Hui Lu - US grants

Titin, a 1(m-long protein (7,800 atoms) found in striated muscle myofibrils, possesses unique elastic and extensibility properties in its I-band region, which is largely composed of a PEVK region and 7-strand (-sandwich immunoglobulin-like (Ig) domains [50]. The behavior of titin as a multi-stage entropic spring has been shown in atomic force microscopy [54] and optical tweezer experiments to partially depend on the reversible unfolding of individual Ig domains. We performed SMD simulations* to stretch single titin Ig domains in solution with pulling speeds of 0.5 and 1.0E/ps [7]. The resulting force-extension profiles exhibit a single dominant peak for each Ig domain unfolding, consistent with the experimentally observed sequential, as opposed to concerted, unfolding of Ig domains under external stretching forces. This force peak can be attributed to an initial burst of backbone hydrogen bonds, which takes place between anti-parallel (-strands A and B and between paral lel (-strands A' and G. Additional features of the simulations, including the position of the force peak and relative unfolding resistance of different Ig domains, can be related to experimental observations. Similar elastic behavior is also found in other protein domains, such as tenascin fibronectin-III-like domains. Simulations of fibronectin-III domain unfolding, and of unfolding of two connected Ig domains, are currently ongoing.

To characterize the dynamic behavior of calmodulin in solution, we have carried out molecular dynamics (MD) simulations of the Ca2+-loaded structure* (see reference [91]). The crystal structure of calmodulin was placed in a solvent sphere of radius 44E, and 6 Cl- and 22 Na+ ions were included to neutralize the system and to model a 150 mM salt concentration. The total number of atoms was 32,867. During the 3 ns simulation the structure exhibits large conformational changes on the nanosecond time scale. The central alpha-helix, which has been shown to unwind locally upon binding of calmodulin to target proteins, bends and unwinds near residue Arg74. We interpret this result as a preparative step in the more extensive structural transition observed in the "flexible linker" region 74-82 of the central helix upon complex formation. The major structural change is a reorientation of the two Ca2+-binding domains with respect to each other and a rearrangement of alpha-helices i n the N-terminus domain which make the hydrophobic target peptide binding site more accessible. This structural rearrangement brings the domains to a more favorable position for target binding, poised to achieve the orientation observed in the complex of calmodulin with myosin-light-chain-kinase. Analysis of solvent structure reveals an inhomogeneity in the mobility of water in the vicinity of the protein which is attributable to the hydrophobic effect exerted by calmodulin's binding sites for target peptides.

Crystal structures of DNA and protein-DNA complexes show the existence of "fixed" water molecules in the minor and major groove of DNA and at the protein-DNA interface [87, 88]. We studied the effect of these water molecules on the structure and bending of DNA, as well as on the binding specificity, by using DNA with analogues*. It was argued theoretically, and supported experimentally, that a water molecule bridges between the N7 of the purine ring and the exocyclic amino group in adenine bases. The 2'-deoxy-7-hydroxymethyl-7-deazaadenosine analogue (hm7c7dA) [89] was suggested to mimic the role of structural water in the major groove of DNA. This analogue replaces the adenine base and the water molecule bound to it. Four distinct systems, based on the Dickerson dodecamer with d(CGCGAATTCGCG) sequence, were constructed: the dodecamer itself, the dodecamer with both adenine bases at position 5 and 6 mutated, the dodecamer with adenine base at position 5 mutated and the dodecamer with adenine base at position 6 mutated. DNA structure and dynamics are known to be sensitive to hydration, therefore, the DNA was embedded in a previously equilibrated cylinder of water molecules. To counterbalance the negative charge on the DNA backbone, 15 sodium ions were added by replacing 15 water molecules with the highest electrostatic energies of the oxygen atom. There are approximately 12,000 atoms in each system. The molecular dynamics program NAMD was used to run the simulations. For each system, 1ns of dynamics was performed: 250 ps of dynamics with soft constraints on the terminal base-pairs of the DNA and 750 ps of free dynamics in order to yield a better hydration of the DNA bases. The structural deviations of DNA from the initial X-ray crystal structure, evaluated on the basis of root mean square deviations (RMSD) for all four systems, show that the analogue does not affect the overall DNA conformation. Bending points develop in the axis of the DNA at the CG-AA and TT-CG steps in all the simulations. In addition, the analogue does not affect the hydrogen bonding and stacking interactions in either of the simulated structures. Since the (hm7c7dA) analogue does not disrupt the conformation and properties of B-form DNA, the interaction of proteins with DNA containing this analogue will be studied further to better delineate the role of water in protein-DNA interactions. The crystal structure of the trp-repressor bound to DNA [90] will be used as the starting point.

? DESCRIPTION (provided by applicant): Neurogenetic studies provided insight into molecular basis of tens of childhood neurological diseases but in the context of intellectual disabilities an autism spectrum disorders (ASDs) the challenge is how one can explain, similar phenotypes in face of vastly different molecular perturbations. This led to the proposal that the observed behaviors result from some shared patterns of circuit dysfunction. There is a pair of disorders with overlapping phenotypes that presents a unique opportunity to explore circuit-level disruption of homeostasis and its sequelae, particularly for learning and memory: Rett syndrome (RTT), caused by loss-of-function mutations in the X-linked MECP2, and MECP2 duplication syndrome, caused by duplications (or triplications) of the gene. The mechanism accounting for overlapping phenotypes in two syndromes with opposite molecular defects (and transcriptional alterations) remains mysterious. My preliminary data show that both loss and gain of MeCP2 function leads to increased cross-correlations of spontaneous calcium activity and increased sensitivity to GABA blockade in acutely isolated hippocampal slices. This hypersynchrony is caused by an imbalance of excitation and inhibition in the hippocampal circuit. The objective of this proposal is to characterize the malfunction of the hippocampal CA1 circuit in mouse models of RTT and MECP2 duplication syndrome and to explore the possibility of intervention and rescue. I hypothesize that loss and gain of MeCP2 function generates similar patterns of malfunction (circuitopathies) in canonical neural circuits, and that these circuitopathies can be rescued by restoring the imbalance of excitation and inhibition. To address this hypothesis, I propose three specific aims: (1) Elucidate the cellular mechanism underlying the malfunction of hippocampal CA1 circuit caused by MeCP2 dysfunction; (2) Determine how the circuit in hippocampal CA1 responds during learning tasks in Mecp2 mutants; (3) Determine whether altering cellular excitability acutely or chronically can rescue circuit malfunction in MeCP2 disorders. Given that circuit function is what eventually determines behavior, these studies will elucidate the circuit-level mechanism accounting for overlapping phenotypes of Rett syndrome and MECP2 duplication syndrome. It will also reveal the circuit's response to a hippocampal dependent learning behavior and uncover potential correlations between circuit malfunction and behavioral deficits. The data will provide insights into the value of manipulations at the circuit level and might lead to the design of new therapeutic approaches. Research proposed in the K99 mentored phase (year 1 and 2) is concentrated on generating multiple genetic mouse lines to elucidate the cellular mechanism of circuit malfunctions caused by Mecp2 mutation and establishing in vivo calcium imaging with a miniature head-mounted microscope on freely moving mice performing a learning task, all of which will be carried out with the supervision of Dr. Huda Y. Zoghbi and Dr. Stelios Smirnakis. During this phase, I will acquire training on new skills to directly prepare me for a career as an independent research scientist through scheduled weekly lab meetings, mentor supervision and discussion sessions, attending weekly departmental seminars, journal clubs and retreats, participation in joint lab and co- institutional meetings, attendance and participation at national scientific conferences, and enrollment in formal courses. The R00 Independent phase (year 3 to 5) will focus on determining how the circuit in hippocampal CA1 responds during learning tasks in Mecp2 mutants and explore the rescue of Mecp2 disorders. During this phase, I will continue an active relationship with my mentors through scheduled phone conversations and email. I will rely on their input and advice towards hiring lab personnel, budget development, and developing a successful R01 grant application.

The networking landscape has changed dramatically along with two main advances: (1) fast hardware has led to high-speed, high-bandwidth computer networks; (2) new networking architectures, such as software-defined networking, have given rise to a flexible way to operate networking services. Unfortunately, traditional systems software, such as commodity operating systems, faces critical challenges to efficiently support such high-speed networks and new networking architectures. This project will conduct a holistic study of network software stacks in commodity operating systems to identify critical bottlenecks, propose new solutions to address these bottlenecks, and finally validate the proposed solutions using real prototype implementations.

Specifically, the project entails three research thrusts: First, to maximize packet-level parallelism, it will develop a stress-testing approach to locate the serialization bottleneck and design a highly efficient pipelining process to parallelize packet processing in virtualized networks. Second, to improve per-packet processing efficiency for small packets, it will develop a multi-level packet coalescing approach, including hardware interrupt coalescing, software interrupt coalescing, and lossless packet coalescing. Third, to strike a good balance between parallelism and data locality, it will design a holistic scheduling algorithm to optimally multiplex in-kernel interrupts and user-level threads for virtualized network functions.

The knowledge developed in this project will help to improve the key aspects of network performance in commodity operating systems, thus benefiting all systems and applications running on these systems. The research outcomes from this project will have influence on the design and implementation of production networking systems and be integrated into core computer science courses. This project will provide training to undergraduate students, graduate students, and students from underrepresented groups.

The project mainly generates four types of data including prototype implementations, software instrumentation benchmarks, detailed reports of empirical evaluations, and curriculum materials. These data will be maintained on the project website during the execution of the project and for a minimum of three years after the project's ending date: http://www.cs.binghamton.edu/~huilu/projects/CNets.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.