Biological Systems Workbook: Data modelling and simulations at molecular level

Nowadays, there are huge quantities of data surrounding the different fields of biology derived from experiments and theoretical simulations, where results are often stored in biological databases that are growing at a vertiginous rate every year. Therefore, there is an increasing research interest in the application of mathematical and physical models able to produce reliable predictions and explanations to understand and rationalize that information. All these investigations are helping to overcome biological questions pushing forward in the solution of problems faced by our society. In this Biological Systems Workbook, we aim to introduce the basic pieces allowing life to take place, from the 3D structural point of view. We will start learning how to look at the 3D structure of molecules from studying small organic molecules used as drugs. Meanwhile, we will learn some methods that help us to generate models of these structures. Then we will move to more complex natural organic molecules as lipid or carbohydrates, learning how to estimate and reproduce their dynamics. Later, we will revise the structure of more complex macromolecules as proteins or DNA. Along this process, we will refer to different computational tools and databases that will help us to search, analyze and model the different molecular systems studied in this course

Relativistic DFT calculation and their effect on the accuracy of results

This study explores the significance of density functional theory (DFT) calculations with relativistic effects for two ethylenediaminetetraacetate (edta) type complexes: trans(O5)-[M(eddadp)]- (M = Rh3+, Co3+). Relativistic effects affect the electronic structure of a molecule and, thus, its chemical and spectroscopic properties. With the use of scalar relativistic corrections (SR-ZORA), as implemented in the ADF package, with the B3LYP functional, the TZP basis set and the COSMO solvation model, structural analyses show improved predictions for the geometries of both complexes. In the case of the Rh3+ complex, the differences in metal-ligand bond lengths with and without the relativistic effects were small. In the case of the Co3+ complex, the changes in metal-ligand bond lengths due to the relativistic effects were slightly more pronounced. Compared to experimental values, excitation energies are better when including relativistic corrections, especially for the Rh3+ complex. These results indicate the importance of relativistic DFT calculations for heavy element compounds

Complexity, Emergent Systems and Complex Biological Systems:\ud Complex Systems Theory and Biodynamics. [Edited book by I.C. Baianu, with listed contributors (2011)]

An overview is presented of System dynamics, the study of the behaviour of complex systems, Dynamical system in mathematics Dynamic programming in computer science and control theory, Complex systems biology, Neurodynamics and Psychodynamics.\u

Cooperation of local motions in the Hsp90 molecular chaperone ATPase mechanism

The Hsp90 chaperone is a central node of protein homeostasis activating a large number of diverse client proteins. Hsp90 functions as a molecular clamp that closes and opens in response to the binding and hydrolysis of ATP. Crystallographic studies define distinct conformational states of the mechanistic core implying structural changes that have not yet been observed in solution. Here, we engineered one-nanometer fluorescence probes based on photo-induced electron transfer into yeast Hsp90 to observe these motions. We found that the ATPase activity of the chaperone was reflected in the kinetics of specific structural rearrangements at remote positions that acted cooperatively. Nanosecond single-molecule fluorescence fluctuation analysis uncovered that critical structural elements that undergo rearrangement are mobile on a sub-millisecond time scale. We identified a two-step mechanism for lid closure over the nucleotide-binding pocket. The activating co-chaperone Aha1 mobilizes the lid of apo Hsp90, suggesting an early role in the catalytic cycle

The Complex Role of Sequence and Structure in the Stability and Function of the TIM Barrel Proteins

Sequence divergence of orthologous proteins enables adaptation to a plethora of environmental stresses and promotes evolution of novel functions. As one of the most common motifs in biology capable of diverse enzymatic functions, the TIM barrel represents an ideal model system for mapping the phenotypic manifestations of protein sequence. Limits on evolution imposed by constraints on sequence and structure were investigated using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS). Exploration of fitness landscapes of phylogenetically distant orthologs provides a strategy for elucidating the complex interrelationship in the context of a protein fold. Fitness effects of point mutations in three phylogenetically divergent IGPS proteins during adaptation to temperature stress were probed by auxotrophic complementation of yeast with prokaryotic, thermophilic IGPS. Significant correlations between the fitness landscapes of distant orthologues implicate both sequence and structure as primary forces in defining the TIM barrel fitness landscape. These results suggest that fitness landscapes of point mutants can be successfully translocated in sequence space, where knowledge of one landscape may be predictive for the landscape of another ortholog. Analysis of a surprising class of beneficial mutations in all three IGPS orthologs pointed to a long-range allosteric pathway towards the active site of the protein. Biophysical and biochemical analyses provided insights into the molecular mechanism of these beneficial fitness effects. Epistatic interactions suggest that the helical shell may be involved in the observed allostery. Taken together, knowledge of the fundamental properties of the TIM protein architecture will provide new strategies for de novo protein design of a highly targeted protein fold

Complementary Mass Spectrometry Methods for Characterizing Protein Folding, Structure, and Dynamics

Proteins are involved in virtually every biochemical process. A comprehensive characterization of factors that govern protein function is essential for understanding the biomedical aspects of human health. This dissertation aims to develop complementary mass spectrometry-based methods and apply them to solve problems pertaining to the area of protein structure, folding and dynamics. ‎Chapter 1 uses fast photochemical oxidation of proteins (FPOP) to characterize partially disordered conformers populated under semi-denaturing conditions. In FPOP, ·OH generated by laser photolysis of H2O2 introduces oxidative modifications at solvent accessible side chains. By contrast, buried sites are protected from radical attack. Using apomyoglobin (aMb), it was demonstrated that under optimized conditions undesired can be almost completely eliminated and detailed structural information can be obtained. ‎Chapter 3 combines FPOP with submillisecond mixing to enable studying early events in protein folding. aMb served as a model system for these measurements. Spatially-resolved changes in solvent accessibility follow the folding process. Data revealed that early aMb folding events are driven by both local and sequence-remote docking of hydrophobic side chains. Assembly of a partially formed scaffold after 0.2 ms is followed by stepwise consolidation that ultimately yields the native state. The submillisecond mixer used improved the time resolution by a factor of 50 compared to earlier FPOP experiments. Submillisecond mixing in conjunction with slower mixing techniques help monitor completes folding pathways, from fractions of a millisecond all the way to minutes. ‎Chapter 4 uses ion mobility mass spectrometry (IM-MS) to explore the structural relationship between semi folded solution and gas phase protein conformers. Collision cross sections (CCSs) provide a measure of analyte size. Mb was used as model system because it follows a sequential unfolding pathway that comprises two partially disordered states. IM-MS data showed that the degree of gas phase unfolding is not strongly correlated with the corresponding solution. Gas phase unfolding as well as collapse events can lead to disparities between gaseous and solution structures for partially unfolded proteins. IM-MS data on non-native conformers should therefore be interpreted with caution. ‎Chapter 5 uses HDX-MS to examine the role of conformational dynamics for the function of multi-protein molecular machines such as FoF1 ATP synthase. HDX-MS monitors backbone deuteration kinetics in the presence of D2O. Disordered segments exchange more rapidly than those in tightly folded regions. Measurements of spatially-resolved deuterium are performed using LC-MS. It was found that the H-bonding network of key power transmission elements is insensitive to PMF-induced mechanical stress. Unexpectedly, HDX-MS reveals a pronounced destabilization of the g C-terminus during rotational catalysis under PMF. The behavior of g is attributed to kinetic friction within the apical rotor bearing

Examination of Aggregation Prone Proteins and their Higher Order Interactions by Ion Mobility-Mass Spectrometry.

Amyloid forming peptides and proteins present an extreme challenge for modern analytical measurement techniques. When natively-folded biomolecules partition into misfolded forms, they produce a myriad of inherently unstable conformations that eventually lead to the presumed cytotoxic species linked to disease. Most often, these cytotoxic states take the form of small oligomeric species that exist within a complex mixture of other oligomers that may, or may not, be related to a disease etiology. In addition, these dynamically-generated oligomers are present in small amounts, within a complex mixture of other biomolecules, small molecules, and metal ions that may also influence the ensemble of states being measured. Ion mobility separation, coupled to mass spectrometry, has recently become a key technology for the analysis of amyloid-forming peptides and proteins due to its ability to analyze low concentrations of complex mixtures. Described here is the application of IM-MS to study protein interactions with small molecules, dipeptides, and neuropeptides. This combine information furthers the knowledge base of neurodegenerative diseases from a structural standpoint. First, the interaction of amyloid beta: leucine enkephalin was discovered in a screen of many neuropeptides. This interaction was characterized using IM-MS through collision cross section and Kd measurements. Multiple copies of leucine enkephalin are found to bind with amyloid beta, each with an approximate binding strength of 60 micromolar. Modeling suggests binding near the structured core region of amyloid beta. Following these initial studies, site directed amino acid substitution of leucine enkephalin reveals that the hydrophobic C-terminal residues phenylalanine and leucine are critical for binding to occur. Alanine substitutions of amyloid beta residues, selected based on simulated annealing results, indicate residues Y10 and Q15 to be most critical for the interaction of amyloid beta with the dipeptide FL. Molecular dynamics models were filtered using IM-MS experimental results, and structures representative of the interaction are shown. Additionally, workflow to study amyloid beta has been applied to the oligomerization of ubiquitin monomer and linear tri-ubiqutin in the presence of copper ions, measuring an increase in the number of dimeric species. Stability measurements using collision induced unfolding, and aggregation propensity of Ubiquilin2 are also studied.PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/116673/1/mtso_1.pd

Exploration of the structural requirements of Aurora Kinase B inhibitors by a combined QSAR, modelling and molecular simulation approach

Aurora kinase B plays an important role in the cell cycle to orchestrate the mitotic process. The amplification and overexpression of this kinase have been implicated in several human malignancies. Therefore, Aurora kinase B is a potential drug target for anticancer therapies. Here, we combine atom-based 3D-QSAR analysis and pharmacophore model generation to identify the principal structural features of acylureidoindolin derivatives that could potentially be responsible for the inhibition of Aurora kinase B. The selected CoMFA and CoMSIA model showed significant results with cross-validation values (q(2)) of 0.68, 0.641 and linear regression values (r(2)) of 0.971, 0.933 respectively. These values support the statistical reliability of our model. A pharmacophore model was also generated, incorporating features of reported crystal complex structures of Aurora kinase B. The pharmacophore model was used to screen commercial databases to retrieve potential lead candidates. The resulting hits were analyzed at each stage for diversity based on the pharmacophore model, followed by molecular docking and filtering based on their interaction with active site residues and 3D-QSAR predictions. Subsequently, MD simulations and binding free energy calculations were performed to test the predictions and to characterize interactions at the molecular level. The results suggested that the identified compounds retained the interactions with binding residues. Binding energy decomposition identified residues Glu155, Trp156 and Ala157 of site B and Leu83 and Leu207 of site C as major contributors to binding affinity, complementary to 3D-QSAR results. To best of our knowledge, this is the first comparison of WaterSwap field and 3D-QSAR maps. Overall, this integrated strategy provides a basis for the development of new and potential AK-B inhibitors and is applicable to other protein targets