Structural and Biophysical Characterization of Variants of the Mechanosensitive Channel of Large Conductance (MSCL)

The ability to sense mechanical force is vital to all organisms to interact with and respond to stimuli in their environment. Mechanosensation is critical to many physiological functions such as the senses of hearing and touch in animals, gravitropism in plants and osmoregulation in bacteria. Of these processes, the best understood at the molecular level involve bacterial mechanosensitive channels. Under hypo-osmotic stress, bacteria are able to alleviate turgor pressure through mechanosensitive channels that gate directly in response to tension in the membrane lipid bilayer. A key participant in this response is the mechanosensitive channel of large conductance (MscL), a non-selective channel with a high conductance of ~3 nS that gates at tensions close to the membrane lytic tension.

It has been appreciated since the original discovery by C. Kung that the small subunit size (~130 to 160 residues) and the high conductance necessitate that MscL forms a homo-oligomeric channel. Over the past 20 years of study, the proposed oligomeric state of MscL has ranged from monomer to hexamer. Oligomeric state has been shown to vary between MscL homologues and is influenced by lipid/detergent environment. In this thesis, we report the creation of a chimera library to systematically survey the correlation between MscL sequence and oligomeric state to identify the sequence determinants of oligomeric state. Our results demonstrate that although there is no combination of sequences uniquely associated with a given oligomeric state (or mixture of oligomeric states), there are significant correlations. In the quest to characterize the oligomeric state of MscL, an exciting discovery was made about the dynamic nature of the MscL complex. We found that in detergent solution, under mild heating conditions (37 °C – 60 °C), subunits of MscL can exchange between complexes, and the dynamics of this process are sensitive to the protein sequence.

Extensive efforts were made to produce high diffraction quality crystals of MscL for the determination of a high resolution X-ray crystal structure of a full length channel. The surface entropy reduction strategy was applied to the design of S. aureus MscL variants and while the strategy appears to have improved the crystallizability of S. aureus MscL, unfortunately the diffraction qualities of these crystals were not significantly improved. MscL chimeras were also screened for crystallization in various solubilization detergents, but also failed to yield high quality crystals.

MscL is a fascinating protein and continues to serve as a model system for the study of the structural and functional properties of mechanosensitive channels. Further characterization of the MscL chimera library will offer more insight into the characteristics of the channel. Of particular interest are the functional characterization of the chimeras and the exploration of the physiological relevance of intercomplex subunit exchange.

Structural Characterizations of the Dimeric Anti-HIV Antibody 2G12 and the HIV-2 Envelope Glycoprotein

More than thirty years after the discovery that Human Immunodeficiency Virus (HIV) was the causative agent of Acquired Immunodeficiency Syndrome (AIDS), the disease remains pandemic as long as no effective universal vaccine is found. Over 34 million individuals in the world are infected with the virus, and the vast majority of them have no access to the antiretroviral therapies that have largely reduced HIV to a chronic disease in the developed world. The first chapter of this thesis introduces the history of the virus. The key to the infectious mechanism of the virus lies in its envelope glycoprotein (Env), a trimeric spike on the viral surface that utilizes host T cell receptors for entry. Though HIV-1 Env is immunogenic, most infected patients do not mount an effective neutralizing antibody response against it. Broadly-neutralizing anti-Env antibodies (bNAbs) present in the serum of a minority of infected individuals are usually sufficient to prevent the progression to full blown AIDS. Thus, the molecular details of these bNAbs as well as the antibody-antigen interface are of prime interest for structural studies, as insight gained would contribute to the design of a more effective immunogen and potential vaccine candidate. The second chapter of this thesis describes the low-resolution crystal structure of one such antibody, 2G12 dimer, which targets a high mannose epitope on the surface of Env. Patients infected with HIV-2, a related virus with ~35% sequence identity in the Env region, can generally mount a robust antibody response sufficient for viral control for reasons still unknown. The final two chapters of this thesis focus on the first reported structural studies of HIV-2 Env, the molecular details of which may inform HIV-1 therapy and immunogen design.

Structural Characterization of Pro-inflammatory and Anti-inflammatory Immunoglobulin G Fc Proteins

Immunoglobulin G (IgG) is central in mediating host defense due to its ability to target and eliminate invading pathogens. The fragment antigen binding (Fab) regions are responsible for antigen recognition; however the effector responses are encoded on the Fc region of IgG. IgG Fc displays considerable glycan heterogeneity, accounting for its complex effector functions of inflammation, modulation and immune suppression. Intravenous immunoglobulin G (IVIG) is pooled serum IgG from multiple donors and is used to treat individuals with autoimmune and inflammatory disorders such as rheumatoid arthritis and Kawasaki’s disease, respectively. It contains all the subtypes of IgG (IgG1-4) and over 120 glycovariants due to variation of an Asparagine 297-linked glycan on the Fc. The species identified as the activating component of IVIG is sialylated IgG Fc. Comparisons of wild type Fc and sialylated Fc X-ray crystal structures suggests that sialylation causes an increase in conformational flexibility, which may be important for its anti-inflammatory properties.

Although glycan modifications can promote the anti-inflammatory properties of the Fc, there are amino acid substitutions that cause Fcs to initiate an enhanced immune response. Mutations in the Fc can cause up to a 100-fold increase in binding affinity to activating Fc gamma receptors located on immune cells, and have been shown to enhance antibody dependent cell-mediated cytotoxicity. This is important in developing therapeutic antibodies against cancer and infectious diseases. Structural studies of mutant Fcs in complex with activating receptors gave insight into new protein-protein interactions that lead to an enhanced binding affinity.

Together these studies show how dynamic and diverse the Fc region is and how both protein and carbohydrate modifications can alter structure, leading to IgG Fc’s switch from a pro-inflammatory to an anti-inflammatory protein.

Exploring the Kinetics of Domain Switching in Ferroelectrics for Structural Applications

The complex domain structure in ferroelectrics gives rise to electromechanical coupling, and its evolution (via domain switching) results in a time-dependent (i.e. viscoelastic) response. Although ferroelectrics are used in many technological applications, most do not attempt to exploit the viscoelastic response of ferroelectrics, mainly due to a lack of understanding and accurate models for their description and prediction. Thus, the aim of this thesis research is to gain better understanding of the influence of domain evolution in ferroelectrics on their dynamic mechanical response. There have been few studies on the viscoelastic properties of ferroelectrics, mainly due to a lack of experimental methods. Therefore, an apparatus and method called Broadband Electromechanical Spectroscopy (BES) was designed and built. BES allows for the simultaneous application of dynamic mechanical and electrical loading in a vacuum environment. Using BES, the dynamic stiffness and loss tangent in bending and torsion of a particular ferroelectric, viz. lead zirconate titanate (PZT), was characterized for different combinations of electrical and mechanical loading frequencies throughout the entire electric displacement hysteresis. Experimental results showed significant increases in loss tangent (by nearly an order of magnitude) and compliance during domain switching, which shows promise as a new approach to structural damping. A continuum model of the viscoelasticity of ferroelectrics was developed, which incorporates microstructural evolution via internal variables and associated kinetic relations. For the first time, through a new linearization process, the incremental dynamic stiffness and loss tangent of materials were computed throughout the entire electric displacement hysteresis for different combinations of mechanical and electrical loading frequencies. The model accurately captured experimental results. Using the understanding gained from the characterization and modeling of PZT, two applications of domain switching kinetics were explored by using Micro Fiber Composites (MFCs). Proofs of concept of set-and-hold actuation and structural damping using MFCs were demonstrated.

Analysis of a concrete arch highway bridge reinforced with structural steel

An article in the Engineering News-Record for March 30, 1923, describes a new concrete arch bridge across the Connecticut River between Springfield and West Springfield, Mass.

Fabrication, Characterization, And Deformation of 3D Structural Meta-Materials

Current technological advances in fabrication methods have provided pathways to creating architected structural meta-materials similar to those found in natural organisms that are structurally robust and lightweight, such as diatoms. Structural meta-materials are materials with mechanical properties that are determined by material properties at various length scales, which range from the material microstructure (nm) to the macro-scale architecture (μm – mm). It is now possible to exploit material size effect, which emerge at the nanometer length scale, as well as structural effects to tune the material properties and failure mechanisms of small-scale cellular solids, such as nanolattices. This work demonstrates the fabrication and mechanical properties of 3-dimensional hollow nanolattices in both tension and compression. Hollow gold nanolattices loaded in uniaxial compression demonstrate that strength and stiffness vary as a function of geometry and tube wall thickness. Structural effects were explored by increasing the unit cell angle from 30° to 60° while keeping all other parameters constant; material size effects were probed by varying the tube wall thickness, t, from 200nm to 635nm, at a constant relative density and grain size. In-situ uniaxial compression experiments reveal an order-of-magnitude increase in yield stress and modulus in nanolattices with greater lattice angles, and a 150% increase in the yield strength without a concomitant change in modulus in thicker-walled nanolattices for fixed lattice angles. These results imply that independent control of structural and material size effects enables tunability of mechanical properties of 3-dimensional architected meta-materials and highlight the importance of material, geometric, and microstructural effects in small-scale mechanics. This work also explores the flaw tolerance of 3D hollow-tube alumina kagome nanolattices with and without pre-fabricated notches, both in experiment and simulation. Experiments demonstrate that the hollow kagome nanolattices in uniaxial tension always fail at the same load when the ratio of notch length (a) to sample width (w) is no greater than 1/3, with no correlation between failure occurring at or away from the notch. For notches with (a/w) > 1/3, the samples fail at lower peak loads and this is attributed to the increased compliance as fewer unit cells span the un-notched region. Finite element simulations of the kagome tension samples show that the failure is governed by tensile loading for (a/w) < 1/3 but as (a/w) increases, bending begins to play a significant role in the failure. This work explores the flaw sensitivity of hollow alumina kagome nanolattices in tension, using experiments and simulations, and demonstrates that the discrete-continuum duality of architected structural meta-materials gives rise to their flaw insensitivity even when made entirely of intrinsically brittle materials.

SteelConverter and Caltech VirtualShaker: Rapid Nonlinear Cloud-Based Structural Model Conversion and Analysis

STEEL, the Caltech created nonlinear large displacement analysis software, is currently used by a large number of researchers at Caltech. However, due to its complexity, lack of visualization tools (such as pre- and post-processing capabilities) rapid creation and analysis of models using this software was difficult. SteelConverter was created as a means to facilitate model creation through the use of the industry standard finite element solver ETABS. This software allows users to create models in ETABS and intelligently convert model information such as geometry, loading, releases, fixity, etc., into a format that STEEL understands. Models that would take several days to create and verify now take several hours or less. The productivity of the researcher as well as the level of confidence in the model being analyzed is greatly increased.

It has always been a major goal of Caltech to spread the knowledge created here to other universities. However, due to the complexity of STEEL it was difficult for researchers or engineers from other universities to conduct analyses. While SteelConverter did help researchers at Caltech improve their research, sending SteelConverter and its documentation to other universities was less than ideal. Issues of version control, individual computer requirements, and the difficulty of releasing updates made a more centralized solution preferred. This is where the idea for Caltech VirtualShaker was born. Through the creation of a centralized website where users could log in, submit, analyze, and process models in the cloud, all of the major concerns associated with the utilization of SteelConverter were eliminated. Caltech VirtualShaker allows users to create profiles where defaults associated with their most commonly run models are saved, and allows them to submit multiple jobs to an online virtual server to be analyzed and post-processed. The creation of this website not only allowed for more rapid distribution of this tool, but also created a means for engineers and researchers with no access to powerful computer clusters to run computationally intensive analyses without the excessive cost of building and maintaining a computer cluster.

In order to increase confidence in the use of STEEL as an analysis system, as well as verify the conversion tools, a series of comparisons were done between STEEL and ETABS. Six models of increasing complexity, ranging from a cantilever column to a twenty-story moment frame, were analyzed to determine the ability of STEEL to accurately calculate basic model properties such as elastic stiffness and damping through a free vibration analysis as well as more complex structural properties such as overall structural capacity through a pushover analysis. These analyses showed a very strong agreement between the two softwares on every aspect of each analysis. However, these analyses also showed the ability of the STEEL analysis algorithm to converge at significantly larger drifts than ETABS when using the more computationally expensive and structurally realistic fiber hinges. Following the ETABS analysis, it was decided to repeat the comparisons in a software more capable of conducting highly nonlinear analysis, called Perform. These analyses again showed a very strong agreement between the two softwares in every aspect of each analysis through instability. However, due to some limitations in Perform, free vibration analyses for the three story one bay chevron brace frame, two bay chevron brace frame, and twenty story moment frame could not be conducted. With the current trend towards ultimate capacity analysis, the ability to use fiber based models allows engineers to gain a better understanding of a building’s behavior under these extreme load scenarios.

Following this, a final study was done on Hall’s U20 structure [1] where the structure was analyzed in all three softwares and their results compared. The pushover curves from each software were compared and the differences caused by variations in software implementation explained. From this, conclusions can be drawn on the effectiveness of each analysis tool when attempting to analyze structures through the point of geometric instability. The analyses show that while ETABS was capable of accurately determining the elastic stiffness of the model, following the onset of inelastic behavior the analysis tool failed to converge. However, for the small number of time steps the ETABS analysis was converging, its results exactly matched those of STEEL, leading to the conclusion that ETABS is not an appropriate analysis package for analyzing a structure through the point of collapse when using fiber elements throughout the model. The analyses also showed that while Perform was capable of calculating the response of the structure accurately, restrictions in the material model resulted in a pushover curve that did not match that of STEEL exactly, particularly post collapse. However, such problems could be alleviated by choosing a more simplistic material model.

Synthesis and structural characterisation of [Cu2[(PDC)2(bpa)(H2O)2]•nH2O•mDMF (n=3 and m=1 for 1, n=7 and m=0 for 2, PDC=2,5-pyrindinedicarboxylate and bpa= 1,2-di(4-pyridil)ethane))

[EN] Combination of polycarboxylate anions and dipyridyl ligands is an effective strategy to produce solid coordination frameworks (SCF) which are crystalline materials based on connections between metal ions through organic ligands. In this sense, combination of polycarboxylate anions and dipyridyl ligands is an effective strategy to produce extended structures. In this context, this work is focused on two novel CuII-based SCFs exhibiting PDC (2,5-pyridinedicarboxylate) and bpa (1,2-di(4-pyridyl)ethane), being the first structures reported in literature containing both ligands. Chemical formula are [Cu2[(PDC)2(bpa)(H2O)2]•3H2O•DMF (1), and [Cu2(PDC)2(bpa)(H2O)2]•7H2O (2), where DMF is dimethylformamide. Compounds 1 and 2 have been characterized by means of XRD, IR, TG/DTG, and DTA analysis.