Multi-factor experiments and modeling

학위논문(석사) -- 서울대학교대학원 : 농업생명과학대학 생태조경.지역시스템공학부(지역시스템공학전공), 2023. 2. 김성배.Acetaminophen (AAP) and Ibuprofen (IPF) are among the most prescribed nonsteroidal anti-inflammatory drugs recently, but they are not readily removed in conventional wastewater treatments. Here, we investigate the adsorption characteristics of contaminants (AAP and IPF) onto spherical carbon materials (SCMs), which was synthesized through hydrothermal carbonization of sucrose followed by calcination. Single-factor experiments were performed by varying the pH, contact time, temperature, adsorbent dose, and initial contaminants concentration. The maximum adsorption capacity for AAP is 92.0 mg/g and IPF is 95.6 mg/g. The SCMs were successfully regenerated after methanol washing. The Raman, FTIR, XPS spectra and pH experiments data suggest that - interaction, n-* interaction, hydrogen-bond formation, and electrostatic repulsion could take place between the SCMs and contaminants. Those mechanisms were explored and visualized with molecular modeling using CHEM3D. A pore-filling mechanism could contribute to the adsorption in view of the molecular size of contaminants and the average pore diameter of the SCMs. Multi-factor adsorption experiments were executed with pH, temperature, SCMs dosage, and initial contaminants concentrations as input variables and contaminants adsorption capacity as an output variable, and an artificial neural network (ANN) model with 2 hidden layers were developed to sufficiently describe the adsorption data. Further analyses with additional experimental data confirm that the ANN model possessed good predictability for multi-factor adsorption. In the ANN model, initial contaminants concentration was most important factor, according to the relative importance of the input variables.아세트아미노펜(AAP)과 이부프로펜(IPF)은 최근 들어 가장 많이 처방되는 비스테로이드성 항염증제(NSAID) 중 하나이지만, 기존의 폐수처리 공정에서는 쉽게 제거되지 않는다. 본 연구에서는 수열합성법과 열처리 공정을 통해 수크로스 기반의 탄소 구체(SCMs)를 합성하고, 오염물질(AAP와 IPF)에 대한 흡착 특성을 조사하였다. 단일 변수 실험(Single-factor experiments)은 pH, 반응 시간, 온도, 흡착제 주입량, 그리고 초기 오염물질 농도를 바꾸어가며 수행하였다. SCMs를 이용한 AAP의 최대흡착능은 92.0 mg/g, IPF의 최대흡착능은 95.6 mg/g으로 나타났으며, 실험에 사용된 흡착제는 메탄올을 이용하여 효율적으로 재생되었다. Raman, FTIR, XPS 스펙트럼과 pH 실험 데이터에 따르면 흡착제와 오염물질 간에 - 상호작용, n-* 상호작용, 수소결합, 그리고 정전기적 반발력이 발생하는 것으로 나타났다. 이러한 메커니즘은 CHEM3D를 이용한 분자 모델링을 통해 재검증하고 시각화하여 나타내었다. 또한, 오염물질 분자의 크기와 흡착제의 평균 기공 직경을 비교하였을 때 pore-filling 메커니즘도 흡착에 기여할 수 있는 것으로 나타났다. 다중 변수 실험(Multi-factor experiments)은 pH, 온도, 흡착제 주입량, 초기 오염물질 농도를 입력변수로 하고 오염물질 흡착능을 출력변수로 하여 수행하였고, 2개의 은닉층을 갖는 인공신경망(ANN) 모델을 개발하였다. 이후, 추가 실험 데이터를 ANN 모델에 적용하여 오염물질 흡착에 대해 우수한 예측 가능성을 가지고 있음을 확인하였다. 완성된 ANN 모델에서 각 입력 변수의 중요도를 평가하였고, 초기 오염물질 농도가 가장 중요한 요인으로 나타났다. 본 연구 결과를 통해 수크로스로 합성한 탄소구체가 수중의 AAP와 IPF를 효율적으로 제거할 수 있는 흡착제임을 확인하였다. 또한, 분자 모델링을 통해 오염물질의 제거 메커니즘을 재검증하였고, ANN 모델링을 통해 오염물질 제거를 최적화하고 예측하는 모델을 구축하였다.1. Introduction 1 1.1. Background 1 1.1.1. Contaminants 2 1.1.2. Spherical carbon materials (SCMs) 4 1.2. Objective 6 2. Literature Reviews 7 2.1. Adsorption of AAP using carbon-based adsorbents 7 2.2. Adsorption of IPF using carbon-based adsorbents 9 2.3. Adsorption of contaminants using SCMs 10 3. Materials and Methods 12 3.1. Synthesis of the SCMs 12 3.2. Single-factor experiments 13 3.2.1. Single-factor experiments for AAP adsorption 13 3.2.2. Single-factor experiments for IPF adsorption 19 3.3. Characterization of the SCMs 22 3.4. Computational studies 25 3.5. Multi-factor experiments and ANN 26 3.5.1. ANN modeling for AAP adsorption 26 3.5.2. ANN modeling for IPF adsorption 31 4. Results and Discussion 35 4.1. Adsorption characteristics onto the SCMs 35 4.1.1. Adsorption characteristics for AAP 35 4.1.2. Adsorption characteristics for IPF 48 4.2. Characterization of the SCMs 62 4.3. Adsorption mechanisms and computational studies 98 4.3.1. Adsorption mechanisms and moleular modeling (AAP) 98 4.3.2. Adsorption mechanisms and moleular modeling (IPF) 114 4.4. Multi-factor experiments and ANN 135 4.4.1. ANN modeling for AAP adsorption 135 4.4.2. ANN modeling for IPF adsorption 146 5. Conclusions 154 5.1. AAP 154 5.2. IPF 155 5.3. General conclusions and recommendations 156 6. References 157 국문 초록 179석

Mapping energy transport networks in proteins

The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the evolution of protein structural change following ligand photolysis, and time-resolved IR and Raman techniques, e.g., have provided detailed pictures of the nature and rate of energy transport in peptides and proteins, including recent advances in identifying transport through individual amino acids of several heme proteins. Computational tools to locate energy transport pathways in proteins have also been advancing. Energy transport pathways in proteins have since some time been identified by molecular dynamics (MD) simulations, and more recent efforts have focused on the development of coarse graining approaches, some of which have exploited analogies to thermal transport in other molecular materials. With the identification of pathways in proteins and protein complexes, network analysis has been applied to locate residues that control protein dynamics and possibly allostery, where chemical reactions at one binding site mediate reactions at distance sites of the protein. In this chapter we review approaches for locating computationally energy transport networks in proteins. We present background into energy and thermal transport in condensed phase and macromolecules that underlies the approaches we discuss before turning to a description of the approaches themselves. We also illustrate the application of the computational methods for locating energy transport networks and simulating energy dynamics in proteins with several examples

Dense point sets have sparse Delaunay triangulations

The spread of a finite set of points is the ratio between the longest and shortest pairwise distances. We prove that the Delaunay triangulation of any set of n points in R^3 with spread D has complexity O(D^3). This bound is tight in the worst case for all D = O(sqrt{n}). In particular, the Delaunay triangulation of any dense point set has linear complexity. We also generalize this upper bound to regular triangulations of k-ply systems of balls, unions of several dense point sets, and uniform samples of smooth surfaces. On the other hand, for any n and D=O(n), we construct a regular triangulation of complexity Omega(nD) whose n vertices have spread D.Comment: 31 pages, 11 figures. Full version of SODA 2002 paper. Also available at http://www.cs.uiuc.edu/~jeffe/pubs/screw.htm

Molecular mechanism of MBX2319 inhibition of Escherichia coli AcrB multidrug efflux pump and comparison with other inhibitors

Efflux pumps of the resistance nodulation division (RND) superfamily, such as AcrB, make a major contribution to multidrug resistance in Gram-negative bacteria. The development of inhibitors of the RND pumps would improve the efficacy of current and next-generation antibiotics. To date, however, only one inhibitor has been cocrystallized with AcrB. Thus, in silico struc- ture-based analysis is essential for elucidating the interaction between other inhibitors and the efflux pumps. In this work, we used computer docking and molecular dynamics simulations to study the interaction between AcrB and the compound MBX2319, a novel pyranopyridine efflux pump inhibitor with potent activity against RND efflux pumps of Enterobacteriaceae species, as well as other known inhibitors (D13-9001, 1-[1-naphthylmethyl]-piperazine, and phenylalanylarginine-ß-naphthyl-amide) and the binding of doxorubicin to the efflux-defective F610A variant of AcrB. We also analyzed the binding of a sub- strate, minocycline, for comparison. Our results show that MBX2319 binds very tightly to the lower part of the distal pocket in the B protomer of AcrB, strongly interacting with the phenylalanines lining the hydrophobic trap, where the hydrophobic por- tion of D13-9001 was found to bind by X-ray crystallography. Additionally, MBX2319 binds to AcrB in a manner that is similar to the way in which doxorubicin binds to the F610A variant of AcrB. In contrast, 1-(1-naphthylmethyl)-piperazine and phenylalanylarginine-ß-naphthylamide appear to bind to somewhat different areas of the distal pocket in the B protomer of AcrB than does MBX2319. However, all inhibitors (except D13-9001) appear to distort the structure of the distal pocket, impairing the proper binding of substrates

Evolutionary conservation of influenza A PB2 sequences reveals potential target sites for small molecule inhibitors.

The influenza A basic polymerase protein 2 (PB2) functions as part of a heterotrimer to replicate the viral RNA genome. To investigate novel PB2 antiviral target sites, this work identified evolutionary conserved regions across the PB2 protein sequence amongst all sub-types and hosts, as well as ligand binding hot spots which overlap with highly conserved areas. Fifteen binding sites were predicted in different PB2 domains; some of which reside in areas of unknown function. Virtual screening of ~50,000 drug-like compounds showed binding affinities of up to 10.3 kcal/mol. The highest affinity molecules were found to interact with conserved residues including Gln138, Gly222, Ile529, Asn540 and Thr530. A library containing 1738 FDA approved drugs were screened additionally and revealed Paliperidone as a top hit with a binding affinity of -10 kcal/mol. Predicted ligands are ideal leads for new antivirals as they were targeted to evolutionary conserved binding sites

The extrinsic proteins of photosystem II: update

© 2016, Springer-Verlag Berlin Heidelberg. Main conclusion: Recent investigations have provided important new insights into the structures and functions of the extrinsic proteins of Photosystem II. This review is an update of the last major review on the extrinsic proteins of Photosystem II (Bricker et al., Biochemistry 31:4623–4628 2012). In this report, we will examine advances in our understanding of the structure and function of these components. These proteins include PsbO, which is uniformly present in all oxygenic organisms, the PsbU, PsbV, CyanoQ, and CyanoP proteins, found in the cyanobacteria, and the PsbP, PsbQ and PsbR proteins, found in the green plant lineage. These proteins serve to stabilize the Mn4CaO5 cluster and optimize oxygen evolution at physiological calcium and chloride concentrations. The mechanisms used to perform these functions, however, remain poorly understood. Recently, important new findings have significantly advanced our understanding of the structures, locations and functions of these important subunits. We will discuss the biochemical, structural and genetic studies that have been used to elucidate the roles played by these proteins within the photosystem and their locations within the photosynthetic complex. Additionally, we will examine open questions needing to be addressed to provide a coherent picture of the role of these components within the photosystem

Density Functional Theory for Hard Particles in N Dimensions

Recently it has been shown that the heuristic Rosenfeld functional derives from the virial expansion for particles which overlap in one center. Here, we generalize this approach to any number of intersections. Starting from the virial expansion in Ree-Hoover diagrams, it is shown in the first part that each intersection pattern defines exactly one infinite class of diagrams. Determining their automorphism groups, we sum over all its elements and derive a generic functional. The second part proves that this functional factorizes into a convolute of integral kernels for each intersection center. We derive this kernel for N dimensional particles in the N dimensional, flat Euclidean space. The third part focuses on three dimensions and determines the functionals for up to four intersection centers, comparing the leading order to Rosenfeld's result. We close by proving a generalized form of the Blaschke, Santalo, Chern equation of integral geometry.Comment: 2 figure

The Roles of Membrane Rafts in CD32A-Mediated Phagocytosis

Membrane rafts are highly dynamic heterogeneous sterol- and sphingolipid-rich micro-domains on cell surfaces. They are generally believed to provide residency for cell surface molecules (e.g., adhesion and signaling molecules) and scaffolding to facilitate the functions of these molecules such as membrane trafficking, receptor transport, cell signaling, and endocytosis.
The governing, or overall hypothesis, for this project is that membrane rafts provide residency for Fc[gamma]RIIA (CD32A) on K562 cells, and that by doing so they provide a platform from which Fc[gamma]RIIA initiate or carry out their functions, which include migration, signaling, phagocytic synapse formation, and internalization of IgG opsonized targets.
Using immuno-fluorescent laser scanning confocal microscopy and reflection interference microscopy (RIM), we studied the spatial and temporal distributions of membrane rafts and surface receptors, signaling molecules, and cell organelles during the formation of phagocytic contact areas. K562 cells, which naturally express CD32A, a cell surface receptor for the Fc portion of Immuno-globulin G(IgG), was chosen as a model for neutrophils. An opsonized target was modeled using a glass supported lipid bilayer reconstituted with IgG. CD32A was found to cluster and co-localize with membrane rafts. Placing the K562 cells on the lipid bilayer triggered a process of contact area formation that includes binding between receptors and ligands, their recruitment to the contact area, a concurrent membrane raft movement to and concentration in the contact area, and transport of CD32A, IgG, and membrane rafts to the Golgi complex. Characterization of these processes was performed using agents known to disrupt detergent resistant membranes (DRMs), dissolve actin microfilaments, and inhibit myosin motor activity, which abolished the CD32A clusters and prevented the contact area formation. 
The relevance to phagocytosis of contact area formation between K562 cells and lipid bilayers was demonstrated using micro-beads coated with a lipid bilayer reconstituted with IgG as the opsonized target instead of the glass supported planar lipid bilayer. Disruption of membrane rafts, salvation of the actin cytoskeleton, and inhibition of myosin II activity were found to inhibit phagocytosis.
These data suggest membrane rafts play several important roles in CD32A mediated phagocytosis including pre-clustering CD32A, transport of CD32A to the phagocytic cup, and transport of the opsonized target towards the Golgi complex. Here we have provided evidence that membrane rafts serve as platforms which are used to cluster CD32A and transport CD32A along the actin cytoskeleton to the site of phagocytic synapse formation thus allowing for the quick assembly of a phagocytic synapse.
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Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation

The accurate description of protein-protein interfaces remains a challenging task. Traditional criteria, based on atomic contacts or changes in solvent accessibility, tend to over or underpredict the interface itself and cannot discriminate active from less relevant parts. A recent simulation study by Mihalek and co-authors (2007, JMB 369, 584-95) concluded that active residues tend to be `dry', that is, insulated from water fluctuations. We show that patterns of `dry' residues can, to a large extent, be predicted by a fast, parameter-free and purely geometric analysis of protein interfaces. We introduce the shelling order of Voronoi facets as a straightforward quantitative measure of an atom's depth inside an interface. We analyze the correlation between Voronoi shelling order, dryness, and conservation on a set of 54 protein-protein complexes. Residues with high shelling order tend to be dry; evolutionary conservation also correlates with dryness and shelling order but, perhaps not surprisingly, is a much less accurate predictor of either property. Voronoi shelling order thus seems a meaningful and efficient descriptor of protein interfaces. Moreover, the strong correlation with dryness suggests that water dynamics within protein interfaces may, in first approximation, be described by simple diffusion models