Protein structure refinement algorithms

Protein structure prediction has remained a major challenge in structural biology for more than half a century. Accelerated and cost efficient sequencing technologies have allowed researchers to sequence new organisms and discover new protein sequences. Novel protein structure prediction technologies will allow researchers to study the structure of proteins and to determine their roles in the underlying biology processes and develop novel therapeutics.

Difficulty of the problem stems from two folds: (a) describing the energy landscape that corresponds to the protein structure, commonly referred to as force field problem; and (b) sampling of the energy landscape, trying to find the lowest energy configuration that is hypothesized to be the native state of the structure in solution. The two problems are interweaved and they have to be solved simultaneously. This thesis is composed of three major contributions. In the first chapter we describe a novel high-resolution protein structure refinement algorithm called GRID. In the second chapter we present REMCGRID, an algorithm for generation of low energy decoy sets. In the third chapter, we present a machine learning approach to ranking decoys by incorporating coarse-grain features of protein structures.

Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry.

In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive.

Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

In Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for "tuning" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious "leak" pathways that compete with desired pathways.

We successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.

Biocombustíveis, governança global e comércio internacional: Rumo a um novo paradigma energético?

Considerando-se este importante momento de transição em que as tradicionais matrizes energéticas são paulatinamente substituídas por um conjunto de fontes renováveis, das quais os biocombustíves sobressaem-se pela capacidade de contribuir para o meio ambiente, trazendo igualmente benefícios econômicos e sociais a seus produtores; o presente trabalho visa contribuir para o panorama energético global que se começa a se delinear. Diante da impotência do Estado em lidar hodiernamente com determinadas questões, testemunha-se a participação de atores privados (organizações não governamentais, empresas transnacionais e sociedade civil, entre outros) atuando como vetores na transmissão de compromissos internacionais junto a estruturas nacionais para a solução de problemas comuns da humanidade. A essa nova arquitetura jurídica e política convencionou-se designar de governança global. Diante da inexistência de uma governança energética global que opere no interesse de países importadores, exportadores e investidores do setor de energia, agindo também como promotora de desenvolvimento social e econômico junto a países em desenvolvimento; e, por fim, em face da ausência de uma regulação internacional exclusiva na área energética, o presente estudo se dedica a investigar as possibilidades de disciplinamento do comércio internacional dos biocombustíveis. Admitindo-se o relevante desempenho que o Brasil detém na produção e exportação deste produto, inclusive na área tecnológica, a presente tese busca identificar o foro adequado, condições justas de produção, investimento, concessão de subsídios, adoção de medidas técnicas, de compra e venda, concorrência entre outros itens que o tema relaciona.

Measuring the kinetics of amyloid fibril elongation using quartz crystal microbalances.

Kinetic measurements of amyloid growth provide insight into the free energy landscape of this supramolecular process and are crucial in the search for potent inhibitors of the main disorders with which it is associated, including Alzheimer's and Parkinson's diseases and Type II diabetes. In recent years, a new class of surface-bound biosensor assays, e.g., those based on surface plasmon resonance (SPR) and the quartz crystal microbalance (QCM) have been established as extremely valuable tools for kinetic measurements of amyloid formation. Here we describe detailed protocols of how QCM techniques can be used to monitor the elongation of amyloid fibrils in real time and to study the influence of external factors on the kinetics of amyloid growth with unprecedented accuracy.

中低能重离子碰撞中x-射线产生截面的理论研究

本工作应用Visual Fortran编写了ECPSSR理论计算程序，修正了ISICS程序中的错误，本程序可以对各种入射离子与靶原子的组合进行计算，给出K，L，M的壳层及次壳层电离截面以及相应的x-射线产生截面，并根据需要选择是否对入射离子运动进行相对论修正。采用所编写的程序计算了一些碰撞体系的电离截面和x-射线产生截面，并与其他程序的计算结果和实验数据分别进行了比较。对于低能离子入射， ECPSSR计算的x-射线产生截面值明显低于实验值。考虑到低能入射离子可能会与靶原子形成准分子，本工作采用联合分离原子(USA, united and separated atom)模型替代ECPSSR中的PSS模型，考虑分子轨道(M)效应得到了基于联合分离原子模型的电离模型－MECUSAR。编写了相应的程序并对部分碰撞系统进行了计算，将计算得到的碰撞截面与实验进行比较，发现对于较低能量重离子碰撞，MECUSAR计算值好于ECPSSR计算值，对于轻离子入射，MECUSAR计算值与ECPSSR值基本相符，而计算K壳层x-射线产生截面时，ECPSSR计算值好于MECUSAR计算值

Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics

We developed a coarse-grained yet microscopic detailed model to study the statistical fluctuations of single-molecule protein conformational dynamics of adenylate kinase. We explored the underlying conformational energy landscape and found that the system has two basins of attractions, open and closed conformations connected by two separate pathways. The kinetics is found to be nonexponential, consistent with single-molecule conformational dynamics experiments. Furthermore, we found that the statistical distribution of the kinetic times for the conformational transition has a long power law tail, reflecting the exponential density of state of the underlying landscape. We also studied the joint distribution of the two pathways and found memory effects.

Optimal specificity and function for flexible biomolecular recognition

Biomolecular associations often accompanied by large conformational changes, sometimes folding and unfolding. By exploring an exactly solvable model, we constructed the free energy landscape and established a general framework for studying the biomolecular flexible binding process. We derived an optimal criterion for the specificity and function for flexible biomolecular binding where the binding and conformational folding are coupled.

Optimal specificity and function for flexible biomolecular recognition

Biomolecular associations often accompanied by large conformational changes, sometimes folding and unfolding. By exploring an exactly solvable model, we constructed the free energy landscape and established a general framework for studying the biomolecular flexible binding process. We derived an optimal criterion for the specificity and function for flexible biomolecular binding where the binding and conformational folding are coupled.

Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path-integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.

In vitro study on the binding of neutral red to bovine serum albumin by molecular spectroscopy

In this paper, the binding of neutral red (NR) to bovine serum albumin (BSA) under physiological conditions has been studied by spectroscopy method including fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. The Stern-Volmer fluorescence quenching constant (K-SV), binding constant (K-b) and the number of binding sites (It) were measured by fluorescence quenching method. Fluorescence experiments were also performed at different ionic strengths. It was found K-SV was ionic strength dependent, which indicated the electrostatic interactions were part of the binding forces. The distance r between donor (BSA) and acceptor (NR) was obtained according to Foster's non-radiative energy transfer theory. CD spectroscopy and FT-IR spectroscopy were used to investigate the structural information of BSA molecules on the binding of NR, and the results showed no change of BSA conformation in our experimental conditions.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Temperature dependence of the distribution of the first passage time: Results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Go-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T-opt*. The optimal folding temperature T-opt* is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T-opt* and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T-opt* and start to diverge when the temperature is lower than T-opt*. The distribution of FPT is close to a log-normal-like distribution at T* greater than or equal to T-opt*. At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.

Studies on plant extracellular calmodulin by lanthanide luminescence probe

Plant extracellular calmodulin (CaM) has been purified from cauliflower and identified with NAD kinase(NADK) activation and inhibition effect of CaM antagonist W7, Tb-3.1 fluorescence titration showed that extracellular CaM contained four metal-binding sites, The excitation spectrum and emission specturm indicated that extracellular CaM contained one tyrosine residue which could transfer energy to bound Tb3+. Based on Forster type nonradiative energy transfer theory, the distances of Tyr-->sites III, IV have been determined, these are 1. 104 nm(Tyr --> III, site) and 1. 056 nm(Tyr --> N, site). By studing the effect of CaM antagonist W7 and CaM antibody on Tb3+-sensitized fluorescence, it was found that the binding sites of W7 and antibody were located on the c-terminal part of plant extracellular CaM which contains domain III and domain IV.

Effect of surface state properties of TiO2 nanoparticle film on its photocatalytic activity

TiO2 nanoparticle film catalysts with different thicknesses were prepared by plasma-enhanced chemical vapor deposition(PECVD) method and the surfaces were subsequently treated by TiCl4 or O-2 plasma. Two kinds of TiO2 films with different surface properties were obtained. Their surface microstructures and energy levels of surface states were tested by AFM, XRD, SPS, The photocatalytic activities of the catalysts were determined via photodegradation experiments of phenol. The results demonstrated that photocatalytic activities of samples whose surface was treated by O-2 plasma were greater than those treated by TiCl4 plasma. Moreover, photodegradation ratio of phenol during the first hour catalyzed by 0. 17 mu m thickness TiO2 nanoparticle film was greater than other samples. Especially, the difference of photocatalytic activities of TiO2 nanoparticle films treated by TiCl4 or O-2 plasma was respectively explained by energy band theory.

On stable non supersymmetric vacua at the bottom of cascading theories

We consider a wide class of cascading gauge theories which usually lead to runaway behaviour in the IR, and discuss possible deformations of the superpotential at the bottom of the cascade which stabilize the runaway direction and provide stable non-supersymmetric vacua. The models we find may allow for a weakly coupled supergravity analysis of dynamical supersymmetric breaking in the context of the gauge/string correspondence. © SISSA 2006.