Structure Prediction of G-Protein Coupled Receptors

G-protein coupled receptors (GPCRs) form a large family of proteins and are very important drug targets. They are membrane proteins, which makes computational prediction of their structure challenging. Homology modeling is further complicated by low sequence similarly of the GPCR superfamily.

In this dissertation, we analyze the conserved inter-helical contacts of recently solved crystal structures, and we develop a unified sequence-structural alignment of the GPCR superfamily. We use this method to align 817 human GPCRs, 399 of which are nonolfactory. This alignment can be used to generate high quality homology models for the 817 GPCRs.

To refine the provided GPCR homology models we developed the Trihelix sampling method. We use a multi-scale approach to simplify the problem by treating the transmembrane helices as rigid bodies. In contrast to Monte Carlo structure prediction methods, the Trihelix method does a complete local sampling using discretized coordinates for the transmembrane helices. We validate the method on existing structures and apply it to predict the structure of the lactate receptor, HCAR1. For this receptor, we also build extracellular loops by taking into account constraints from three disulfide bonds. Docking of lactate and 3,5-dihydroxybenzoic acid shows likely involvement of three Arg residues on different transmembrane helices in binding a single ligand molecule.

Protein structure prediction relies on accurate force fields. We next present an effort to improve the quality of charge assignment for large atomic models. In particular, we introduce the formalism of the polarizable charge equilibration scheme (PQEQ) and we describe its implementation in the molecular simulation package Lammps. PQEQ allows fast on the fly charge assignment even for reactive force fields.

Quantifying Earthquake Collapse Risk of Tall Steel Braced Frame Buildings Using Rupture-to-Rafters Simulations

This thesis examines collapse risk of tall steel braced frame buildings using rupture-to-rafters simulations due to suite of San Andreas earthquakes. Two key advancements in this work are the development of (i) a rational methodology for assigning scenario earthquake probabilities and (ii) an artificial correction-free approach to broadband ground motion simulation. The work can be divided into the following sections: earthquake source modeling, earthquake probability calculations, ground motion simulations, building response, and performance analysis.

As a first step the kinematic source inversions of past earthquakes in the magnitude range of 6-8 are used to simulate 60 scenario earthquakes on the San Andreas fault. For each scenario earthquake a 30-year occurrence probability is calculated and we present a rational method to redistribute the forecast earthquake probabilities from UCERF to the simulated scenario earthquake. We illustrate the inner workings of the method through an example involving earthquakes on the San Andreas fault in southern California.

Next, three-component broadband ground motion histories are computed at 636 sites in the greater Los Angeles metropolitan area by superposing short-period (0.2~s-2.0~s) empirical Green's function synthetics on top of long-period ($>$ 2.0~s) spectral element synthetics. We superimpose these seismograms on low-frequency seismograms, computed from kinematic source models using the spectral element method, to produce broadband seismograms.

Using the ground motions at 636 sites for the 60 scenario earthquakes, 3-D nonlinear analysis of several variants of an 18-story steel braced frame building, designed for three soil types using the 1994 and 1997 Uniform Building Code provisions and subjected to these ground motions, are conducted. Model performance is classified into one of five performance levels: Immediate Occupancy, Life Safety, Collapse Prevention, Red-Tagged, and Model Collapse. The results are combined with the 30-year probability of occurrence of the San Andreas scenario earthquakes using the PEER performance based earthquake engineering framework to determine the probability of exceedance of these limit states over the next 30 years.

Quantifying Earthquake Collapse Risk of Tall Steel Moment Frame Buildings Using Rupture-to-Rafters Simulations

There is a sparse number of credible source models available from large-magnitude past earthquakes. A stochastic source model generation algorithm thus becomes necessary for robust risk quantification using scenario earthquakes. We present an algorithm that combines the physics of fault ruptures as imaged in laboratory earthquakes with stress estimates on the fault constrained by field observations to generate stochastic source models for large-magnitude (Mw 6.0-8.0) strike-slip earthquakes. The algorithm is validated through a statistical comparison of synthetic ground motion histories from a stochastically generated source model for a magnitude 7.90 earthquake and a kinematic finite-source inversion of an equivalent magnitude past earthquake on a geometrically similar fault. The synthetic dataset comprises of three-component ground motion waveforms, computed at 636 sites in southern California, for ten hypothetical rupture scenarios (five hypocenters, each with two rupture directions) on the southern San Andreas fault. A similar validation exercise is conducted for a magnitude 6.0 earthquake, the lower magnitude limit for the algorithm. Additionally, ground motions from the Mw7.9 earthquake simulations are compared against predictions by the Campbell-Bozorgnia NGA relation as well as the ShakeOut scenario earthquake. The algorithm is then applied to generate fifty source models for a hypothetical magnitude 7.9 earthquake originating at Parkfield, with rupture propagating from north to south (towards Wrightwood), similar to the 1857 Fort Tejon earthquake. Using the spectral element method, three-component ground motion waveforms are computed in the Los Angeles basin for each scenario earthquake and the sensitivity of ground shaking intensity to seismic source parameters (such as the percentage of asperity area relative to the fault area, rupture speed, and risetime) is studied.

Under plausible San Andreas fault earthquakes in the next 30 years, modeled using the stochastic source algorithm, the performance of two 18-story steel moment frame buildings (UBC 1982 and 1997 designs) in southern California is quantified. The approach integrates rupture-to-rafters simulations into the PEER performance based earthquake engineering (PBEE) framework. Using stochastic sources and computational seismic wave propagation, three-component ground motion histories at 636 sites in southern California are generated for sixty scenario earthquakes on the San Andreas fault. The ruptures, with moment magnitudes in the range of 6.0-8.0, are assumed to occur at five locations on the southern section of the fault. Two unilateral rupture propagation directions are considered. The 30-year probabilities of all plausible ruptures in this magnitude range and in that section of the fault, as forecast by the United States Geological Survey, are distributed among these 60 earthquakes based on proximity and moment release. The response of the two 18-story buildings hypothetically located at each of the 636 sites under 3-component shaking from all 60 events is computed using 3-D nonlinear time-history analysis. Using these results, the probability of the structural response exceeding Immediate Occupancy (IO), Life-Safety (LS), and Collapse Prevention (CP) performance levels under San Andreas fault earthquakes over the next thirty years is evaluated.

Furthermore, the conditional and marginal probability distributions of peak ground velocity (PGV) and displacement (PGD) in Los Angeles and surrounding basins due to earthquakes occurring primarily on the mid-section of southern San Andreas fault are determined using Bayesian model class identification. Simulated ground motions at sites within 55-75km from the source from a suite of 60 earthquakes (Mw 6.0 − 8.0) primarily rupturing mid-section of San Andreas fault are considered for PGV and PGD data.

Studies of response to earthquake ground motion

A study is made of the accuracy of electronic digital computer calculations of ground displacement and response spectra from strong-motion earthquake accelerograms. This involves an investigation of methods of the preparatory reduction of accelerograms into a form useful for the digital computation and of the accuracy of subsequent digital calculations. Various checks are made for both the ground displacement and response spectra results, and it is concluded that the main errors are those involved in digitizing the original record. Differences resulting from various investigators digitizing the same experimental record may become as large as 100% of the maximum computed ground displacements. The spread of the results of ground displacement calculations is greater than that of the response spectra calculations. Standardized methods of adjustment and calculation are recommended, to minimize such errors.

Studies are made of the spread of response spectral values about their mean. The distribution is investigated experimentally by Monte Carlo techniques using an electric analog system with white noise excitation, and histograms are presented indicating the dependence of the distribution on the damping and period of the structure. Approximate distributions are obtained analytically by confirming and extending existing results with accurate digital computer calculations. A comparison of the experimental and analytical approaches indicates good agreement for low damping values where the approximations are valid. A family of distribution curves to be used in conjunction with existing average spectra is presented. The combination of analog and digital computations used with Monte Carlo techniques is a promising approach to the statistical problems of earthquake engineering.

Methods of analysis of very small earthquake ground motion records obtained simultaneously at different sites are discussed. The advantages of Fourier spectrum analysis for certain types of studies and methods of calculation of Fourier spectra are presented. The digitizing and analysis of several earthquake records is described and checks are made of the dependence of results on digitizing procedure, earthquake duration and integration step length. Possible dangers of a direct ratio comparison of Fourier spectra curves are pointed out and the necessity for some type of smoothing procedure before comparison is established. A standard method of analysis for the study of comparative ground motion at different sites is recommended.

The classification and prediction of macroinvertebrate communities in British rivers

This article describes the progress of the River Communities Project which commenced in 1977. This project aimed to develop a sensitive and practical system for river site classification using macroinvertebrates as an objective means of appraising the status of British rivers. The relationship between physical and chemical features of sites and their biological communities were examined. Sampling was undertaken on 41 British rivers. Ordination techniques were used to analyze data and the sites were classified into 16 groups using multiple discrimination analysis. The potential for using the environmental data to predict to which group a site belonged and the fauna likely to be present was investigated.

Investigation of strong earthquake ground motion

The pattern of energy release during the Imperial Valley, California, earthquake of 1940 is studied by analysing the El Centro strong motion seismograph record and records from the Tinemaha seismograph station, 546 km from the epicenter. The earthquake was a multiple event sequence with at least 4 events recorded at El Centro in the first 25 seconds, followed by 9 events recorded in the next 5 minutes. Clear P, S and surface waves were observed on the strong motion record. Although the main part of the earthquake energy was released during the first 15 seconds, some of the later events were as large as M = 5.8 and thus are important for earthquake engineering studies. The moment calculated using Fourier analysis of surface waves agrees with the moment estimated from field measurements of fault offset after the earthquake. The earthquake engineering significance of the complex pattern of energy release is discussed. It is concluded that a cumulative increase in amplitudes of building vibration resulting from the present sequence of shocks would be significant only for structures with relatively long natural period of vibration. However, progressive weakening effects may also lead to greater damage for multiple event earthquakes.

The model with surface Love waves propagating through a single layer as a surface wave guide is studied. It is expected that the derived properties for this simple model illustrate well several phenomena associated with strong earthquake ground motion. First, it is shown that a surface layer, or several layers, will cause the main part of the high frequency energy, radiated from the nearby earthquake, to be confined to the layer as a wave guide. The existence of the surface layer will thus increase the rate of the energy transfer into the man-made structures on or near the surface of the layer. Secondly, the surface amplitude of the guided SH waves will decrease if the energy of the wave is essentially confined to the layer and if the wave propagates towards an increasing layer thickness. It is also shown that the constructive interference of SH waves will cause the zeroes and the peaks in the Fourier amplitude spectrum of the surface ground motion to be continuously displaced towards the longer periods as the distance from the source of the energy release increases.

Influence of local geology on earthquake ground motion

As a simplified approach for estimating theoretically the influence of local subsoils upon the ground motion during an earthquake, the problem of an idealized layered system subjected to vertically incident plane body waves was studied. Both the technique of steady-state analysis and the technique of transient analysis have been used to analyze the problem.

In the steady-state analysis, a recursion formula has been derived for obtaining the response of a layered system to sinusoidally steady-state input. Several conclusions are drawn concerning the nature of the amplification spectrum of a nonviscous layered system having its layer stiffnesses increasing with depth. Numerical examples are given to demonstrate the effect of layer parameters on the amplification spectrum of a layered system.

In the transient analysis, two modified shear beam models have been established for obtaining approximately the response of a layered system to earthquake-like excitation. The method of continuous modal analysis was adopted for approximate analysis of the models, with energy dissipation in the layers, if any, taken into account. Numerical examples are given to demonstrate the accuracy of the models and the effect of a layered system in modifying the input motion.

Conditions are established, under which the theory is applicable to predict the influence of local subsoils on the ground motion during an earthquake. To demonstrate the applicability of the models to actual cases, three examples of actually recorded earthquake events are examined. It is concluded that significant modification of the incoming seismic waves, as predicted by the theory, is likely to occur in well defined soft subsoils during an earthquake, provided that certain conditions concerning the nature of the incoming seismic waves are satisfied.