The thermodynamics and statistical mechanics of protein folding

The physics of self-organization and complexity is manifested on a variety of biological scales, from large ecosystems to the molecular level. Protein molecules exhibit characteristics of complex systems in terms of their structure, dynamics, and function. Proteins have the extraordinary ability to fold to a specific functional three-dimensional shape, starting from a random coil, in a biologically relevant time. How they accomplish this is one of the secrets of life. In this work, theoretical research into understanding this remarkable behavior is discussed. Thermodynamic and statistical mechanical tools are used in order to investigate the protein folding dynamics and stability. Theoretical analyses of the results from computer simulation of the dynamics of a four-helix bundle show that the excluded volume entropic effects are very important in protein dynamics and crucial for protein stability. The dramatic effects of changing the size of sidechains imply that a strategic placement of amino acid residues with a particular size may be an important consideration in protein engineering. Another investigation deals with modeling protein structural transitions as a phase transition. Using finite size scaling theory, the nature of unfolding transition of a four-helix bundle protein was investigated and critical exponents for the transition were calculated for various hydrophobic strengths in the core. It is found that the order of the transition changes from first to higher order as the strength of the hydrophobic interaction in the core region is significantly increased. Finally, a detailed kinetic and thermodynamic analysis was carried out in a model two-helix bundle. The connection between the structural free-energy landscape and folding kinetics was quantified. I show how simple protein engineering, by changing the hydropathy of a small number of amino acids, can enhance protein folding by significantly changing the free energy landscape so that kinetic traps are removed. The results have general applicability in protein engineering as well as understanding the underlying physical mechanisms of protein folding. ^

Global relativistic folding optical potential and the relativistic Green's function model

Optical potentials provide critical input for calculations on a wide variety of nuclear reactions, in particular, for neutrino-nucleus reactions, which are of great interest in the light of the new neutrino oscillation experiments. We present the global relativistic folding optical potential (GRFOP) fits to elastic proton scattering data from C-12 nucleus at energies between 20 and 1040 MeV. We estimate observables, such as the differential cross section, the analyzing power, and the spin rotation parameter, in elastic proton scattering within the relativistic impulse approximation. The new GRFOP potential is employed within the relativistic Green's function model for inclusive quasielastic electron scattering and for (anti) neutrino-nucleus scattering at MiniBooNE kinematics.

Development and Application of Covalent-Labeling Strategies for the Large-Scale Thermodynamic Analysis of Protein Folding and Ligand Binding

Thermodynamic stability measurements on proteins and protein-ligand complexes can offer insights not only into the fundamental properties of protein folding reactions and protein functions, but also into the development of protein-directed therapeutic agents to combat disease. Conventional calorimetric or spectroscopic approaches for measuring protein stability typically require large amounts of purified protein. This requirement has precluded their use in proteomic applications. Stability of Proteins from Rates of Oxidation (SPROX) is a recently developed mass spectrometry-based approach for proteome-wide thermodynamic stability analysis. Since the proteomic coverage of SPROX is fundamentally limited by the detection of methionine-containing peptides, the use of tryptophan-containing peptides was investigated in this dissertation. A new SPROX-like protocol was developed that measured protein folding free energies using the denaturant dependence of the rate at which globally protected tryptophan and methionine residues are modified with dimethyl (2-hydroxyl-5-nitrobenzyl) sulfonium bromide and hydrogen peroxide, respectively. This so-called Hybrid protocol was applied to proteins in yeast and MCF-7 cell lysates and achieved a ~50% increase in proteomic coverage compared to probing only methionine-containing peptides. Subsequently, the Hybrid protocol was successfully utilized to identify and quantify both known and novel protein-ligand interactions in cell lysates. The ligands under study included the well-known Hsp90 inhibitor geldanamycin and the less well-understood omeprazole sulfide that inhibits liver-stage malaria. In addition to protein-small molecule interactions, protein-protein interactions involving Puf6 were investigated using the SPROX technique in comparative thermodynamic analyses performed on wild-type and Puf6-deletion yeast strains. A total of 39 proteins were detected as Puf6 targets and 36 of these targets were previously unknown to interact with Puf6. Finally, to facilitate the SPROX/Hybrid data analysis process and minimize human errors, a Bayesian algorithm was developed for transition midpoint assignment. In summary, the work in this dissertation expanded the scope of SPROX and evaluated the use of SPROX/Hybrid protocols for characterizing protein-ligand interactions in complex biological mixtures.

How Vladimir Putin’s Divorce Story Was Constructed and Received, or When the President Divorced His Wife and Married the Country Instead

When the Russian president divorced his wife in 2013, social media crowds coined plenty of the Internet memes to interpret the news. Anastasia Denisova, Doctoral Researcher at CAMRI, examined the framing of the story in traditional and new media and came to the surprising findings.

Enhancing the Manufacturing Knowledge of Undergraduate Engineering Students: A Case Study of a Design-Build-Test Challenge Involving Folding Bicycles

Many engineers currently in professional practice will have gained a degree level qualification which involved studying a curriculum heavy with mathematics and engineering science. While this knowledge is vital to the engineering design process so also is manufacturing knowledge, if the resulting designs are to be both technically and commercially viable.
The methodology advanced by the CDIO Initiative aims to improve engineering education by teaching in the context of Conceiving, Designing, Implementing and Operating products, processes or systems. A key element of this approach is the use of Design-Built-Test (DBT) projects as the core of an integrated curriculum. This approach facilitates the development of professional skills as well as the application of technical knowledge and skills developed in other parts of the degree programme. This approach also changes the role of lecturer to that of facilitator / coach in an active learning environment in which students gain concrete experiences that support their development.
The case study herein describes Mechanical Engineering undergraduate student involvement in the manufacture and assembly of concept and functional prototypes of a folding bicycle.

Who makes the news : Australia : global media monitoring project 2010 national report

The Australian report for the Global Media Monitoring Project 2010 (GMMP 2010) involved a study of 374 stories that were sampled from 26 Australian newspapers, radio and television stations, and internet news services on 10 November 2009. This snapshot of reporting on that day suggests that women are under-represented in the Australian news media as both the sources and creators of news. Females made up only 24% of the 1012 news sources who were heard, read about or seen in the stories that were studied. Neglect of female sources was particularly noticeable in sports news. Women made up only 1% of the 142 sources who were talked about or quoted in sports stories. Female sources of news were disproportionately portrayed as celebrities and victims. Although women made up only 24% of sources overall, they comprised 44% of victims of crimes, accidents, war, health problems, or discrimination. Unsurprisingly, women made up 32% of sources in stories about violent crimes and 29% in stories about disasters, accidents or emergencies – usually in the role of victim. Females were commonly defined in terms of their status as a mother, daughter, wife, sister or other family relationship. Family status was mentioned for 33% of women quoted or discussed in the news stories compared to only 13% of male sources. Women also made up 75% of sources described as homemakers or parents. The Australian GMMP 2010 study also indicates a gender division among the journalists who wrote or presented the news. Only 32% of the stories were written or presented by female reporters and newsreaders. The gender inequality was again most evident in sports journalism. Findings from the Australian report also contributed to the GMMP 2010 Global Report and the Pacific GMMP 2010 Regional Report, which are available at http://whomakesthenews.org/gmmp/gmmp-reports/gmmp-2010-reports

The factor V HR2 haplotype: Prevalence and association of the A4070G and A6755G polymorphisms

Recently, a polymorphism was identified in exon 25 of the factor V gene that is possibly a functional candidate for the HR2 haplotype. This haplotype is characterized by a single base substitution named R2 (A4070G) in the B domain of the protein. A mutation (A6755G; 2194Asp→Gly) located near the C terminus has been hypothesized to influence protein folding and glycosylation, and might be responsible for the shift in factor V isoform (FV1 / FV2) ratio. This study investigated the prevalence of these two factor V HR2 haplotype polymorphisms in a cohort of normal blood donors, patients with osteoarthritis and women with complications during pregnancy, and in families of factor V Leiden individuals. A high allele frequency for the two polymorphisms was found in the blood donor group (6.2% R2, 5.6% A6755G). No significant difference in allele frequency was observed in the clinical groups (obstetric complications and osteoarthritis, 4.1-4.9% for the two polymorphisms) when compared with that of healthy blood donors. We confirm that the factor V A6755G polymorphism shows strong linkage to the R2 allele, although it is not exclusively inherited with the exon 13 A4070G variant and can occur independently. © 2001 Lippincott Williams & Wilkins.

Reconstructing the event stratigraphy from the complex structural - stratigraphic architecture of an Archaean volcanic – intrusive – sedimentary succession : the Boorara Domain, Eastern Goldfields Superterrane, Western Australia

Two main deformational phases are recognised in the Archaean Boorara Domain of the Kalgoorlie Terrane, Eastern Goldfields Superterrane, Yilgarn Craton, Western Australia, primarily involving southover- north thrust faulting that repeated and thickened the stratigraphy, followed by east northeast – west-southwest shortening that resulted in macroscale folding of the greenstone lithologies. The domain preserves mid-greenschist facies metamorphic grade, with an increase to lower amphibolite metamorphic grade towards the north of the region. As a result of the deformation and metamorphism, individual stratigraphic horizons are difficult to trace continuously throughout the entire domain. Volcanological and sedimentological textures and structures, primary lithological contacts, petrography and geochemistry have been used to correlate lithofacies between faultbounded structural blocks. The correlated stratigraphic sequence for the Boorara Domain comprises quartzo-feldspathic turbidite packages, overlain by high-Mg tholeiitic basalt (lower basalt), coherent and clastic dacite facies, intrusive and extrusive komatiite units, an overlying komatiitic basalt unit (upper basalt), and at the stratigraphic top of the sequence, volcaniclastic quartz-rich turbidites. Reconstruction of the stratigraphy and consideration of emplacement dynamics has allowed reconstruction of the emplacement history and setting of the preserved sequence. This involves a felsic, mafic and ultramafic magmatic system emplaced as high-level intrusions, with localised emergent volcanic centres, into a submarine basin in which active sedimentation was occurring.

The genesis of 'the new geography and the new imperialism : 1870-1918', or 'how I came to Jamaica and joined the UWI Geography Department

In this article, Brian Hudson relates how he came to write the paper published in the journal Antipode, for which he gained recognition as a radical geographer in the late 1970's. It is a tale of a journey in which the loves of his life, geography, history, travel and his wife of over 40 years, came together through living in a number of different places: the United Kingdom, Ghana, Hong Kong, and Jamaica. After leaving UWI, Brian and his family settled in Brisbane, Australia where he taught at Queensland University of Technology until his retirement.

The promise of Iceland

Memoir, 288 pages. An account of journeys made by the author from Australia to Iceland as a way of interrogating notions of cultural belonging, family, and homecoming. "In 1990, Kári Gíslason travelled to Iceland to meet his father for the first time. What he finds is not what he expected. Born from a secret liaison between a British mother and an Icelandic father, Kári Gíslason was the subject of a promise – a promise elicited from his father to not reveal his identity. The Icelandic city of Reykjavík, where Kári was born, was also home to his father and his father’s wife and five children – none of whom knew of Kári’s existence. Moving regularly between Iceland and Australia, he grew up aware of his father’s identity, but understanding that it was the subject of a secret pact between his parents. At the age of 27, he makes a decision to break the pact and contacts his father’s other family. What follows, and what leads him there, makes for a riveting journey over landscapes, time and memory. Kári travels from the freezing cold winters of Iceland to the shark net at Sydney’s Balmoral, an unsettled life in the English countryside and the harsh yellow summer of Brisbane, and back again. He traces the steps of his mother who answered an ad in The Times for an English-speaking secretary in 1970 and found herself in Iceland among the ‘Army of Foreign Secretaries’, and in the arms of a secret lover. Iceland becomes the substitute for the father Kári never really knew as he discovers the meaning of ‘home’ and closes the circle of his own fatherless life."-- publisher website

Restoration of native folding of single-stranded DNA sequences through reverse mutations: an indication of a new epigenetic mechanism

We used in vivo (biological), in silico (computational structure prediction), and in vitro (model sequence folding) analyses of single-stranded DNA sequences to show that nucleic acid folding conservation is the selective principle behind a high-frequency single-nucleotide reversion observed in a three-nucleotide mutated motif of the Maize streak virus replication associated protein (Rep) gene. In silico and in vitro studies showed that the three-nucleotide mutation adversely affected Rep nucleic acid folding, and that the single-nucleotide reversion [C(601)A] restored wild-type-like folding. In vivo support came from infecting maize with mutant viruses: those with Rep genes containing nucleotide changes predicted to restore a wild-type-like fold [A(601)/G(601)] preferentially accumulated over those predicted to fold differently [C(601)/T(601)], which frequently reverted to A(601) and displaced the original population. We propose that the selection of native nucleic acid folding is an epigenetic effect, which might have broad implications in the evolution of plants and their viruses.

Role of kilometer-scale weak circular heterogeneities on upper crustal deformation patterns: Evidence from scaled analogue modeling and the Sudbury Basin, Canada

The Sudbury Basin is a non-cylindrical fold basin occupying the central portion of the Sudbury Impact Structure. The impact structure lends itself excellently to explore the structural evolution of continental crust containing a circular region of long-term weakness. In a series of scaled analogue experiments various model crustal configurations were shortened horizontally at a constant rate. In mechanically weakened crust, model basins formed that mimic several first-order structural characteristics of the Sudbury Basin: (1) asymmetric, non-cylindrical folding of the Basin, (2) structures indicating concentric shortening around lateral basin termini and (3) the presence of a zone of strain concentration near the hinge zones of model basins. Geometrically and kinematically this zone corresponds to the South Range Shear Zone of the Sudbury Basin. According to our experiments, this shear zone is a direct mechanical consequence of basin formation, rather than the result of thrusting following folding. Overall, the models highlight the structurally anomalous character of the Sudbury Basin within the Paleoproterozoic Eastern Penokean Orogen. In particular, our models suggest that the Basin formed by pure shear thickening of crust, whereas transpressive deformation prevailed elsewhere in the orogen. The model basin is deformed by thickening and non-cylindrical synformal buckling, while conjugate transpressive shear zones propagated away from its lateral tips. This is consistent with pure shear deformation of a weak circular inclusion in a strong matrix. The models suggest that the Sudbury Basin formed as a consequence of long-term weakening of the upper crust by meteorite impact.

Dying for the bonds of marriage : forced marriages as a weapon of genocide

‘Forced marriages’ involve a woman or girl being abducted and declared the ‘wife’ of her captor without her consent or her family’s consent. The practice generally occurs during wartime and the ‘wife’ is normally subjected to rape, forced impregnation and sexual slavery. Moreover, she is coerced into an intimate relationship with a man who is often the perpetrator of crimes against her and her community. While forced marriages have recently been recognised as a crime against humanity, this Article contends that this does not constitute full recognition of the destructive nature of forced marriages. Instead, this Article mirrors and extends the Akayesu decision that rape can be used as a tool of genocide and maintains that forced marriages can also be a form of genocide.

Wife abuse : are we detecting it?

Our objective was to measure the prevalence of wife abuse in an urban teaching hospital family practice unit and compare this to the frequency of documentation by family physicians. A modified Conflicts Tactics Scale Questionnaire was administered to all female patients either married or common-law older than 16 years during the study period. The respective patients' charts were reviewed for documentation of wife abuse. Three hundred eighty-three charts were reviewed, and 275 surveys were completed (72% response rate). Physical and mental abuse were reported in 8% and 23%, respectively, of the respondents. Four percent of respondents had considered suicide. One percent of the charts had wife assault documented (p = 0.0001). Wife abuse is reported in at least 8% of our patients. There appear to be significant health risks to these women, including homicide, suicide, and rape. Family physician documentation of wife abuse was poor.

The role of HtrA as a chaperone and protease in bacterial pathogenesis

HtrA (High Temperature Requirement A) is a critical stress response protease and chaperone for many bacteria. HtrA is a multitasking protein which can degrade unfolded proteins, conduct specific proteolysis of some substrates for correct assembly, interact with substrates to ensure correct folding, assembly or localisation, and chaperone unfolded proteins. These functions are critical for the virulence of a number of bacterial pathogens, in some cases not simply due to the broad activities of HtrA in protection against the protein stress conditions which occur during virulence. But also due to the role of HtrA in either specific proteolysis or assembly of key protein substrates which function directly in virulence. Remarkably, these activities are all conducted without any requirement for ATP. The biochemical mechanism of HtrA relies both on the chymotryptic serine protease active site as well as the presence of two PDZ (protein binding) domains. The mechanism is a unique combination of activation by substrate motifs to alter the confirmation of the active site, and assembly into a multimeric complex which has enhanced degradation and may also act as a protective cage for proteins which are not degraded. The role of this protease in the pathogenesis of a number of bacteria and the details of its distinctive biochemical activation and assembly mechanisms are discussed in this chapter.