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Protein Science: a Publication of the Protein Society

Przemyslaw J Porebski, Piotr Sroka, Heping Zheng, David R Cooper, Wladek Minor
Our understanding of the world of biomolecular structures is based upon the interpretation of macromolecular models, of which ∼ 90% are themselves the interpretation of electron density maps. This structural information guides scientific progress and exploration in many biomedical disciplines. The Protein Data Bank's web portals have made these structures available for mass scientific consumption and greatly broaden the scope of information presented in scientific publications. The portals provide numerous quality metrics; however, the portion of the structure that is most vital for interpretation of the function may have the most difficult to interpret electron density and this ambiguity is not reflected by any single metric...
August 17, 2017: Protein Science: a Publication of the Protein Society
Alexander Miguel Monzon, Diego Javier Zea, Cristina Marino-Buslje, Gustavo Parisi
A key concept in template-based modeling is the high correlation between sequence and structural divergence, with the practical consequence that homologous proteins that are similar at the sequence level will also be similar at the structural level. However, conformational diversity of the native state will reduce the correlation between structural and sequence divergence, because structural variation can appear without sequence diversity. In this work, we explore the impact that conformational diversity has on the relationship between structural and sequence divergence...
August 17, 2017: Protein Science: a Publication of the Protein Society
Akira R Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata, Naohiro Kobayashi, Toshimichi Fujiwara, Genji Kurisu, Haruki Nakamura
The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated. Here, we report the new RDB PDBj Mine 2, the WebGL molecular viewer Molmil, the ProMode-Elastic server for normal mode analysis, a virtual reality system for the eF-site protein electrostatic molecular surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches...
August 17, 2017: Protein Science: a Publication of the Protein Society
Yu-Ru Lin, Nobuyasu Koga, Sergey M Vorobiev, David Baker
We have previously shown that monomeric globular αβ- proteins can be designed de novo with considerable control over topology, size and shape. In this paper, we investigate the design of cyclic homo-oligomers from these starting points. We experimented with both keeping the original monomer backbones fixed during the cyclic docking and design process, and allowing the backbone of the monomer to conform to that of adjacent subunits in the homo-oligomer. The latter flexible backbone protocol generated designs with shape complementarity approaching that of native homo-oligomers, but experimental characterization showed that the fixed backbone designs were more stable and less aggregation prone...
August 12, 2017: Protein Science: a Publication of the Protein Society
Ryan L Melvin, Jiajie Xiao, Ryan C Godwin, Kenneth S Berenhaut, Freddie R Salsbury
Correlated motion analysis provides a method for understanding communication between and dynamic similarities of biopolymer residues and domains. The typical equal-time correlation matrices - frequently visualized with pseudo-colorings or heat maps - quickly convey large regions of highly correlated motion but hide more subtle similarities of motion. Here we propose a complementary method for visualizing correlations within proteins (or general biopolymers) that quickly conveys intuition about which residues have a similar dynamic behavior...
August 11, 2017: Protein Science: a Publication of the Protein Society
Gunnar Jeschke
Structural characterization of proteins and their complexes may require integration of restraints from various experimental techniques. MMM is a Matlab-based open-source modelling toolbox for this purpose with a particular emphasis on distance distribution restraints obtained from electron paramagnetic resonance experiments on spin-labelled proteins and nucleic acids and their combination with atomistic structures of domains or whole protomers, small-angle scattering data, secondary structure information, homology information, and elastic network models...
August 11, 2017: Protein Science: a Publication of the Protein Society
Cyril F Reboul, Michael Eager, Dominika Elmlund, Hans Elmlund
Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. We developed the SIMPLE open-source image-processing suite for analysing cryo-EM images of single-particles. A core component of SIMPLE is the probabilistic PRIME algorithm for identifying clusters of images in 2D and determine relative orientations of single-particle projections in 3D. Here we extend our previous work on PRIME and introduce new stochastic optimisation algorithms that improve the robustness of the approach...
August 10, 2017: Protein Science: a Publication of the Protein Society
Lye Siang Lee, Nicholas Brunk, Daniel G Haywood, David Keifer, Elizabeth Pierson, Panagiotis Kondylis, Joseph Che-Yen Wang, Stephen C Jacobson, Martin F Jarrold, Adam Zlotnick
Hepatitis B virus (HBV) core protein is a model system for studying assembly and disassembly of icosahedral structures. Controlling disassembly will allow re-engineering the 120 subunit HBV capsid, making it a molecular breadboard. We examined removal of subunits from partially crosslinked capsids to form stable incomplete particles. To characterize incomplete capsids, we used two single molecule techniques, resistive-pulse sensing and charge detection mass spectrometry. We expected to find a binomial distribution of capsid fragments...
August 10, 2017: Protein Science: a Publication of the Protein Society
Jinghua Ge, Furong Huang, Yuri E Nesmelov
Myosin is an enzyme that utilizes ATP to produce a conformational change generating a force. The kinetics of the myosin reverse recovery stroke depend on the metal cation complexed with ATP. The reverse recovery stroke is slow for MgATP and fast for MnATP. The metal ion coordinates the γ phosphate of ATP in the myosin active site. It is accepted that the reverse recovery stroke is correlated with the phosphate release, therefore magnesium "holds" phosphate tighter than manganese. Magnesium and manganese are similar ions in terms of their chemical properties and the shell complexation, hence we propose to use these ions to study the mechanism of the phosphate release...
August 10, 2017: Protein Science: a Publication of the Protein Society
Anna Rising, Ella Cederlund, Carina Palmberg, Henrik Uhlhorn, Stefan Gaunitz, Kerstin Nordling, Erik Ågren, Elisabet Ihse, Gunilla Westermark, Lars Tjernberg, Hans Jörnvall, Jan Johansson, Per Westermark
Amyloid A (AA) amyloidosis occurs spontaneously in many mammals and birds, but the prevalence varies considerably among different species, and even among subgroups of the same species. The Blue fox and the Gray fox seem to be resistant to the development of AA amyloidosis, while Island foxes have a high prevalence of the disease. Herein, we report on the identification of AA amyloidosis in the Red fox (Vulpes vulpes). Edman degradation and tandem MS analysis of proteolyzed amyloid protein revealed that the amyloid partly was composed of full-length SAA...
August 9, 2017: Protein Science: a Publication of the Protein Society
Md Nuruddin Mahmud, Masayuki Oda, Daiki Usui, Yasuo Inoshima, Naotaka Ishiguro, Yuji O Kamatari
A monoclonal antibody (mAb) G2 possesses an unusual characteristic of reacting with at least three proteins (ATP6V1C1, SEPT3, and C6H10orf76) other than its original antigen, chicken prion protein (ChPrP). The epitopes on ChPrP and ATP6V1C1 have been identified previously. In this study, we identified the epitope in the third protein, SEPT3. Interestingly, there was no amino acid sequence similarity among the epitopes on the three proteins. These epitopes had high binding affinities to G2 (KD = ∼10(-7) M for monovalent binding and KD = ∼10(-9) M for divalent binding), as determined using a SPR biosensor...
August 9, 2017: Protein Science: a Publication of the Protein Society
Charles D Schwieters, Guillermo A Bermejo, G Marius Clore
Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data sources. Here, some of Xplor-NIH's most useful data-associated energy terms are reviewed, including newer alternative options for using residual dipolar coupling data in structure calculations. Further, we discuss new developments in the implementation of strict symmetry for the calculation of symmetric homo-oligomers, and in the representation of the system as an ensemble of structures to account for motional effects...
August 2, 2017: Protein Science: a Publication of the Protein Society
Nathan S Alexander, Krzysztof Palczewski
Dedicated computing resources are expensive to develop, maintain, and administrate. Frequently, research groups require bursts of computing power, during which progress is still limited by available computing resources. One way to alleviate this bottleneck would be to utilize additional computing resources. Today, many computing devices remain idle most of the time. Passive volunteer computing exploits this unemployed reserve of computing power by allowing device-owners to donate computing time on their own devices...
August 1, 2017: Protein Science: a Publication of the Protein Society
Andrew E Brereton, P Andrew Karplus
Ensembles of protein structures are increasingly used to represent the conformational variation of a protein as determined by experiment and/or by molecular simulations, as well as uncertainties that may be associated with structure determinations or predictions. Making the best use of such information requires the ability to quantitatively compare entire ensembles. For this reason, we recently introduced the Ensemblator (Clark et al. [2015] Protein Sci 24, 1528), a novel approach to compare user-defined groups of models, in residue level detail...
August 1, 2017: Protein Science: a Publication of the Protein Society
Xiao-Yun Yang, Zong-Qiang Li, Zeng-Qiang Gao, Wen-Jia Wang, Zhi Geng, Jian-Hua Xu, Zhun She, Yu-Hui Dong
Widely spread in gram-negative bacteria, the type VI secretion system (T6SS) secretes many effector-immunity protein pairs to help the bacteria compete against other prokaryotic rivals, and infect their eukaryotic hosts. Tle5 and Tle5B are two phospholipase effector protein secreted by T6SS of Pseudomonas aeruginosa. They can facilitate the bacterial internalization process into human epithelial cells by interacting with Akt protein of the PI3K-Akt signal pathway. Tli5 and PA5086-5088 are cognate immunity proteins of Tle5 and Tle5B, respectively...
July 30, 2017: Protein Science: a Publication of the Protein Society
Junya Kobayashi, Yoshiyuki Matsuura
In the budding yeast Saccharomyces cerevisiae, the protein phosphatase Cdc14p orchestrates various events essential for mitotic exit. We have determined the X-ray crystal structures at 1.85 Å resolution of the catalytic domain of Cdc14p in both the apo state, and as a complex with S160-phosphorylated Swi6p peptide. Each asymmetric unit contains two Cdc14p chains arranged in an intimately associated homodimer, consistent with its oligomeric state in solution. The dimerization interface is located on the backside of the substrate-binding cleft...
July 30, 2017: Protein Science: a Publication of the Protein Society
Yurong Wen, Zhenlin Ouyang, Bart Devreese, Wangxiao He, Yongping Shao, Wuyuan Lu, Fang Zheng
The master regulator CsgD switches planktonic growth to biofilm formation by activating synthesis of curli fimbriae and cellulose in Enterobacteriaceae. CsgD was classified to be the LuxR response regulatory family, while its cognate sensor histidine kinase has not been identified yet. CsgD consists of a C-terminal DNA binding domain and an N-terminal regulatory domain that provokes the upstream signal transduction to further modulate its function. We provide the crystal structure of Salmonella Typhimurium CsgD regulatory domain, which reveals an atypical β5α5 response regulatory receiver domain folding with the α2 helix representing as a disorder loop compared to the LuxR/FixJ canonical response regulator, and the structure indicated a noteworthy α5 helix similar to the non-canonical master regulator VpsT receiver domain α6...
July 30, 2017: Protein Science: a Publication of the Protein Society
Azade S Hosseini, Christopher J Pace, Adam A Esposito, Jianmin Gao
It has been a long-standing goal to understand the structure-stability relationship of proteins, as optimal stability is essential for protein function and highly desirable for protein therapeutics. Halogenation has emerged as a minimally invasive strategy to probe the physical characteristics of proteins in solution, as well as enhance the structural stabilities of proteins for therapeutic applications. Although advances in synthetic chemistry and genetic code expansion have allowed for the rapid synthesis of proteins with diverse chemical sequences, much remains to be learned regarding the impact of these mutations on their structural integrity...
July 24, 2017: Protein Science: a Publication of the Protein Society
Yangjie Wei, Newton Wahome, Greta VanSlyke, Neal Whitaker, Prashant Kumar, Michael L Barta, Wendy L Picking, David B Volkin, Nicholas J Mantis, C Russell Middaugh
Polyvalent antigen display is an effective strategy to enhance the immunogenicity of subunit vaccines by clustering them in an array-like manner on a scaffold system. This strategy results in a higher local density of antigens, increased high avidity interactions with B cells and other antigen presenting cells, and therefore a more effective presentation of vaccine antigens. In the present study, we used lumazine synthase (LS), an icosahedral symmetry capsid derived from Bacillus anthracis, as a scaffold to present 60 copies of a linear B cell epitope (PB10) from the ricin toxin fused to the C terminus of LS via four different linkers...
July 24, 2017: Protein Science: a Publication of the Protein Society
Valjean R Bacot-Davis, Angelia V Bassenden, Tara Sprules, Albert M Berghuis
The aminoglycoside modifying enzyme (AME) ANT(2″)-Ia is a significant target for next generation antibiotic development. Structural studies of a related aminoglycoside-modifying enzyme, ANT(3″)(9), revealed this enzyme contains dynamic, disordered, and well-defined segments that modulate thermodynamically before and after antibiotic binding. Characterizing these structural dynamics is critical for in situ screening, design, and development of contemporary antibiotics that can be implemented in a clinical setting to treat potentially lethal, antibiotic resistant, human infections...
July 21, 2017: Protein Science: a Publication of the Protein Society
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