Showing papers by "David E. Shaw published in 2011"

How Fast-Folding Proteins Fold

Abstract: An outstanding challenge in the field of molecular biology has been to understand the process by which proteins fold into their characteristic three-dimensional structures. Here, we report the results of atomic-level molecular dynamics simulations, over periods ranging between 100 μs and 1 ms, that reveal a set of common principles underlying the folding of 12 structurally diverse proteins. In simulations conducted with a single physics-based energy function, the proteins, representing all three major structural classes, spontaneously and repeatedly fold to their experimentally determined native structures. Early in the folding process, the protein backbone adopts a nativelike topology while certain secondary structure elements and a small number of nonlocal contacts form. In most cases, folding follows a single dominant route in which elements of the native structure appear in an order highly correlated with their propensity to form in the unfolded state.

Structure and function of an irreversible agonist-β2 adrenoceptor complex

Abstract: G-protein-coupled receptors (GPCRs) are eukaryotic integral membrane proteins that modulate biological function by initiating cellular signalling in response to chemically diverse agonists. Despite recent progress in the structural biology of GPCRs, the molecular basis for agonist binding and allosteric modulation of these proteins is poorly understood. Structural knowledge of agonist-bound states is essential for deciphering the mechanism of receptor activation, and for structure-guided design and optimization of ligands. However, the crystallization of agonist-bound GPCRs has been hampered by modest affinities and rapid off-rates of available agonists. Using the inactive structure of the human β(2) adrenergic receptor (β(2)AR) as a guide, we designed a β(2)AR agonist that can be covalently tethered to a specific site on the receptor through a disulphide bond. The covalent β(2)AR-agonist complex forms efficiently, and is capable of activating a heterotrimeric G protein. We crystallized a covalent agonist-bound β(2)AR-T4L fusion protein in lipid bilayers through the use of the lipidic mesophase method, and determined its structure at 3.5 A resolution. A comparison to the inactive structure and an antibody-stabilized active structure (companion paper) shows how binding events at both the extracellular and intracellular surfaces are required to stabilize an active conformation of the receptor. The structures are in agreement with long-timescale (up to 30 μs) molecular dynamics simulations showing that an agonist-bound active conformation spontaneously relaxes to an inactive-like conformation in the absence of a G protein or stabilizing antibody.

How does a drug molecule find its target binding site

Abstract: Although the thermodynamic principles that control the binding of drug molecules to their protein targets are well understood, detailed experimental characterization of the process by which such binding occurs has proven challenging. We conducted relatively long, unguided molecular dynamics simulations in which a ligand (the cancer drug dasatinib or the kinase inhibitor PP1) was initially placed at a random location within a box that also contained a protein (Src kinase) to which that ligand was known to bind. In several of these simulations, the ligand correctly identified its target binding site, forming a complex virtually identical to the crystallographically determined bound structure. The simulated trajectories provide a continuous, atomic-level view of the entire binding process, revealing persistent and noteworthy intermediate conformations and shedding light on the role of water molecules. The technique we employed, which does not assume any prior knowledge of the binding site's location, may prove particularly useful in the development of allosteric inhibitors that target previously undiscovered binding sites.

Pathway and mechanism of drug binding to G-protein-coupled receptors

Abstract: How drugs bind to their receptors--from initial association, through drug entry into the binding pocket, to adoption of the final bound conformation, or "pose"--has remained unknown, even for G-protein-coupled receptor modulators, which constitute one-third of all marketed drugs. We captured this pharmaceutically critical process in atomic detail using the first unbiased molecular dynamics simulations in which drug molecules spontaneously associate with G-protein-coupled receptors to achieve final poses matching those determined crystallographically. We found that several beta blockers and a beta agonist all traverse the same well-defined, dominant pathway as they bind to the β(1)- and β(2)-adrenergic receptors, initially making contact with a vestibule on each receptor's extracellular surface. Surprisingly, association with this vestibule, at a distance of 15 A from the binding pocket, often presents the largest energetic barrier to binding, despite the fact that subsequent entry into the binding pocket requires the receptor to deform and the drug to squeeze through a narrow passage. The early barrier appears to reflect the substantial dehydration that takes place as the drug associates with the vestibule. Our atomic-level description of the binding process suggests opportunities for allosteric modulation and provides a structural foundation for future optimization of drug-receptor binding and unbinding rates.

Activation mechanism of the β2-adrenergic receptor

Abstract: A third of marketed drugs act by binding to a G-protein-coupled receptor (GPCR) and either triggering or preventing receptor activation. Although recent crystal structures have provided snapshots of both active and inactive functional states of GPCRs, these structures do not reveal the mechanism by which GPCRs transition between these states. Here we propose an activation mechanism for the β2-adrenergic receptor, a prototypical GPCR, based on atomic-level simulations in which an agonist-bound receptor transitions spontaneously from the active to the inactive crystallographically observed conformation. A loosely coupled allosteric network, comprising three regions that can each switch individually between multiple distinct conformations, links small perturbations at the extracellular drug-binding site to large conformational changes at the intracellular G-protein-binding site. Our simulations also exhibit an intermediate that may represent a receptor conformation to which a G protein binds during activation, and suggest that the first structural changes during receptor activation often take place on the intracellular side of the receptor, far from the drug-binding site. By capturing this fundamental signaling process in atomic detail, our results may provide a foundation for the design of drugs that control receptor signaling more precisely by stabilizing specific receptor conformations.

Parallel random numbers: as easy as 1, 2, 3

Abstract: Most pseudorandom number generators (PRNGs) scale poorly to massively parallel high-performance computation because they are designed as sequentially dependent state transformations. We demonstrate that independent, keyed transformations of counters produce a large alternative class of PRNGs with excellent statistical properties (long period, no discernable structure or correlation). These counter-based PRNGs are ideally suited to modern multi-core CPUs, GPUs, clusters, and special-purpose hardware because they vectorize and parallelize well, and require little or no memory for state. We introduce several counter-based PRNGs: some based on cryptographic standards (AES, Threefish) and some completely new (Philox). All our PRNGs pass rigorous statistical tests (including TestU01's BigCrush) and produce at least 264 unique parallel streams of random numbers, each with period 2128 or more. In addition to essentially unlimited parallel scalability, our PRNGs offer excellent single-chip performance: Philox is faster than the CURAND library on a single NVIDIA GPU.

Targeting the Urokinase Plasminogen Activator Receptor Inhibits Ovarian Cancer Metastasis

Abstract: Purpose: To understand the functional and preclinical efficacy of targeting the urokinase plasminogen activator receptor (u-PAR) in ovarian cancer. Experimental Design: Expression of u-PAR was studied in 162 epithelial ovarian cancers, including 77 pairs of corresponding primary and metastatic tumors. The effect of an antibody against u-PAR (ATN-658) on proliferation, adhesion, invasion, apoptosis, and migration was assessed in 3 (SKOV3ip1, HeyA8, and CaOV3) ovarian cancer cell lines. The impact of the u-PAR antibody on tumor weight, number, and survival was examined in corresponding ovarian cancer xenograft models and the mechanism by which ATN-658 blocks metastasis was explored. Results: Only 8% of all ovarian tumors were negative for u-PAR expression. Treatment of SKOV3ip1, HeyA8, and CaOV3 ovarian cancer cell lines with the u-PAR antibody inhibited cell invasion, migration, and adhesion. In vivo , anti-u-PAR treatment reduced the number of tumors and tumor weight in CaOV3 and SKOV3ip1 xenografts and reduced tumor weight and increased survival in HeyA8 xenografts. Immunostaining of CaOV3 xenograft tumors and ovarian cancer cell lines showed an increase in active-caspase 3 and TUNEL staining. Treatment with u-PAR antibody inhibited α 5 -integrin and u-PAR colocalization on primary human omental extracellular matrix. Anti-u-PAR treatment also decreased the expression of urokinase, u-PAR, β 3 -integrin, and fibroblast growth factor receptor-1 both in vitro and in vivo . Conclusions: This study shows that an antibody against u-PAR reduces metastasis, induces apoptosis, and reduces the interaction between u-PAR and α 5 -integrin. This provides a rationale for targeting the u-PAR pathway in patients with ovarian cancer and for further testing of ATN-658 in this indication. Clin Cancer Res; 17(3); 459–71. ©2010 AACR .

Insights into the conformational flexibility of Bruton's tyrosine kinase from multiple ligand complex structures.

Abstract: Bruton's tyrosine kinase (BTK) plays a key role in B cell receptor signaling and is considered a promising drug target for lymphoma and inflammatory diseases. We have determined the X-ray crystal structures of BTK kinase domain in complex with six inhibitors from distinct chemical classes. Five different BTK protein conformations are stabilized by the bound inhibitors, providing insights into the structural flexibility of the Gly-rich loop, helix C, the DFG sequence, and activation loop. The conformational changes occur independent of activation loop phosphorylation and do not correlate with the structurally unchanged WEI motif in the Src homology 2-kinase domain linker. Two novel activation loop conformations and an atypical DFG conformation are observed representing unique inactive states of BTK. Two regions within the activation loop are shown to structurally transform between 310- and α-helices, one of which collapses into the adenosine-5′-triphosphate binding pocket. The first crystal structure of a Tec kinase family member in the pharmacologically important DFG-out conformation and bound to a type II kinase inhibitor is described. The different protein conformations observed provide insights into the structural flexibility of BTK, the molecular basis of its regulation, and the structure-based design of specific inhibitors.

Radix-8 Digit-by-Rounding: Achieving High-Performance Reciprocals, Square Roots, and Reciprocal Square Roots

Abstract: We describe a high-performance digit-recurrence algorithm for computing exactly rounded reciprocals, square roots, and reciprocal square roots in hardware at a rate of three result bits -- one radix-8 digit -- per recurrence iteration. To achieve a single-cycle recurrence at a short cycle time, we adapted the digit-by-rounding algorithm, which is normally applied at much higher radices, for efficient operation at radix 8. Using this approach avoids in the recurrence step the lookup table required by SRT -- the usual algorithm used for hardware digit recurrences. The increasing access latency of this table, the size of which grows super linearly in the radix, limits high-frequency SRT implementations to radix 4 or lower. We also developed a series of novel optimizations focused on further reducing the critical path through the recurrence. We propose, for example, decreasing data path widths to a point where erroneous results sometimes occur and then correcting these errors off the critical path. We present a specific implementation that computes any of these functions to 31 bits of precision in 13 cycles. Our implementation achieves a cycle time only 11% longer than the best reported SRT design for the same functions, yet delivers results in five fewer cycles. Finally, we show that even at lower radices, a digit-by-rounding design is likely to have a shorter critical path than one using SRT at the same radix.

Overcoming Communication Latency Barriers in Massively Parallel Scientific Computation

Abstract: Anton, a massively parallel special-purpose machine that accelerates molecular dynamics simulations by orders of magnitude, uses a combination of specialized hardware mechanisms and restructured software algorithms to reduce and hide communication latency. Anton delivers end-to-end internode latency significantly lower than any other large-scale parallel machine, and its critical-path communication time for molecular dynamics simulations is less than 3 percent that of the next-fastest platform.

Chapter 20:Probing the Conformational Dynamics of GPCRs with Molecular Dynamics Simulation

Abstract: A mounting body of evidence indicates that G-protein–coupled receptors (GPCRs), which represent the largest class of both human membrane proteins and drug targets, can interconvert between numerous conformational states with distinct intracellular signaling profiles. Molecular dynamics (MD) simulation represents a promising method for characterizing these states, their role in signal transduction, and the mechanisms by which drugs and endogenous ligands select among them. Dramatic increases in achievable simulation length and an explosion in the number of available GPCR crystal structures are beginning to remove the major obstacles that have hindered MD simulations of GPCRs in the past. Here, we summarize the factors determining the applicability of MD simulation to the study of GPCR conformational dynamics, provide a brief history of GPCR simulations, and discuss future prospects for using MD to elucidate the dynamical behavior of GPCRs as well as their interactions with ligands and intracellular signaling proteins.

Tight Certification Techniques for Digit-by-Rounding Algorithms with Application to a New 1/sqrt(x) Design

Abstract: Digit-by-rounding algorithms enable efficient hardware implementations of algebraic functions such as the reciprocal, square root, or reciprocal square root, but certifying the correctness of such algorithms is a nontrivial endeavor. Traditionally, sufficient conditions for correctness are derived as closed-form formulae relating key design parameters. These sufficient conditions, however, often prove stricter than necessary, excluding correct and efficient designs. In this paper, we present a rigorous, computer-aided method for correctness certification that better approximates the necessary conditions, lowering the risk of rejecting correct designs. We also present two specific applications of this method. First, when applied to a conventional digit-by-rounding reciprocal square root design, our method enabled a fourfold reduction in lookup table size relative to the minimum dictated by a standard sufficient condition. Second, our method certified the correctness of a novel reciprocal square root design that we developed to parallelize two computational steps whose sequential execution lies on the critical path of conventional designs. The difficulty in deriving closed-form sufficient conditions to ascertain this design's correctness provided the original motivation for development of the new certification method.

Zonal methods for computation of particle interactions

Abstract: A generalized approach to particle interaction can confer advantages over previously described method in terms of one or more of communications bandwidth and latency and memory access characteristics. These generalizations can involve one or more of at least spatial decomposition, import region rounding, and multiple zone communication scheduling. An architecture for computation of particle interactions makes use various forms of parallelism. In one implementation, the parallelism involves using multiple computation nodes arranged according to a geometric partitioning of a simulation volume.

***WITHDRAWN PATENT AS PER THE LATEST USPTO WITHDRAWN LIST***Approaches and architectures for computation of particle interactions

Abstract: A generalized approach to particle interaction can confer advantages over previously described method in terms of one or more of communications bandwidth and latency and memory access characteristics. These generalizations can involve one or more of at least spatial decomposition, import region rounding, and multiple zone communication scheduling. An architecture for computation of particle interactions makes use various forms of parallelism. In one implementation, the parallelism involves using multiple computation nodes arranged according to a geometric partitioning of a simulation volume.