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Chang H.-J.,Academia Sinica, Taiwan | Chang H.-J.,Institute of Biological Chemistry | Chang H.-J.,National Taiwan University | Jian J.-W.,Academia Sinica, Taiwan | And 17 more authors.
Structure | Year: 2014

Protein loops are frequently considered as critical determinants in protein structure and function. Recent advances in high-throughput methods for DNA sequencing and thermal stability measurement have enabled effective exploration of sequence-structure-function relationships in local protein regions. Using these data-intensive technologies, we investigated the sequence-structure- function relationships of six complementarity-determining regions (CDRs) and ten non-CDR loops in the variable domains of a model vascular endothelial growth factor (VEGF)-binding single-chain antibody variable fragment (scFv) whose sequence had been optimized via a consensus-sequence approach. The results show that only a handful of residues involving long-range tertiary interactions distant from the antigen-binding site are strongly coupled with antigen binding. This implies that the loops are passive regions in protein folding; the essential sequences of these regions are dictated by conserved tertiary interactions and the consensus local loop-sequence features contribute little to protein stability and function. © 2014 Elsevier Ltd All rights reserved. Source

Kamalov M.,Institute of Biological Chemistry | Kaur H.,University of Auckland | Brimble M.A.,University of Auckland
Chemistry - A European Journal | Year: 2016

Synthetic methods aimed at preparing peptides cross-linked by diaminodiacids remain an important chemical challenge. These cross-links are known to play a crucial role on the activity, structural stability, and folding of the host peptides and proteins. Recent developments in the syntheses of such systems have led to intriguing advances in the understanding of intermolecular side-chain cross-linking and the role that these structural motifs play in the biochemistry of proteins. Herein we provide an overview of the existing synthetic methodology that has been developed to effect protein cross-linking using diaminodiacids. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Kirchhoff H.,Institute of Biological Chemistry
Plant signaling & behavior | Year: 2013

The thylakoid membrane system inside plants chloroplasts defines the structural framework for photosynthetic conversion of sunlight into metabolic energy forms (ATP, NADPH + H(+)). An architectural hallmark of these thylakoid membranes is the tight stacking of part of the membrane into cylindrical flat grana thylakoids, with a diameter of about 500 nm, that are interconnected by unstacked stroma lamellae forming a complex 3D network of alternating grana piles and stroma lamellae. The structural differentiation in the stacked and unstacked thylakoid regions is the basis for a pronounced spatial separation of multisubunit pigment-protein complexes that catalyze energy transformation. The main part of photosystem II (PSII) associated with light-harvesting complex II (LHCII) is concentrated in the grana thylakoids whereas PSI-LHCI and the ATPase complex are excluded from the stacked grana and accumulate in the unstacked thylakoid regions. The fifth protein complex, the cytochrome b 6f complex, is assumed to be homogenously distributed. It is important to recognize that this structural arrangement is not static but highly dynamic and responsive to environmental factors like light intensity and quality or temperature. Knowledge about the interplay between dynamic structural features of the intricate thylakoid architecture, and the functionality, regulation, repair and biogenesis of the photosynthetic machinery is essential for understanding the plasticity of energy conversion in plants living in a fluctuating multi-factorial environment. Source

Chang H.-J.,Institute of Biological Chemistry | Chang H.-J.,National Taiwan University | Yang A.-S.,Academia Sinica, Taiwan
Methods in Molecular Biology | Year: 2014

Cystine-stabilized mini-proteins are important scaffolds in the combinatorial search of binders for molecular recognition. The structural determinants of a cystine-stabilized scaffold are the critical residues determining the formation of the native disulfide-bonding configuration, and thus should remain unchanged in the combinatorial libraries so as to allow a large portion of the library sequences to be compatible with the scaffold structure. A high-throughput molecular evolution procedure has been developed to select and screen for the polypeptide sequences folding into a specific cystine-stabilized structure. Patterns of sequence preference that emerge from the resultant sequence profiles provide structural determinant information, which facilitates the designs of combinatorial libraries for combinatorial approaches as in phage display. This methodology enables artificial cystine-stabilized proteins to be engineered with enhanced folding and binding properties. © 2014 Springer Science+Business Media, LLC . Source

Guh Y.-J.,Institute of Biological Chemistry | Guh Y.-J.,Academia Sinica, Taiwan | Yang C.-Y.,Academia Sinica, Taiwan | Liu S.-T.,National Taiwan Normal University | And 2 more authors.
Proceedings of the Royal Society B: Biological Sciences | Year: 2016

Oestrogen-related receptor α (ERRα) is an orphan nuclear receptor which is important for adaptive metabolic responses under conditions of increased energy demand, such as cold, exercise and fasting. Importantly, metabolism under these conditions is usually accompanied by elevated production of organic acids, which may threaten the body acid-base status. Although ERRα is known to help regulate ion transport by the renal epithelia, its role in the transport of acidbase equivalents remains unknown. Here, we tested the hypothesis that ERRα is involved in acidbase regulation mechanisms by using zebrafish as the model to examine the effects of ERRα on transepithelial H+ secretion. ERRα is abundantly expressed in H+-pump-rich cells (HR cells), a group of ionocytes responsible for H+ secretion in the skin of developing embryos, and its expression is stimulated by acidic (pH 4) environments. Knockdown of ERRα impairs both basal and low pH-induced H+ secretion in the yolk-sac skin, which is accompanied by decreased expression of H+secreting-related transporters. The effect of ERRα on H+ secretion is achieved through regulating both the total number of HR cells and the function of individual HR cells. These results demonstrate, for the first time, that ERRα is required for transepithelial H+ secretion for systemic acid-base homeostasis. © 2016 The Author(s) Published by the Royal Society. All rights reserved. Source

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