Early Folding Research Articles

3D hydrodynamic flow focusing-based micromixer enables high-resolution imaging for studying the early folding kinetics of G-quadruplex

Hydrodynamic flow focusing-based micromixers (laminar micromixers) have been widely applied to the investigation of the folding kinetics of biomacromolecules, due to their capability to resolve the folding events in a microsecond time scale. Although most existing laminar micromixers attempted to reduce mixing time, our work focused on developing a system that can generate high-resolution images under a more stable flow, which results in more accurate kinetic analysis. Specifically, we developed a simple three-dimensional (3D) laminar micromixer, which distributes the sample stream to a 3D profile to address flow-instability issues caused by Dean vortices in a two-dimensional mixer. In the 3D mixer, the sample stream was successfully focused to a one-pixel width at the resolution of ˜200 nm/pixel, which approached the resolving power of an optical microscope and represented the highest imaging resolution ever achieved using a 3D mixer. Furthermore, we used the device to investigate the early folding kinetics of G-quadruplex under various sodium cation concentrations. Interestingly, a lag phase was found before the exponential phase during the folding process. Moreover, we obtained the G-quadruplex’s observed kinetics of (1.51 ± 0.02) ×104 s−1, (1.68 ± 0.04) ×104 s−1 and (2.01 ± 0.02) ×104 s−1 at 50-, 100- and 200 mM NaCl, respectively.

Aberrant gyrification contributes to the link between gestational age and adult IQ after premature birth.

Gyrification is a hallmark of human brain development, starting in the second half of gestation in primary cortices, followed by unimodal and then transmodal associative cortices. Alterations in gyrification have been noted in premature-born newborns and children, suggesting abnormal cortical folding to be a permanent feature of prematurity. Furthermore, both gyrification and prematurity are tightly linked with cognitive performance, indicating a link between prematurity, gyrification, and cognitive performance. To investigate this triangular relation, we tested the following two hypotheses: (i) gyrification is aberrant in premature-born adults; and (ii) aberrant gyrification contributes to the impact of prematurity on adult cognitive performance. One hundred and one very premature-born adults (i.e. adults born before 32 weeks of gestation, and/or with birth weight <1500 g) and 111 mature-born adults were assessed by structural MRI and cognitive testing at 27 years of age. Gyrification was measured by local cortical absolute mean curvature (AMC), evaluated through structural MRI. Cognitive performance was assessed by the Wechsler Adult Intelligence Scale, full-scale IQ test. Two-sample t-tests, regression and mediation analyses were used to assess AMC group differences and the relation between AMC, birth-related variables, and full-scale IQ. Three key findings were identified. First, local AMC was widely increased in fronto-temporo-parietal primary and associative cortices of very premature-born adults. Increase of AMC was inversely associated with gestational age and birth weight and positively associated with medical complications at birth, respectively. Second, increased AMC of temporal associative cortices specifically contributed to the association between prematurity and reduced adult IQ (two-path mediation), indicating that aberrant gyrification of temporal associative cortices is critical for impaired cognitive performance after premature birth. Finally, further investigation of the relationship of gyrification between the early folding postcentral cortices and associative temporal cortices, folding later during neurodevelopment, revealed that the effect of gyrification abnormalities in associative temporal cortices on adult IQ is influenced itself by gyrification abnormalities occurring in the early folding postcentral cortices (three-path mediation). These results indicate that gyrification development across cortical areas in the brain conveys prematurity effects on adult IQ. Overall, these results provide evidence that premature birth leads to permanently aberrant gyrification patterns suggesting an altered neurodevelopmental trajectory. Statistical mediation modelling suggests that both aberrant gyrification itself as well as its propagation across the cortex express aspects of impaired neurodevelopment after premature birth and lead to reduced cognitive performance in adulthood. Thus, markers of gyrification appear as potential candidates for prognosis and treatment of prematurity effects.

Nature's Shortcut to Protein Folding.

This Feature Article presents a view of the protein folding transition based on the hypothesis that Nature has built features within the sequences that enable a Shortcut to efficient folding. Nature's Shortcut is proposed to be the early establishment of a set of nonlocal weak contacts, constituting protein loops that significantly constrain regions of the collapsed disordered protein into a native-like low-resolution fluctuating topology of major sections of the backbone. Nature's establishment of this scaffold of nonlocal contacts is claimed to bypass what would otherwise be a nearly hopeless unaided search for the final three-dimensional structure in proteins longer than ∼100 amino acids. To support this main contention of the Feature Article, the loop hypothesis (LH) description of early folding events is experimentally tested with time-resolved Förster resonance energy transfer techniques for adenylate kinase, and the data are shown to be consistent with theoretical predictions from the sequential collapse model (SCM). The experimentally based LH and the theoretically founded SCM are argued to provide a unified picture of the role of nonlocal contacts as constituting Nature's Shortcut to protein folding. Importantly, the SCM is shown to reliably predict key nonlocal contacts utilizing only primary sequence information. This view on Nature's Shortcut is open to the protein community for further detailed assessment, including its practical consequences, by suitable application of advanced experimental and computational techniques.

The Ribosome Cooperates with a Chaperone to Guide Multi-domain Protein Folding

Multi-domain proteins, containing several structural units within a single polypeptide, constitute a large fraction of all proteomes. Co-translational folding is assumed to simplify the conformational search problem for large proteins, but the events leading to correctly folded, functional structures remain poorly characterized. Similarly, how the ribosome and molecular chaperones promote efficient folding remains obscure. Using optical tweezers, we have dissected early folding events of nascent elongation factor G, a multi-domain protein that requires chaperones forfolding. The ribosome and the chaperone trigger factor reduce inter-domain misfolding, permitting folding of the N-terminal G-domain. Successful completion of this step is a crucial prerequisite for folding of the next domain. Unexpectedly, co-translational folding does not proceed unidirectionally; emerging unfolded polypeptide can denature an already-folded domain. Trigger factor, but not theribosome, protects against denaturation. The chaperone thus serves a previously unappreciated function, helping multi-domain proteins overcome inherent challenges during co-translational folding.

Chaperone Interactions at the Ribosome.

The continuous refreshment of the proteome is critical to maintain protein homeostasis and to adapt cells to changing conditions. Thus, de novo protein biogenesis by ribosomes is vitally important to every cellular system. This process is delicate and error-prone and requires, besides cytosolic chaperones, the guidance by a specialized set of molecular chaperones that bind transiently to the translation machinery and the nascent protein to support early folding events and to regulate cotranslational protein transport. These chaperones include the bacterial trigger factor (TF), the archaeal and eukaryotic nascent polypeptide-associated complex (NAC), and the eukaryotic ribosome-associated complex (RAC). This review focuses on the structures, functions, and substrates of these ribosome-associated chaperones and highlights the most recent findings about their potential mechanisms of action.

Application of an interpretable classification model on Early Folding Residues during protein folding

BackgroundMachine learning strategies are prominent tools for data analysis. Especially in life sciences, they have become increasingly important to handle the growing datasets collected by the scientific community. Meanwhile, algorithms improve in performance, but also gain complexity, and tend to neglect interpretability and comprehensiveness of the resulting models.ResultsGeneralized Matrix Learning Vector Quantization (GMLVQ) is a supervised, prototype-based machine learning method and provides comprehensive visualization capabilities not present in other classifiers which allow for a fine-grained interpretation of the data. In contrast to commonly used machine learning strategies, GMLVQ is well-suited for imbalanced classification problems which are frequent in life sciences. We present a Weka plug-in implementing GMLVQ. The feasibility of GMLVQ is demonstrated on a dataset of Early Folding Residues (EFR) that have been shown to initiate and guide the protein folding process. Using 27 features, an area under the receiver operating characteristic of 76.6% was achieved which is comparable to other state-of-the-art classifiers. The obtained model is accessible at https://biosciences.hs-mittweida.de/efpred/.ConclusionsThe application on EFR prediction demonstrates how an easy interpretation of classification models can promote the comprehension of biological mechanisms. The results shed light on the special features of EFR which were reported as most influential for the classification: EFR are embedded in ordered secondary structure elements and they participate in networks of hydrophobic residues. Visualization capabilities of GMLVQ are presented as we demonstrate how to interpret the results.

Descriptive text to the Geological map of Greenland, 1:100 000, Kilen 81 Ø.1 Syd

The geological map sheet of Kilen in 1:100 000 scale covers the south-eastern part of the Carboniferous–Palaeogene Wandel Sea Basin in eastern North Greenland. The map area is dominated by the Flade Isblink ice cap, which separates several minor isolated landmasses. On the semi-nunatak of Kilen, the map is mainly based on oblique photogrammetry and stratigraphical field work while in Erik S. Henius Land, Nordostrundingen and northern Amdrup Land the map is based on field data collected during previous, 1:500 000 scale regional mapping. Twenty-one Palaeozoic–Mesozoic mappable units were identified on Kilen, while the surrounding areas comprise the Late Cretaceous Nakkehoved Formation to the north-east and the Late Carboniferous Foldedal Formation to the south-west. On Kilen, the description of Jurassic–Cretaceous units follows a recently published lithostratigraphy. The Upper Palaeozoic–lowermost Cretaceous strata comprise seven formations and an informal mélange unit. The overlying Lower–Upper Cretaceous succession comprises the Galadriel Fjeld and Sølverbæk Formations, which are subdivided into six and five units, respectively. In addition, the Quaternary Ymer Formation was mapped on south-east Kilen. The Upper Palaeozoic to Mesozoic strata of Kilen are faulted and folded. Several post-Coniacian NNW–SSE-trending normal faults are identified and found to be passively folded by a later N–S compressional event. A prominent subhorizontal fault, the Central Detachment, separates two thrust sheets, the Kilen Thrust Sheet in the footwall and the Hondal Elv Thrust Sheet in the hanging wall. The style of deformation and the structures found on Kilen are caused by compressional tectonics resulting in post-extensional, presumably Early Eocene, folding and thrusting and basin inversion. The structural history of the surrounding areas and their relation to Kilen await further studies.

Descriptive text to the Geological map of Greenland, 1:100 000, Kilen 81 Ø.1 Syd

The geological map sheet of Kilen in 1:100 000 scale covers the south-eastern part of the Carboniferous– Palaeogene Wandel Sea Basin in eastern North Greenland. The map area is dominated by the Flade Isblink ice cap, which separates several minor isolated landmasses. On the semi-nunatak of Kilen, the map is mainly based on oblique photogrammetry and stratigraphical field work while in Erik S. Henius Land, Nordostrundingen and northern Amdrup Land the map is based on field data collected during previous, 1:500 000 scale regional mapping. Twenty-one Palaeozoic–Mesozoic mappable units were identified on Kilen, while the surrounding areas comprise the Late Cretaceous Nakkehoved Formation to the north-east and the Late Carboniferous Foldedal Formation to the south-west. On Kilen, the description of Jurassic–Cretaceous units follows a recently published lithostratigraphy. The Upper Palaeozoic–lowermost Cretaceous strata comprise seven formations and an informal mélange unit. The overlying Lower–Upper Cretaceous succession comprises the Galadriel Fjeld and Sølverbæk Formations, which are subdivided into six and five units, respectively. In addition, the Quaternary Ymer Formation was mapped on south-east Kilen. The Upper Palaeozoic to Mesozoic strata of Kilen are faulted and folded. Several post-Coniacian NNW–SSE-trending normal faults are identified and found to be passively folded by a later N–S compressional event. A prominent subhorizontal fault, the Central Detachment, separates two thrust sheets, the Kilen Thrust Sheet in the footwall and the Hondal Elv Thrust Sheet in the hanging wall. The style of deformation and the structures found on Kilen are caused by compressional tectonics resulting in post-extensional, presumably Early Eocene, folding and thrusting and basin inversion. The structural history of the surrounding areas and their relation to Kilen await further studies.

Polyphase tectonic history of the Southern Peninsula, Haiti: from folding-and-thrusting to transpressive strike-slip

The Southern Peninsula of Haiti is a seismically active east – west trending transpressive mountain range with elevations over 2 km. Present-day deformation is mainly partitioned along the left-lateral Enriquillo – Plantain Garden Fault Zone (EPGFZ) and associated oblique reverse faults and/or folds. The configuration of these faults, their respective timing, and the role of structural heritage on their development is poorly understood. To address these questions we present the results of extensive field campaigns, combined with satellite imagery interpretation and published data, which allows us to constrain the Cenozoic evolution of the Southern Peninsula. Our results show a polyphase tectonic history consisting of three major tectonic events: 1) Maastrichtian to early Paleocene crustal-scale folding that developed coevally with predominantly north to northeast dipping thrusts, resulting in uplift and erosion of the Cretaceous sedimentary cover in large parts of the Southern Peninsula. 2) Early Miocene uplift and erosion, which was strongest in the southwestern part of the peninsula and decreased eastwards, did not affect the Massif de la Selle. Uplift is most likely unrelated to strike-slip activity but resulted from folding in response to NE – SW shortening that possibly reactivated older, predominantly N- to NE-dipping thrusts. 3) Late Miocene to present-day deformation and uplift. Spatially distributed strike-slip started during the late Miocene and became progressively focused along the EPGFZ in the latest Miocene. Oblique and thrust faults locally post-date strike-slip activity from the Pliocene onward. Increase in compressional deformation from west to east is reflected by a change in structural style, with predominantly strike-slip faults in the west and transpressional faults in the east, the latter possibly rooted on the EPGFZ at depth. Paleo-stresses associated with a strike-slip regime are at a significantly high angle to the trace of the EPGFZ, indicating that the EPGFZ is a mechanically weak fault.

Characterizing the relation of functional and Early Folding Residues in protein structures using the example of aminoacyl-tRNA synthetases.

Proteins are chains of amino acids which adopt a three-dimensional structure and are then able to catalyze chemical reactions or propagate signals in organisms. Without external influence, many proteins fold into their native structure, and a small number of Early Folding Residues (EFR) have previously been shown to initiate the formation of secondary structure elements and guide their respective assembly. Using the two diverse superfamilies of aminoacyl-tRNA synthetases (aaRS), it is shown that the position of EFR is preserved over the course of evolution even when the corresponding sequence conservation is small. Folding initiation sites are positioned in the center of secondary structure elements, independent of aaRS class. In class I, the predicted position of EFR resembles an ancient structural packing motif present in many seemingly unrelated proteins. Furthermore, it is shown that EFR and functionally relevant residues in aaRS are almost entirely disjoint sets of residues. The Start2Fold database is used to investigate whether this separation of EFR and functional residues can be observed for other proteins. EFR are found to constitute crucial connectors of protein regions which are distant at sequence level. Especially, these residues exhibit a high number of non-covalent residue-residue contacts such as hydrogen bonds and hydrophobic interactions. This tendency also manifests as energetically stable local regions, as substantiated by a knowledge-based potential. Despite profound differences regarding how EFR and functional residues are embedded in protein structures, a strict separation of structurally and functionally relevant residues cannot be observed for a more general collection of proteins.

Early Injection Laryngoplasty After Surgery: 30 Cases and Proposed Aspiration Assessment Protocol

Vocal fold movement impairment may significantly compromise postoperative recovery and quality of life of patients following thoracic or cardiothoracic surgery or prolonged intubation. The literature is limited and there is no standard screening protocol for the optimal postoperative swallowing and aspiration evaluations. We performed retrospective review of adult patients undergoing early vocal fold (VF) injection laryngoplasty for acute postoperative Vocal fold movement impairment (<30 days) that had both pre- and postinjection speech language pathologist (SLP) performed swallowing/aspiration evaluations. Records were reviewed for demographics, clinical characteristics, procedural details, and short-term outcome measures of oral intake. In total, 30 patients were included, and had data on swallowing/aspiration studies before and after the VF injection laryngoplasty. Most of the patients were injected within 5 days following the laryngologist evaluation and within 14 days following the iatrogenic recurrent laryngeal nerve injury (23/30, 76.7%). The majority of patients were injected at the bedside by awake transcutaneous injection (22/30, 73.3%), six patients were injected in the operating room under general anesthesia, and two at the outpatient clinic. Pre- and postinjection SLP evaluations included clinical bedside assessment or instrumental evaluation. Following VF injection laryngoplasty, oral diet advancement was noted in 81.8% of the patients that were nil per os before the injection (18/22). No complications were noted. In conclusions, acute VFMI following surgery requires immediate diagnosis and therapeutic strategy to minimize postoperative complications and to overcome impairments in the voice, swallow, and cough. Otolaryngology-SLP interdisciplinary aspiration and swallowing assessment protocol is proposed based on our experience and an extensive literature review.

Local and non‐local topological information in the denatured state ensemble of a β‐barrel protein

The folding of predominantly β-sheet proteins is complicated by the presence of a large number of non-local interactions in their native states, which increase the ruggedness of their folding energy landscapes. However, forming non-local contacts early in folding or even in the unfolded state can smooth the energy landscape and facilitate productive folding. We report that several sequence regions of a β-barrel protein, cellular retinoic acid-binding protein 1 (CRABP1), populate native-like secondary structure to a significant extent in the denatured state in 8 M urea. In addition, we provide evidence for both local and non-local interactions in the denatured state of CRABP1. NMR chemical shift perturbations (CSPs) under denaturing conditions upon substitution of single residues by mutation support the presence of several non-local interactions in topologically key sites, arguing that the denatured state is conformationally restricted and contains topological information for the native fold. Among the most striking non-local interactions are those between the N- and C-terminal regions, which are involved in closure of the native β-barrel. In addition, CSPs support the presence of two features in the denatured state: a major hydrophobic cluster involving residues from various parts of the sequence and a native-like interaction similar to one identified in previous studies as forming early in folding (Budyak et al., Structure 21, 476 [2013]). Taken together, our data support a model in which transient structures involving nonlocal interactions prime early folding interactions in CRABP1, determine its barrel topology, and may protect this predominantly β-sheet protein against aggregation.

Integrating kinematic restoration and forward finite element simulations to constrain the evolution of salt diapirism and overburden deformation in evaporite basins

In evaporite basins, salt deformation including inflation, diapirism, and salt canopy emplacement is inherently non-coaxial and ductile and thus it presents challenges for two-dimensional kinematic restorations that rely on line-length and area-balancing assumptions. Also, because salt flow and the resulting deformation of adjacent cover units can be driven by temporally and spatially transient salt pressure gradients, kinematic restorations are generally unable to predict the magnitude and distribution of subseismic deformation that results from a particular structural scenario. Here, we use a case study from the Atwater fold belt, Gulf of Mexico, to test a new workflow that involves comparison of kinematic restoration models with forward numerical (finite-element) models of structural evolution to examine the physical validity of solutions derived from the kinematic restorations and to determine the nature and spatial distribution of the resultant subseismic deformation. In the Atwater fold belt, which represents the downdip portion of a linked updip (landward) extensional-downdip (seaward) contractional system, our kinematic restorations indicated that major anticlines likely result from early short wavelength folding followed by (1) inflation of the autochthonous salt to drive failure of the overburden, (2) collapse of the updip limb of the major salt-cored anticline as the salt evacuates updip, and (3) rapid emplacement of the allochthonous salt canopy. In margin scale finite element models of the same system, progradation of the sedimentary wedge above the weak salt substrate leads to basinward migration of the salt and produces inflation of the major downdip salt-cored folds, as predicted by the kinematic model. However, in relatively strong overburden materials (equivalent friction angle = 32°), such salt flow only sustains inflation of the anticlines and is unable to reproduce the interpreted collapse of the anticlinal backlimb or emplacement of the salt canopy. Alternate model runs that include a significant reduction in material strength (equivalent friction angle = 18°) allow salt in the anticlinal crest to drive both reactive and active diapirism and ultimately lead to rapid emplacement of allochthonous canopies. In all of these models, diapirism drives substantial seismically-resolvable and subseismic deformation of wall rocks. Additionally, these models clearly show that the stress field, and particularly the K value (horizontal-vertical stress ratio) of the sediments adjacent to salt structures used for estimating stress magnitudes for drilling predictions, is fundamentally dependent on what point along the evolutionary path from autochthonous salt, to diapir, to salt sheet, that each structure resides. These results highlight the need to test complex kinematic restorations with physics-based techniques. Additionally, they demonstrate that integrating kinematic restorations with these finite element solutions can substantially increase our ability to predict both subseismic reservoir damage in sediments adjacent to salt structures and the K values used for forecasting drilling conditions, particularly in young basins filled with poorly consolidated sediments.

Late Cretaceous to Miocene and Quaternary deformation history of the Chalk: Channels, slumps, faults, folds and glacitectonics

Late Cretaceous Chalk sedimentation history across the British Isles included (i) fault controlled uplift and subsidence in Northern Ireland and the Inner Hebrides and (ii) uplift along the lines of en echelon folds in Southern Britain and northern France. Synsedimentary slump folds and downslope displacement structures are compared with penecontemporaneous interbed slides and later tectonic folds and faults. Compressional strike-slip tectonic processes at Flamborough Head, Yorkshire, illustrate intra-Chalk slump beds in a half-graben setting. Progressive ‘growth’ of structures characterises early downslope slump folding, interbed sliding and some listric faulting. Sheet-flints replacing slide shear planes and early fractures provide evidence for early movements. Availability of open-slopes or the depth of burial under which the range of structures developed is reflected in the degree of disruption and fragmentation of chalk and flint. Fragmentation provides clues to the timing of events and origin of the Late Campanian Altachuile Breccia (Northern Ireland) and the Coniacian Hope Gap slides (Sussex). Fragmentation and formation of sheet flints together help distinguish intra-Chalk tectonics from Quaternary glacitectonic structures.The role of marl seams, high porosity chalk beds and hardgrounds on bed-sliding, décollement zones and disruption of chalk blocks from bedrock in glacitectonics is discussed. Chalk formations with marl seams develop a special style of fracturing related to early interbed sliding and pore-fluid escape structures. Marl-seams are shown to be primary sedimentary features and not the products of post depositional pressure-solution. More than any other formation the Late Santonian – Early Campanian Newhaven Chalk contains extensive sheet-flints and shows great lateral variation in thickness and lithology across the fold belts of southern England and northern France.

The Palaeoproterozoic Grythyttan Field in the Svecofennian Orogen, West Bergslagen, Central Sweden: structure, stratigraphy and age

A number of discrete slate belts of limited size occur in the Paleoproterozoic volcano-sedimentary Bergslagen Group of western Bergslagen in the Fennoscandian shield of south central Sweden. The Grythyttan Slate Belt, studied for more than a century, forms a single basin with the nearby Saxan Slate Belt. We use the lithostratigraphy of the Grythyttan Slate Formation of the Grythyttan belt, based on basin scale sedimentary facies associations of the volcaniclastic sediments in time and space, as a method to interpret overall tectonic structure. Contrary to traditional views, we reconstruct the GSB as a single overturned limb of a km-scale anticline with horizontal axis in the hanging wall of an east vergent thrust fault, reactivating a listric extensional fault. The fold connects the GSB to the neighboring SSB. Folding and thrusting were related to tectonic closure of a volcanic back- or intra-arc basin. The early folds were subsequently affected by strike-slip shearing and folding around vertical fold axes, which partitioned preferentially into the least competent lithologies (slates and marbles), significantly modifying the map appearance of the slate belt. The late shearing and folding resulted from accretion of Bergslagen onto the Fennoscandian continental margin during the late, Svecobaltic phase of the Svecofennian orogeny. The GSB forms a thin, intraformational wedge in the Bergslagen Group and represents a relatively short interlude with a conglomeratic alluvial fan and turbiditic volcaniclastics followed by more felsic volcanic rocks resembling those of the Bergslagen Group. We suggest that the GSB, and by inference the other slate belts, stem from calderas, as either terrestrial volcanic lakes or shallow submarine eruption centers. The conglomerates are pre-orogenic, not a post-orogenic molasse, as traditionally conceived, and their clast fabric has resulted from sedimentary processes only. Newly determined SIMS U-Pb zircon ages constrain the age of the GSB at ca. 1895 Ma.

Effects of Preferential Counterion Interactions on the Specificity of RNA Folding.

The real-time search for native RNA structure is essential for the operation of regulatory RNAs. We previously reported that a fraction of the Azoarcus ribozyme achieves a compact structure in less than a millisecond. To scrutinize the forces that drive initial folding steps, we used time-resolved SAXS to compare the folding dynamics of this ribozyme in thermodynamically isostable concentrations of different counterions. The results show that the size of the fast-folding population increases with the number of available counterions and correlates with the flexibility of initial RNA structures. Within 1 ms of folding, Mg2+ exhibits a smaller preferential interaction coefficient per charge, ΔΓ+/ Z, than Na+ or [Co(NH3)6]3+. The lower ΔΓ+/ Z corresponds to a smaller yield of folded RNA, although Mg2+ stabilizes native RNA more efficiently than other ions at equilibrium. These results suggest that strong Mg2+-RNA interactions impede the search for globally native structure during early folding stages.

Early thrusting and folding in the Snow Lake camp, Manitoba: tectonic implications and effects on volcanogenic massive sulfide deposits

The Chisel sequence occurs within the Snow Lake arc assemblage (SLA) of the Paleoproterozoic Trans-Hudson Orogen. It is host to six economic volcanogenic massive sulfide (VMS) deposits that formed within a single time-stratigraphic ore interval. The SLA was previously interpreted to share the same deformation history as the ca. 1.86–1.84 Ga Burntwood Group turbidites of the Kisseynew Basin to the north; however, early isoclinal folds identified in the arc assemblage cannot be correlated with structures in the turbidites and therefore developed prior to Burntwood Group deposition. This indicates that the SLA underwent a significant deformation event prior to 1.86 Ga, likely due to intraoceanic accretion or pre-1.86 Ga accretion to the Amisk collage during closure of the ancestral Manikewan Ocean. Evidence for this early folding event is recorded in the Chisel sequence deposits where it has influenced the geometry of the deposits and the location of the ore interval. The deposits are isoclinally folded by these folds, and a major early thrust fault at the Lalor deposit, the Lalor-Chisel fault, displaced the hanging-wall rocks of the deposit and the ore interval. Further flattening, transposition, and elongation of the ore lenses occurred during post-1.84 Ga collision of the SLA with the partially hidden Archean Sask craton. Although the VMS deposits are polydeformed and sulfides and precious metals were mechanically and hydrothermally remobilized at the metre scale, their primary base metal zoning remains intact and provides a tool to reconstruct the geometry of the deposits.

Abstract 4798: Targeting hTERT for treatment of glioblastoma (GBM)

Abstract Approximately 86% of GBM tumors exhibit a mutation at -124 or -146 bp upstream from the ATG start site in the transcription activating promoter region of Human telomerase reverse transcriptase (hTERT). Mutations in the hTERT promoter are known to impair repression, leading to overexpression of hTERT and tumor maintenance. Yet, complete understanding of mechanistic implications is still necessary. While overexpressed hTERT is associated with oncogenesis and resistance to apoptosis, we also observe phenotypes unrelated to the reverse transcription function. We characterized long-term glioma cell lines and glioma PDX models by hTERT promoter mutation status, hTERT mRNA expression, and hTERT protein expression in subcellular fractions. The -124 and -146 mutations are located in the major 5-12 G-quadruplex and result in misfolding of the silencer element, thus causing over-expression of hTERT. Using a diverse small molecule library, we identified a small drug-like pharmacological chaperone (pharmacoperone) molecule, TG-4260, which binds to the 26 mer base-pair heteroduplex loop, which is the nucleation site for cooperative folding of the major 5-12 G-quadruplex. The chaperone effect of TG-4260 corrects DNA hTERT G-quadruplex misfolding resulting from the promoter mutations and restores the silencer function of the G-quadruplex. TG-4260 directly decreases the transcription activity of the −124, −124/125, −138/139, and −146 mutants to a similar extent and suppresses the downstream gene BCL2, which activates caspase-3 and produces cell-cycle arrest, leading to cell death. This is the first example of the use of a pharmacoperone molecule to correct the misfolding of a DNA G-quadruplex element resulting from mutations in an early folding intermediate. We screened GBM cell models against this novel small molecule inhibitor that interferes with mutated hTERT promoter and demonstrated that TG-4260 selectively suppresses glioma cell viability without affecting non-transformed normal human astrocytes. Finally, telomere phenotypes from treated cells indicate non-canonical functions of telomerase may also contribute to glioma pathogenesis. Citation Format: Saumya Reddy Bollam, Hyun-Jin Kang, Sen Peng, Vijay Gokhale, Laurence Hurley, Michael Berens, Harshil Dhruv. Targeting hTERT for treatment of glioblastoma (GBM) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4798.

A two-domain folding intermediate of RuBisCO in complex with the GroEL chaperonin

The chaperonins (GroEL and GroES in Escherichia coli) are ubiquitous molecular chaperones that assist a subset of essential substrate proteins to undergo productive folding to the native state. Using single particle cryo EM and image processing we have examined complexes of E. coli GroEL with the stringently GroE-dependent substrate enzyme RuBisCO from Rhodospirillum rubrum. Here we present snapshots of non-native RuBisCO - GroEL complexes. We observe two distinct substrate densities in the binary complex reminiscent of the two-domain structure of the RuBisCO subunit, so that this may represent a captured form of an early folding intermediate. The occupancy of the complex is consistent with the negative cooperativity of GroEL with respect to substrate binding, in accordance with earlier mass spectroscopy studies.

Inverted fold hinge: An end member of hinge rotation by superposed buckle folding in the Precambrian terrain of western India

Plunge reversal by hinge rotation due to superposed buckle folding ends when one of the hinge segments rotates to a reclined (sensu stricto) geometry. Rotation beyond this limit (called the critical stage of hinge rotation) inverts the rotating hinge segment from an antiform to a synform or vice versa. In the Sawar-Bajta area in the Precambrian terrain of western India, a segment of a synformal early fold has been inverted to an antiform, producing an antiform-synform fold pair with a common hinge and a common axial surface. Later compression folded the limbs and axial surface of the early synform, and rotated its two adjacent hinge segments in opposite directions. Unequal rotation inverted one of the segments and bowed the common hinge upward to produce a mega sheath fold with 46° hinge angle. The sheath folded basement-cover rock contact delineates an eye-fold with more than 30 km long perimeter on map profile. The inverted segment rotated more than 17° beyond the critical position to what is probably the end member of hinge rotation. The interlimb angle of the inverted segment increased, indicating progressive opening up of the fold, which inhibits further rotation beyond the limit set by the end member.