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GEOMETRIC ANALYSIS OF CROSS-LINKABILITY FOR PROTEIN FOLD DISCRIMINATION

S. POTLURI, A.A. KHAN, A. KUZMINYKH, J.M. BUJNICKI, A.M. FRIEDMAN, C. BAILEY-KELLOGG
2003 Biocomputing 2004  
We are pursuing a minimalist approach to protein fold identification that characterizes possible folds in terms of consistency of their geometric features with restraints derived from relatively cheap,  ...  This paper presents a suite of novel lower-and upper-bounding algorithms for analyzing the distance between surface cross-link sites and thereby validating predicted models against experimental cross-linking  ...  Thanks to Mike Stoppelman, Xiaoduan Ye, and other members of our labs for helpful discussions and related work.  ... 
doi:10.1142/9789812704856_0042 fatcat:s7puzvflsja7be6ou275yfotq4

Geometric analysis of cross-linkability for protein fold discrimination

S Potluri, A A Khan, A Kuzminykh, J M Bujnicki, A M Friedman, C Bailey-Kellogg
2004 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
We are pursuing a minimalist approach to protein fold identification that characterizes possible folds in terms of consistency of their geometric features with restraints derived from relatively cheap,  ...  This paper presents a suite of novel lower- and upper-bounding algorithms for analyzing the distance between surface cross-link sites and thereby validating predicted models against experimental cross-linking  ...  Thanks to Mike Stoppelman, Xiaoduan Ye, and other members of our labs for helpful discussions and related work.  ... 
pmid:14992524 fatcat:pk2ixt6u4fa6lav5nopyri2u7a

Protein structure prediction guided by crosslinking restraints – A systematic evaluation of the impact of the crosslinking spacer length

Tommy Hofmann, Axel W. Fischer, Jens Meiler, Stefan Kalkhof
2015 Methods  
In this study, the number of cross-links and their discriminative power was systematically analyzed in silico on a set of 2,055 non-redundant protein folds considering Lys-Lys, Lys-Asp, Lys-Glu, Cys-Cys  ...  Next, simulated restraints of variable length were used to de novo predict the tertiary structure of fifteen proteins using the BCL::Fold algorithm.  ...  Further, 605 the geometrical restraints derived from XL-MS allow for the discrimination of a significant 606 fraction of models representing incorrect topologies and therefore improve the 607 discriminative  ... 
doi:10.1016/j.ymeth.2015.05.014 pmid:25986934 pmcid:PMC4803439 fatcat:k6otwxpasjaflelxt3rt73t3kq

Trapped translocation intermediates establish the route for export of capsular polysaccharides across Escherichia coli outer membranes

N. N. Nickerson, I. L. Mainprize, L. Hampton, M. L. Jones, J. H. Naismith, C. Whitfield
2014 Proceedings of the National Academy of Sciences of the United States of America  
Residues within the lumen of Wza were targeted for site-specific incorporation of the UV photo-cross-linkable unnatural amino acid p-benzoyl-L-phenylalanine.  ...  Wza is the prototype for the large family of OM polysaccharide export proteins.  ...  We thank Catrien Bouwman for construction of the ΔgalE mutant of E. coli E69, Bradley R. Clarke for technical advice, and members of the laboratory of C.W. for helpful discussions.  ... 
doi:10.1073/pnas.1400341111 pmid:24843147 pmcid:PMC4050593 fatcat:ybabs3movnhddnmxejsgvtxypy

High-density chemical cross-linking for modeling protein interactions

Julian Mintseris, Steven P. Gygi
2019 Proceedings of the National Academy of Sciences of the United States of America  
The resulting model suggests a scaffold for development of a class of protein-based inhibitors of the CA family of enzymes.  ...  coverage of 1 unique cross-linked position pair for every 7 amino acids at a 1% false discovery rate.  ...  Finley for the proteasome sample and critical reading of the manuscript. We are also grateful to J. Paolo and R. Kunz for instrument help. We thank A.B. Mason and M.P.  ... 
doi:10.1073/pnas.1902931116 pmid:31848235 pmcid:PMC6955236 fatcat:g72u2fg6p5aqnahmz747w2ha6e

The trimeric solution structure and fucose-binding mechanism of the core fucosylation-specific lectin PhoSL

Kazuhiko Yamasaki, Tomoko Yamasaki, Hiroaki Tateno
2018 Scientific Reports  
NMR analysis with an excess amount of fucose revealed the structural basis for the molecular recognition.  ...  The structure possesses a β-prism motif with a three-fold rotational symmetry, where three antiparallel β-sheets are tightly connected by swapping of β-strands.  ...  Acknowledgements This project was supported by Leading Engine program for Accelerating Drug discovery (LEAD) of AIST. We thank Mr. O. Tani of AIST for his support in the mass spectrometry, and Drs.  ... 
doi:10.1038/s41598-018-25630-2 pmid:29773815 pmcid:PMC5958098 fatcat:wjgbjyybn5b4fodml4u4hg4kc4

Non‐homology‐based prediction of gene functions in maize ( Zea mays ssp. mays )

Xiuru Dai, Zheng Xu, Zhikai Liang, Xiaoyu Tu, Silin Zhong, James C. Schnable, Pinghua Li
2020 The Plant Genome  
Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging.  ...  As a result, homology is widely used for gene function prediction. This means functional annotation errors also propagate from one species to another.  ...  The remaining 80% of data was used to train each algorithm for each GO term. A 10-fold cross validation was used.  ... 
doi:10.1002/tpg2.20015 pmid:33016608 fatcat:lldl4wonu5eh3fll27ebd4hhma

Role of integrative structural biology in understanding transcriptional initiation

Michael J. Trnka, Riccardo Pellarin, Philip J. Robinson
2019 Methods  
The precision of these modelled solutions is limited by the sparseness of cross-links observed, the length of the cross-linking reagent, the ambiguity arisen from the presence of multiple copies of the  ...  same protein, and structural and compositional heterogeneity.  ...  fluctuations (RMSF), and protein-protein contact analysis.  ... 
doi:10.1016/j.ymeth.2019.03.009 pmid:30890443 pmcid:PMC6617507 fatcat:pgdbipcqmbfzdmqhg22fzs6hsy

The 13th International Conference on Advances in Quantitative Laryngology, Voice and Speech Research (June 2–4, 2019, Montreal, Quebec, Canada)

Mongeau
2019 Applied Sciences  
The conference and workshops provide a unique opportunity for partnership and collaboration in the advancement of quantitative methods for the measurement and modelling of voice and speech.  ...  The AQL accomplishes this mandate by facilitating an interprofessional scientific conference and training intended for an international community of otolaryngologists, speech–language pathologists and  ...  for vowel voicing (at least at the speech planning level).  ... 
doi:10.3390/app9132665 fatcat:xg47la5zkngzxaqe4cdeyv63rq

Advances in Non-Animal Testing Approaches towards Accelerated Clinical Translation of Novel Nanotheranostic Therapeutics for Central Nervous System Disorders

Mark J. Lynch, Oliviero L. Gobbo
2021 Nanomaterials  
This review aims to identify the most contemporary non-invasive approaches for BBB crossing using nanotheranostics as a novel drug delivery strategy and current non-animal-based models for assessing the  ...  By generating predictive data for prospective nanomedicines using validated in vitro models for supporting clinical applications in lieu of requiring extensive use of in vivo animal models that have notable  ...  They would also like to acknowledge the work of all researchers included in this review, and to Elsevier Publications and Richard Kollath for the reproduction of figures.  ... 
doi:10.3390/nano11102632 pmid:34685073 fatcat:oecwqiht3vgklixirhp35lnc6q

DOCK 6: Combining techniques to model RNA-small molecule complexes

P. T. Lang, S. R. Brozell, S. Mukherjee, E. F. Pettersen, E. C. Meng, V. Thomas, R. C. Rizzo, D. A. Case, T. L. James, I. D. Kuntz
2009 RNA: A publication of the RNA Society  
With an increasing interest in RNA therapeutics and for targeting RNA to treat disease, there is a need for the tools used in protein-based drug design, particularly DOCKing algorithms, to be extended  ...  Our studies also suggest that RNA-directed ligands often differ from typical protein-ligand complexes in their electrostatic properties, but these differences can be accommodated through the choice of  ...  This work was supported in part by an allocation of computing time from the Ohio Supercomputer Center. Received January 18, 2009; accepted February 25, 2009.  ... 
doi:10.1261/rna.1563609 pmid:19369428 pmcid:PMC2685511 fatcat:7u6e5l3gonchpd23mt2xipseka

Liprotides: a New Class of Protein Lipid-Complexes

Jannik N. Pedersen, Henriette Kristina S. Frislev, Jan S. Pedersen, Daniel E. Otzen
2016 Biophysical Journal  
, Python based beamline control, web based applications for data acquisition and analysis, virtualization, and new sample environments.  ...  The set of coordinates is used for the calculation of the scattering intensity, either for an oriented particle (as shown in figure 1 ) for for randomly oriented systems.  ...  influence the folding and compactness of the protein.  ... 
doi:10.1016/j.bpj.2015.11.3085 fatcat:eqeeb47atfc4lisnurb25n55gu

Deutsche Gesellschaft für Experimentelle und Klinische Pharmakologie und Toxikologie e.V. Abstracts of the 81th Annual Meeting, March 10-12, 2015, Kiel, Germany

2015 Naunyn-Schmiedeberg's Archives of Pharmacology  
Acknowledgement: This work was supported by the German Research Foundation (DFG, FOR 1406, FU 691/9-2). Acknowledgements: Bavarian State Ministry of the Environment and Consumer Protection.  ...  Indeed, disulfide trapping confirmed that the side chains of the pairs Glu84/Arg290 and Glu167/Arg290 are in close proximity when the channel is in the apo closed state, but in weakly cross-linkable and  ...  The 90 % CI of the ratio of the geometric means for MRFLB (with/without omeprazole) was between 115 and 127 %.  ... 
doi:10.1007/s00210-015-1087-4 pmid:25630830 fatcat:wxewzlugk5hvbglugeap75es5u

Guidelines for the use of flow cytometry and cell sorting in immunological studies

Andrea Cossarizza, Hyun-Dong Chang, Andreas Radbruch, Mübeccel Akdis, Immanuel Andrä, Francesco Annunziato, Petra Bacher, Vincenzo Barnaba, Luca Battistini, Wolfgang M. Bauer, Sabine Baumgart, Burkhard Becher (+224 others)
2017 European Journal of Immunology  
Guidelines for the use of flow cytometry and cell sorting in immunological studies  ...  By using covalently-linkable DNA staining probes (such as ethidium monoazide bromide), it is also possible to combine live/dead discrimination with cell fixation [409] .  ...  In contrast, stimulation of CD8 + T cells with whole proteins is not reliable, since MHC class I epitopes are not easily generated from endocytosed proteins which depends on cross-presenting capacity of  ... 
doi:10.1002/eji.201646632 pmid:29023707 pmcid:PMC9165548 fatcat:2lswztuwwzfnnjomgr2cxnhugu

One-pot synthesis of hyperbranched polyamines based on novel amino glycidyl ether

Gyunhyeok Ahn, Songa Kweon, Chungmi Yang, Ji Eun Hwang, Kyuseok Kim, Byeong-Su Kim
2017 Journal of Polymer Science Part A: Polymer Chemistry  
We present a recently developed, universal approach for the preparation of a new class of protein-based nanoparticles for the delivery of therapeutics.  ...  It features a new concept for the formation of particles based on the assembly of surface-modified proteins.  ...  On the material level, a recent development covering urethane-containing cross-linkable macromonomers for 3D printing will be highlighted.  ... 
doi:10.1002/pola.28865 fatcat:r5jaobn7tzg7rojmelsdnr5v2u
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