Publication date: Available online 25 September 2015
Source:Journal of Molecular Biology

Author(s): Cardine N. Nokwe, Manuel Hora, Martin Zacharias, Hisashi Yagi, Christine John, Bernd Reif, Yuji Goto, Johannes Buchner

The association of light chains (LCs) and heavy chains is the basis for functional antibodies that are essential for adaptive immune responses. However, in some cases, LCs and especially fragments consisting of the LC variable (VL) domain are pathologically deposited in fatal aggregation diseases. The two domains of the LC are connected by a highly conserved linker. We show here that, unexpectedly, the linker residue Arg108 affects the conformational stability and folding of both VLκ and LC constant (CLκ) domains. Interestingly, the extension of VL by Arg108 results in its resistance to amyloid formation, which suggests that the nature of the truncation of the LC plays a crucial role in disease progression. Increased solvation due to the exposed charged C-terminal Arg108 residue explains its stabilizing effects on the VL domain. For the CL domain, the interaction of N-terminal loop residues with Arg108 is important for the integrity of the domain, as the disruption of this interaction results in fluctuation, partial opening of the protein’s interior and the exposure of hydrophobic residues that destabilize the domain. This establishes new principles for antibody domain architecture and amyloidogenicity.
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Publication date: Available online 25 September 2015
Source:Journal of Molecular Biology

Author(s): Filipa L. Sousa, Daniel J. Parente, David L. Shis, Jacob A. Hessman, Allen Chazelle, Matthew R. Bennett, Sarah A. Teichmann, Liskin Swint-Kruse

Protein families evolve functional variation by accumulating point-mutations at functionally-important amino acid positions. Homologs in the LacI/GalR family of transcription regulators have evolved to bind diverse DNA sequences and allosteric regulatory molecules. In addition to playing key roles in bacterial metabolism, these proteins have been widely used as a model family for benchmarking structural and functional prediction algorithms. We have collected manually-curated sequence alignments for >3000 sequences, in vivo phenotypic and biochemical data for >5750 LacI/GalR mutational variants, and non-covalent residue contact networks for 65 LacI/GalR homolog structures. Using this rich data resource, we compared the non-covalent residue contact networks of the LacI/GalR subfamilies to design and experimentally validate an allosteric mutant of a synthetic LacI/GalR repressor for use in biotechnology. The AlloRep database (freely available at www.AlloRep.org) is a key resource for future evolutionary studies of LacI/GalR homologs and for benchmarking computational predictions of functional change.
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Publication date: Available online 25 September 2015
Source:Journal of Molecular Biology

Author(s): Joseph S. Harrison, Tim M. Jacobs, Kevin Houlihan, Koenraad Van Doorslaer, Brian Kuhlman

The structurally defined ubiquitin-like homology fold (UBL) can engage in several unique protein-protein interactions (PPI) and many of these complexes have been characterized with high-resolution techniques. Using Rosetta's structural classification tools we have created the Ubiquitin Structural Relational Database (UbSRD), an SQL database of features for all 509 UBL-containing structures in the PDB, allowing users to browse these structures by PPI and providing a platform for quantitative analysis of structural features. We used UbSRD to define the recognition features of ubiquitin (UBQ) and SUMO observed in the PDB and the orientation of the UBQ tail while interacting with certain types of proteins. While some of the interaction surfaces on UBQ and SUMO overlap, each molecule has distinct features that aid in molecular discrimination. Additionally, we find that the UBQ tail is malleable and can adopt a variety of conformations upon binding. UbSRD is accessible as an online resource at rosettadesign.med.unc.edu/ubsrd.

Publication date: Available online 24 September 2015
Source:Journal of Molecular Biology

Author(s): Julia L.E. Willett, Zachary C. Ruhe, Celia W. Goulding, David A. Low, Christopher S. Hayes

Bacteria have developed several strategies to communicate and compete with one another in complex environments. One important mechanism of inter-bacterial competition is contact-dependent growth inhibition (CDI), in which some Gram-negative bacteria use CdiB/CdiA two-partner secretion proteins to suppress the growth of neighboring target cells. CdiB is an Omp85 outer-membrane protein that exports and assembles CdiA exoproteins onto the inhibitor-cell surface. CdiA binds to receptors on susceptible bacteria and subsequently delivers its C-terminal toxin domain (CdiA-CT) into the target cell. CDI systems also encode CdiI immunity proteins, which specifically bind to the CdiA-CT and neutralize its toxin activity, thereby protecting CDI+ cells from auto-inhibition. Remarkably, CdiA-CT sequences are highly variable between bacteria, as are the corresponding CdiI immunity proteins. Variations in CDI toxin/immunity proteins suggest that these systems function in bacterial self/nonself recognition and thereby play an important role in microbial communities. In this review, we discuss recent advances in the biochemistry, structural biology and physiology of CDI.
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Publication date: Available online 24 September 2015
Source:Journal of Molecular Biology

Author(s): Tami Kingsbury

Publication date: Available online 12 September 2015
Source:Journal of Molecular Biology

Author(s): Shanshan Cheng, Charles L. Brooks

Viral capsids exhibit elaborate and symmetrical architectures of defined sizes and remarkable mechanical properties not seen with cellular macromolecular complexes. Given the uniqueness of the higher order organization of viral capsid proteins in the virosphere, we explored the question of whether the patterns of protein-protein interactions within viral capsids are distinct from those in generic protein complexes. Our comparative analysis involving a non-redundant set of 551 inter-subunit interfaces in viral capsids from VIPERdb and 20014 protein-protein interfaces in non-capsid protein complexes from the PDB found 418 generic protein-protein interfaces that share similar physicochemical patterns with some protein-protein interfaces in the capsid set, using the program PCalign we developed for comparing protein-protein interfaces. This overlap in the structural space of protein-protein interfaces is significantly small, with a p-value < 0.0001, based on a permutation test on the total set of protein-protein interfaces. Furthermore, the generic protein-protein interfaces that bear similarity in their spatial and chemical arrangement with capsid ones are mostly small in size with fewer than 20 interfacial residues, which results from the relatively limited choices of natural design for small interfaces, rather than having significant biological implications in terms of functional relationships. We conclude based on this study that protein-protein interfaces in viral capsids are non-representative of patterns in the smaller, more compact cellular protein complexes. Our finding highlights the design principle of building large biological containers from repeated, self-assembling units, and provides insights into specific targets for antiviral drug design for improved efficacy.
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Publication date: 11 September 2015
Source:Journal of Molecular Biology, Volume 427, Issue 18

Publication date: 11 September 2015
Source:Journal of Molecular Biology, Volume 427, Issue 18

Publication date: 11 September 2015
Source:Journal of Molecular Biology, Volume 427, Issue 18

Author(s): Marina Ostankovitch, Johannes Buchner

Publication date: 11 September 2015
Source:Journal of Molecular Biology, Volume 427, Issue 18

Author(s): Julia M. Flynn, Parul Mishra, Daniel N.A. Bolon

Hsp90 is a molecular chaperone that facilitates the maturation of signaling proteins including many kinases and steroid hormone receptors. Through these client proteins, Hsp90 is a key mediator of many physiological processes and has emerged as a promising drug target in cancer. Additionally, Hsp90 can mask or potentiate the impact of mutations in clients with remarkable influence on evolutionary adaptations. The influential roles of Hsp90 in biology and disease have stimulated extensive research into the molecular mechanism of this chaperone. These studies have shown that Hsp90 is a homodimeric protein that requires ATP hydrolysis and a host of accessory proteins termed co-chaperones to facilitate the maturation of clients to their active states. Flexible hinge regions between its three structured domains enable Hsp90 to sample dramatically distinct conformations that are influenced by nucleotide, client, and co-chaperone binding. While it is clear that Hsp90 can exist in symmetrical conformations, recent studies have indicated that this homodimeric chaperone can also assume a variety of asymmetric conformations and complexes that are important for client maturation. The visualization of Hsp90-client complexes at high resolution together with tools to independently manipulate each subunit in the Hsp90 dimer are providing new insights into the asymmetric function of each subunit during client maturation.
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Publication date: 11 September 2015
Source:Journal of Molecular Biology, Volume 427, Issue 18

Author(s): Hideki Taguchi

Chaperonin GroEL is an essential chaperone that assists in protein folding in the cell. Since one GroEL ring binds one GroES heptamer, the GroEL double ring permits the formation of two types of GroEL:GroES complexes: asymmetric 1:1 “bullet”-shaped and symmetric 1:2 “football”-shaped GroEL:GroES2 complexes. There have been continuing debates about the mechanism and which complex is critical to the chaperonin-assisted folding. In this review, I summarize the recent progress on the football complex.
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Publication date: 11 September 2015
Source:Journal of Molecular Biology, Volume 427, Issue 18

Author(s): Tom Lopez, Kevin Dalton, Judith Frydman

Protein folding in the cell requires the assistance of enzymes collectively called chaperones. Among these, the chaperonins are 1-MDa ring-shaped oligomeric complexes that bind unfolded polypeptides and promote their folding within an isolated chamber in an ATP-dependent manner. Group II chaperonins, found in archaea and eukaryotes, contain a built-in lid that opens and closes over the central chamber. In eukaryotes, the chaperonin TRiC/CCT is hetero-oligomeric, consisting of two stacked rings of eight paralogous subunits each. TRiC facilitates folding of approximately 10% of the eukaryotic proteome, including many cytoskeletal components and cell cycle regulators. Folding of many cellular substrates of TRiC cannot be assisted by any other chaperone. A complete structural and mechanistic understanding of this highly conserved and essential chaperonin remains elusive. However, recent work is beginning to shed light on key aspects of chaperonin function and how their unique properties underlie their contribution to maintaining cellular proteostasis.
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Publication date: 11 September 2015
Source:Journal of Molecular Biology, Volume 427, Issue 18

Author(s): Kristoffer R. Brandvold, Richard I. Morimoto

Protein homeostasis (proteostasis) is inextricably tied to cellular health and organismal lifespan. Aging, exposure to physiological and environmental stress, and expression of mutant and metastable proteins can cause an imbalance in the protein-folding landscape, which results in the formation of non-native protein aggregates that challenge the capacity of the proteostasis network (PN), increasing the risk for diseases associated with misfolding, aggregation, and aberrant regulation of cell stress responses. Molecular chaperones have central roles in each of the arms of the PN (protein synthesis, folding, disaggregation, and degradation), leading to the proposal that modulation of chaperone function could have therapeutic benefits for the large and growing family of diseases of protein conformation including neurodegeneration, metabolic diseases, and cancer. In this review, we will discuss the current strategies used to tune the PN through targeting molecular chaperones and assess the potential of the chemical biology of proteostasis.
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Non-coding RNA: Antibiotic tricks a switch

Nature 526, 7575 (2015). doi:10.1038/nature15635

Authors: Thomas Hermann

A screen for compounds that block a bacterial biosynthetic pathway has uncovered an antibiotic lead that shuts off pathogen growth by targeting a molecular switch in a regulatory RNA structure. See Article p.672

Selective small-molecule inhibition of an RNA structural element

Nature 526, 7575 (2015). doi:10.1038/nature15542

Authors: John A. Howe, Hao Wang, Thierry O. Fischmann, Carl J. Balibar, Li Xiao, Andrew M. Galgoci, Juliana C. Malinverni, Todd Mayhood, Artjohn Villafania, Ali Nahvi, Nicholas Murgolo, Christopher M. Barbieri, Paul A. Mann, Donna Carr, Ellen Xia, Paul Zuck, Dan Riley, Ronald E. Painter, Scott S. Walker, Brad Sherborne, Reynalda de Jesus, Weidong Pan, Michael A. Plotkin, Jin Wu, Diane Rindgen, John Cummings, Charles G. Garlisi, Rumin Zhang, Payal R. Sheth, Charles J. Gill, Haifeng Tang & Terry Roemer

Riboswitches are non-coding RNA structures located in messenger RNAs that bind endogenous ligands, such as a specific metabolite or ion, to regulate gene expression. As such, riboswitches serve as a novel, yet largely unexploited, class of emerging drug targets. Demonstrating this potential, however, has proven

by Naiqian Zhang, Haiyun Wang, Yun Fang, Jun Wang, Xiaoqi Zheng, X. Shirley Liu

The ability to predict the response of a cancer patient to a therapeutic agent is a major goal in modern oncology that should ultimately lead to personalized treatment. Existing approaches to predicting drug sensitivity rely primarily on profiling of cancer cell line panels that have been treated with different drugs and selecting genomic or functional genomic features to regress or classify the drug response. Here, we propose a dual-layer integrated cell line-drug network model, which uses both cell line similarity network (CSN) data and drug similarity network (DSN) data to predict the drug response of a given cell line using a weighted model. Using the Cancer Cell Line Encyclopedia (CCLE) and Cancer Genome Project (CGP) studies as benchmark datasets, our single-layer model with CSN or DSN and only a single parameter achieved a prediction performance comparable to the previously generated elastic net model. When using the dual-layer model integrating both CSN and DSN, our predicted response reached a 0.6 Pearson correlation coefficient with observed responses for most drugs, which is significantly better than the previous results using the elastic net model. We have also applied the dual-layer cell line-drug integrated network model to fill in the missing drug response values in the CGP dataset. Even though the dual-layer integrated cell line-drug network model does not specifically model mutation information, it correctly predicted that BRAF mutant cell lines would be more sensitive than BRAF wild-type cell lines to three MEK1/2 inhibitors tested.

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b07788

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b07898

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b09138

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b08215