Abstract Five species belonging to order Chelonia, two families and four genera, namely, Taiwanese soft-shelled turtle, Pelodiscus sinensis japonicus; American soft-shelled turtle, Apalone ferox; alligator snapping turtle, Macroclemys temminck; pitted shelled turtle, Carettochelys insculpta and side-necked turtle, Chelodina siebernrocki were investigated in order to fully understand the structural basis for the multiple lactate dehydrogenase (LDH) isozymes in turtles and soft-shelled turtles. Starch gel electrophoretic patterns of LDH isozymes from muscle, heart, liver, testis and eye were analyzed. Chelonia possess the two fundamental LDH loci-A¡]muscle¡^and B¡]heart¡^as the case of all other vertebrates. The major forms of LDH isozymes in the tissues of Chelonia are homotetrameric LDH-A4 and B4.While some of these Chelonia do not form two heterotetrameric A3B1 and/or A1B3 isozymes. This phenomenon is also observed among some lower vertebrates and fishes of other classes. I have determined the LDH-A and LDH-B cDNA sequences of protein-coding region from these five species. The 3D-structure of tetrameric LDH isozymes from Taiwanese soft-shelled turtle was predicted by homologous modeling and the substitutive residues in subunit contact sites were examined in oder to explain different multiple forms of tetrameric LDH isozymes present in various species. The LDH isozymes are housekeeping genes in most eukaryotic cells and therefore the LDH DNA or protein sequences can be an ideal marker for studying the molecular phylogenetics and evolution among different organisms. However, whether this marker can also be used to investigate the systematic relationship among the closely related species remains to be demonstrated. In this study, the newly determined LDH-A and LDH-B cDNA sequences and their deduced protein sequences from several different turtles and soft-shelled turtles, as well as the previously published LDH sequences, are analyzed by phylogenetic tree reconstruction methods of neighbor-joining, minimum evolution, maximum parsimony and maximum likelihood. These results confirm the traditional classification based on morphology of Chelonia as the two different families belonging to the same order Chelonia. Furthermore, these results clearly classify these Chelonia species into side-necked turtle, rough-shelled hide-necked turtle and smooth-shelled hide-neck turtle. Finally, these results also demonstrate that LDH can indeed be used as a molecular systematic marker for analyzing closely related species.

<p>  </p> <p>Proteins are the active biomolecules of the cell. They perform metabolic action, give the cell structure, protect the cell from antigens, give the cell motility, and much more. The function of proteins are intrinsically linked to their structures, so it is therefore necessary to characterize the structure of a protein to fully understand its function and operation. In this research the application of computational methods, primarily molecular dynamics, towards protein structure determination, refinement, and quality assessment were studied. I applied molecular dynamics techniques to four major projects; the determination of relative error of atomic models deposited with electron microscopy maps in the EMDB, solving and refining atomics structure models for the PhageG major capsid proteins, the elucidation of the structure the protein USP7 and the binding pose of a of a candidate therapeutic drug, and the determination of relative stability of candidate protein folds to distinguish near native models from not. Each year an increasing number of protein structures have been solved using electron microscopy (EM). The influx of solved structure has proven to be a boon to the community, but it is necessary to note that the quality EM maps vary substantially. To understand to what extent atomic structure models generated from EM matched their respective maps, two computational structure refinement methods were used to examine how much structures could be refined. The deviation from the starting structure by refinement, as well as the disagreement between refined models produced by the two computational methods, scaled inversely with both the global and local map resolutions. The results suggested that the observed discrepancy between the deposited maps and refined models is due to the lack of resolvable structural data present in EM maps at low to moderate resolutions, and therefore these annotations must be used with caution in further applications. I also successfully implemented molecular dynamics as a method for protein structure quality assessment. Proteins tend towards shapes which minimize their energy. Experimentally, the stability of a protein can be measured through several techniques, one such technique includes the controlled application of tension to proteins in an atomic force microscopy (AFM) framework.  This kind of tension-based approach is of interest as it probes the force required to unfold individual domains of a protein rather than a bulk characteristic like molting point or activity. It has been shown that key features observed in an AFM experiment can be well reproduced with molecular dynamics simulation, which has been applied to characterize the mechanisms of unfolding of proteins as well as ligand-protein interactions.  Steered molecular dynamics (SMD) was applied to pull and unfold proteins and determine the force required to unfold them. The relative force required to unfold different models with the same sequence was used to estimate relative model accuracy.  This follows from the hypothesis that the structural stability of a given model’s conformation would positively correlate with its accuracy, i.e. how close that model is to its native fold. It was found that near-native models could be successfully selected by comparing the forces required to unfold models, indicating that high unfolding forces indeed indicated high model stability, which in turn correlated with model accuracy. I also applied molecular dynamics-based approaches for refinement of protein structures that are determined from cryo-EM density maps. Computational approaches for protein structure refinement are often developed with the design aim of requiring a user input and experimental data. I modeled the atomic structure of the major capsid protein gp27 and the decoration protein gp26 of PhageG to a 6.1Å resolution electron microscopy map. PhageG modeling was done by mapping the sequences to a presumed homolog (Hk97), arranging the subunits into hexamers and trimmers as suggested by mass spectroscopy data, rigid docking to respective map segments, refinement against half maps using MDFF across a range of weights, and then finally refinement to the whole map using the optimized weight. I also modeled the atomic structure of the protein USP7 to an 8.2 Å resolution map. USP7 modeling was done by combining crystalized domains of the whole structure, rigidly docking the model to the EM map by hand, and then refining in a similar manner as PhageG, with the added approach of weight scaling to overcome local minima along the relaxation. The USP7 model was further validated by exhibiting a ligand-protein binding pose, determined by glide, which corresponded to enzymatic activity mutation assays. In summary I applied molecular dynamics, in conjunction with other computational methods, towards protein structure determination, refinement, and quality assessment.</p>

Dynamic development of nuclear magnetic resonance spectroscopy (NMR) allowed fast acquisition of experimental data which determine structure and dynamics of macromolecules. Nevertheless, due to lack of appropriate computational methods, NMR spectra are still analyzed manually by researchers what takes weeks or years depending on protein complexity. Therefore automation of this process is extremely desired and can significantly reduce time of protein structure solving. In presented work, a new approach to automated three-dimensional protein NMR spectra analysis is presented. It is based on Histogram of Oriented Gradients and Bayesian Network which have not been ever applied in that context in the history of research in the area. Proposed method was evaluated using benchmark data which was established by manual labeling of 99 spectroscopic images taken from 6 different NMR experiments. Afterwards subsequent validation was made using spectra of upstream of N-ras protein. With the use of proposed method, a three-dimensional structure of mentioned protein was calculated. Comparison with reference structure from protein databank reveals no significant differences what has proven that proposed method can be used in practice in NMR laboratories.

The 23 pairs of chromosomes comprising the human genome are intricately folded within the nucleus of each cell in a manner that promotes efficient gene regulation and cell function. Consequently, active gene rich regions are compartmentally segregated from inactive gene poor regions of the genome. To better understand the mechanisms driving compartmentalization we investigated what would occur if this system was disrupted. By digesting the genome to varying sizes and analyzing the fragmented 3D structure over time, our work revealed essential laws governing nuclear compartmentalization. At a finer resolution within compartments, chromatin forms loop structures capable of regulating gene expression. Genome wide association studies have identified numerous single nucleotide polymorphisms (SNPs) associated with the neuropsychiatric disease schizophrenia. When these SNPs are not located within a gene it is difficult to gain insight into disease pathology; however, in some cases chromatin loops may link these noncoding schizophrenia risk variants to their pathological gene targets. By generating 3D genome maps, we identified and analyzed loops of glial cells, neural progenitor cells, and neurons thereby expanding the set of genes conferring schizophrenia risk. The binding of T-cell receptors (TCRs) to foreign peptides on the surface of diseased cells triggers an immune response against the foreign invader. Utilizing available structural information of the TCR antigen interface, we developed computational methods for successful prediction of TCR-antigen binding. As this binding is a prerequisite for immune response, such improvements in binding prediction could lead to important advancements in the fields of autoimmunity and TCR design for cancer therapeutics.

AlphaFold [Jumper et al., 2021, Evans et al., 2022] is a deep learning-based method that can accurately predict the structure of single- and multiple-chain proteins. However, its accuracy decreases with an increasing number of chains, and GPU memory limits the size of protein complexes that can be predicted. Recently, Elofsson’s groupintroduced a Monte Carlo tree search method, MoLPC, that can predict the structure of large complexes from predictions of sub-components [Bryant et al., 2022b]. However, MoLPC cannot adjust for errors in the sub-component predictions and requires knowledge of the correct protein stoichiometry. Large protein complexes are responsible for many essential cellular processes, such as mRNA splicing [Will and Lührmann, 2011], protein degradation [Tanaka, 2009], and protein folding [Ditzel et al., 1998]. However, the lack of structural knowledge of many large protein complexes remains challenging. Only a fraction of the eukaryoticcore complexes in CORUM [Giurgiu et al., 2019] have homologous structures covering all chains in PDB, indicating a significant gap in our structural understanding of protein complexes. AlphaFold-Multimer [Evans et al., 2022] is the only deep learning method that can predict the structure of more than two protein chains, trained on proteins of up to 20 chains, and can predict complexes of up to a few thousand residues, where memory limitations come into play. Another approach, MoLPC, is to predict the structure of sub-components of large complexes and assemble them. It has shown that it is possible to manually assemble large complexes from dimers manually [Burke et al., 2021] or use Monte Carlo tree search [Bryant et al., 2022b]. One limitation of the previous MoLPC approach is its inability to account for errors in sub-component prediction. The addition of small errors in each sub-component can propagate to a significant error when building the entire complex, leading toMoLPC’s failure. To overcome this challenge, the Monte Carlo Tree Search algorithms in MoLPC2 is enhanced to assemble protein complexes while simultaneously predicting their stoichiometry. Using MoLPC2, we accurately predicted the structures of 50 out of 175 non-redundant protein complexes (TM-score &gt;0.8), while MoLPC only predicted 30. It should be noted that improvements introduced in AlphaFold version 2.3 enable the prediction of larger complexes, and if stoichiometry is known, it can accurately predict the structures of 74 complexes. Our findings suggest that assembling symmetrical complexes from sub-components results in higher accuracy while assembling asymmetrical complexes remains challenging.

No description available.

The SUMO protein was named Small Ubiquitin-like MOdifier because its 3-D structure was similar to Ubiquitin. In human, three SUMO proteins were discovered, namely, SUMO-1/2/3. The recombinant ¡µ1-8, 94-95 SUMO-2 protein with 10 histidine residues at its N-terminus was expressed using E. coli. BL-21(DE3), purified at 4 oC and crystallized at room temperature. The surface properties of human SUMO-1/2/3 proteins and 3-D structure of ¡µ1-8, 94-95 SUMO-2 protein were analyzed using computer modeling and X-ray diffraction technology respectively. The two-step purification by immobilized metal ion affinity chromatography(IMAC) was developed to yield ¡µ1-8, 94-95 SUMO-2 protein that reached 60 mg/ml for crystallization. On protein expression, 120 mg protein was obtained from 6 L bacterial growth broth. Crystals of ¡µ1-8, 94-95 SUMO-2 were obtained by the hanging-drop vapor diffusion method and many different crystal forms were observed. One of single crystal with triangular plate polyhedron form diffracted to 1.6 &#x00C5; resolution, the other one with rectangular polyhedron form diffracted to 1.2 &#x00C5;. Analysis of the diffraction pattern suggests the crystals belong to R3 space group, the former one owned unit cell parameters a= b=75.3 &#x00C5;, c=29.2 &#x00C5;, £\=90¢X, £]=90¢X,£^=120¢X, and the later one owned unit cell parameters a= b=74.9 &#x00C5;, c=33.2 &#x00C5; and the same angles respectively. The R factor and Rfree of refinement are 0.133 and 0.190 with highly precise phase on 3-D structure of SUMO-2 protein. Comparison of crystal structure between human SUMO-2 and yeast SMT3 showed that the r.m.s. deviation of C£\ coordinate is 1.054 &#x00C5;. In addition, comparison of SUMO-1 NMR structure and SMT3 crystal structure showed that the r.m.s. deviation of C£\ coordinates is 2.736 &#x00C5;. Hence, the structures of SUMO-2 and SMT3 are more similar each other than those of SUMO-1and SMT3.

Orientador: João Pessoa Araujo Junior / Resumo: A suinocultura vem alcançando grande desenvolvimento de técnicas eficientes associadas ao melhoramento genético, nutrição, manejo e sanidade. Entretanto, devido aos métodos intensivos de criação, os suínos se tornaram mais susceptíveis a um grande número de doenças infecciosas. Entre os mais importantes patógenos que afetam a indústria suinícola mundial está o circovírus suíno 2 (PCV2), um pequeno vírus icosaédrico, não-envelopado, de DNA circular, de fita simples (ssDNA), ambisenso, composta por 1767-1768 nucleotídeos. Este vírus é altamente resistente a variações ambientais e agentes desinfetantes, é endêmico no mundo todo e está associado a várias manifestações clínicas distintas, que acarretam importantes perdas econômicas aos produtores. Um dos fatores possivelmente implicados na patogenicidade do PCV2 é a proteína Cap, a unidade fundamental constituinte do capsídeo deste vírus. Estudos realizados pela equipe do Prof. Dr. João Pessoa Araújo Jr., do Instituto de Biotecnologia da Unesp em Botucatu/SP, comprovaram que vírus com mutações em suas proteínas Cap isolados a partir de cultivo celular aumentavam a morte celular em culturas celulares infectadas. Estes resultados evidenciaram a importância do capsídeo nos mecanismos de infecção e patogenicidade do PCV2, tornando interessante a realização de estudos estruturais com as proteínas Cap mutantes. A execução de estudos estruturais in silico mostrou a baixa frequência das mutações identificadas na proteína Cap dos vírus pro... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Swine breeding has achieved a high development based on genetic improvement, nutrition, management and sanity. However, due to the intensive breeding methods, swine have become more susceptible to a higher number of infectious diseases. Among the most important pathogens that affect the swine world industry is the porcine circovirus 2 (PCV2), a small, icosahedral, non-enveloped virus, ambisense single-stranded circular DNA, composed by 1,767-1,768 nucleotides. This virus is highly resistant to environmental variations and disinfecting agents, endemic worldwide and has been associated to several distinct clinical manifestations that entail important economic losses to the producers. One of the factors possibly implicated on the PCV2 pathogenicity is the Cap protein, the fundamental unity that constitutes this virus capsid. Studies performed by the group of Dr. João Pessoa Araújo Jr. rom the Instituto de Biotecnologia da Unesp em Botucatu/SP, confirmed that viruses with mutated Cap proteins from cell culture increased cell death in infected cultures. Such results highlight the importance of capsid in the infection mechanisms and pathogenicity of PCV2 and the importance of structural and comparative studies with Cap protein structures. In silico structural studies showed the low frequency of the mutations identified in the mutant Cap proteins and also indicated a clear difference between the physico-chemical properties of the new amino acid residues in comparison to those found ... (Complete abstract click electronic access below) / Mestre

Submitted by Pâmela Merlo Marson (pam.marson@aluno.ibb.unesp.br) on 2018-06-05T17:11:43Z No. of bitstreams: 1 Dissertação_Mestrado_Pamela-Merlo-Marson_2018_vf.pdf: 1757229 bytes, checksum: ed7b8faed4d956e7a1ba89178199507d (MD5) / Approved for entry into archive by Sulamita Selma C Colnago null (sulamita@btu.unesp.br) on 2018-06-07T14:10:28Z (GMT) No. of bitstreams: 1 marson_pm_me_bot.pdf: 1757229 bytes, checksum: ed7b8faed4d956e7a1ba89178199507d (MD5) / Made available in DSpace on 2018-06-07T14:10:28Z (GMT). No. of bitstreams: 1 marson_pm_me_bot.pdf: 1757229 bytes, checksum: ed7b8faed4d956e7a1ba89178199507d (MD5) Previous issue date: 2018-02-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A suinocultura vem alcançando grande desenvolvimento de técnicas eficientes associadas ao melhoramento genético, nutrição, manejo e sanidade. Entretanto, devido aos métodos intensivos de criação, os suínos se tornaram mais susceptíveis a um grande número de doenças infecciosas. Entre os mais importantes patógenos que afetam a indústria suinícola mundial está o circovírus suíno 2 (PCV2), um pequeno vírus icosaédrico, não-envelopado, de DNA circular, de fita simples (ssDNA), ambisenso, composta por 1767-1768 nucleotídeos. Este vírus é altamente resistente a variações ambientais e agentes desinfetantes, é endêmico no mundo todo e está associado a várias manifestações clínicas distintas, que acarretam importantes perdas econômicas aos produtores. Um dos fatores possivelmente implicados na patogenicidade do PCV2 é a proteína Cap, a unidade fundamental constituinte do capsídeo deste vírus. Estudos realizados pela equipe do Prof. Dr. João Pessoa Araújo Jr., do Instituto de Biotecnologia da Unesp em Botucatu/SP, comprovaram que vírus com mutações em suas proteínas Cap isolados a partir de cultivo celular aumentavam a morte celular em culturas celulares infectadas. Estes resultados evidenciaram a importância do capsídeo nos mecanismos de infecção e patogenicidade do PCV2, tornando interessante a realização de estudos estruturais com as proteínas Cap mutantes. A execução de estudos estruturais in silico mostrou a baixa frequência das mutações identificadas na proteína Cap dos vírus provenientes do cultivo in vitro e também indicou uma clara diferença entre as propriedades físico-químicas dos novos resíduos de aminoácidos em relação àqueles substituídos. Estas alterações, associadas à localização dos resíduos na superfície viral e a menor flexibilidade das proteínas Cap dos vírus mutantes, indicaram a possibilidade de alterações estruturais/funcionais relevantes, incluindo a alteração da afinidade por receptores celulares e diminuição da efetividade de anticorpos produzidos contra vírus vacinais. Foram também realizados trabalhos experimentais para a produção heteróloga da proteína Cap de um vírus selvagem, os quais envolveram ensaios de subclonagem da sequência de interesse em um vetor de expressão, testes de transcrição e experimentos de expressão protéica. Os resultados destes procedimentos foram compatíveis com a produção da proteína Cap, porém novos estudos são necessários para confirmar a produção da molécula alvo e melhorar o rendimento dos ensaios de expressão. / Swine breeding has achieved a high development based on genetic improvement, nutrition, management and sanity. However, due to the intensive breeding methods, swine have become more susceptible to a higher number of infectious diseases. Among the most important pathogens that affect the swine world industry is the porcine circovirus 2 (PCV2), a small, icosahedral, non-enveloped virus, ambisense single-stranded circular DNA, composed by 1,767-1,768 nucleotides. This virus is highly resistant to environmental variations and disinfecting agents, endemic worldwide and has been associated to several distinct clinical manifestations that entail important economic losses to the producers. One of the factors possibly implicated on the PCV2 pathogenicity is the Cap protein, the fundamental unity that constitutes this virus capsid. Studies performed by the group of Dr. João Pessoa Araújo Jr. rom the Instituto de Biotecnologia da Unesp em Botucatu/SP, confirmed that viruses with mutated Cap proteins from cell culture increased cell death in infected cultures. Such results highlight the importance of capsid in the infection mechanisms and pathogenicity of PCV2 and the importance of structural and comparative studies with Cap protein structures. In silico structural studies showed the low frequency of the mutations identified in the mutant Cap proteins and also indicated a clear difference between the physico-chemical properties of the new amino acid residues in comparison to those found in the wild-type virus. These mutations, associated with the location of the mutated residues on the viral surface and the lower mutated Cap protein flexibility, could lead to relevant structural/functional changes, including alteration of affinity for cellular receptors and decreased effectiveness of antibodies produced against vaccine viruses. Experimental works aiming the heterologous production of a wild-type Cap protein were also carried out, which involved expression vector subcloning, transcription tests and protein expression experiments. The results of these procedures were compatible with the production of the Cap protein, but further studies are needed to confirm the production of the target molecule and improve the yield of the expression assays.

No description available.