS coexist in solution. PdxT is a monomer in solution. PLP synthase is composed of a PdxS dodecamer core plus 12 PdxT subunits. The structures of PdxS and PLP synthase in solution were studied by small angle X-ray scattering (SAXS). The PdxS structure in solution is consistent with the crystal structure. The structure determination of PLP synthase in solution turned to be a much more difficult case than expected and more investigations are needed. A model of PLP synthase was proposed based on the distribution of conserved surfaces in the PdxS dodecdamer, the results from AUC experiments, and the information from SAXS experiments

Numerical Investigation of Passive Vortex Generators on a Wind Turbine Airfoil Undergoing Pitch Oscillations

Passive vortex generators (VGs) are widely used to suppress the flow separation of wind turbine blades, and hence, to improve rotor performance. VGs have been extensively investigated on stationary airfoils; however, their influence on unsteady airfoil flow remains unclear. Thus, we evaluated the unsteady aerodynamic responses of the DU-97-W300 airfoil with and without VGs undergoing pitch oscillations, which is a typical motion of the turbine unsteady operating conditions. The airfoil flow is simulated by numerically solving the unsteady Reynolds-averaged Navier-Stokes equations with fully resolved VGs. Numerical modelling is validated by good agreement between the calculated and experimental data with respect to the unsteady-uncontrolled flow under pitch oscillations, and the steady-controlled flow with VGs. The dynamic stall of the airfoil was found to be effectively suppressed by VGs. The lift hysteresis intensity is greatly decreased, i.e., by 72.7%, at moderate unsteadiness, and its sensitivity to the reduced frequency is favorably reduced. The influences of vane height and chordwise installation are investigated on the unsteady aerodynamic responses as well. In a no-stall flow regime, decreasing vane height and positioning VGs further downstream can lead to relatively high effectiveness. Compared with the baseline VG geometry, the smaller VGs can decrease the decay exponent of nondimensionalized peak vorticity by almost 0.02, and installation further downstream can increase the aerodynamic pitch damping by 0.0278. The obtained results are helpful to understand the dynamic stall control by means of conventional VGs and to develop more effective VG designs for both steady and unsteady wind turbine airfoil flow