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Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts

Guido Capitani, Jose M. Duarte, Kumaran Baskaran, Spencer Bliven, Joseph C. Somody
2015 Bioinformatics  
Since the mid-1990s, several approaches have been applied to obtain high-accuracy classification of crystal contacts and biological protein-protein interfaces.  ...  A key issue linked to protein interface classification is the identification of the biological assembly of a crystal structure and the analysis of its symmetry.  ...  Research Program of the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (support to S.B.). Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btv622 pmid:26508758 pmcid:PMC4743631 fatcat:y5taf2mmlfgtxjjqjb7ghiqvxu

Thermotropic Liquid Crystal-Assisted Chemical and Biological Sensors

Nicolai Popov, Lawrence W. Honaker, Maia Popova, Nadezhda Usol'tseva, Elizabeth K. Mann, Antal Jákli, Piotr Popov
2017 Materials  
In this review article, we analyze recent progress in the application of liquid crystal-assisted advanced functional materials for sensing biological and chemical analytes.  ...  We review trends in implementing LC sensing techniques and identify common problems related to the stability and reliability of the sensing materials as well as to experimental set-ups.  ...  ., E.K.M. and A.J. were supported in part by a NSF DMR-0907055 and 1506018. P.P., E.K.M. and A.J. were additionally supported by NSF I-Corps grant. P.  ... 
doi:10.3390/ma11010020 pmid:29295530 pmcid:PMC5793518 fatcat:earsvgxlxbfnhln6ojsmwpqxsu

Introduction to protein crystallization

A MCPHERSON
2004 Methods  
The crystallization of proteins, nucleic acids and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule but exhibits conditions  ...  Protein crystallization was discovered by chance about 150 years ago and was developed in the late 19th century as a powerful purification tool and as a demonstration of chemical purity.  ...  In these cases the antibody fragment enhanced the solubility of the otherwise insoluble protein and provided additional lattice contacts in the resultant crystals.  ... 
doi:10.1016/j.ymeth.2004.03.019 pmid:15325645 fatcat:ou5ddllubzfx7llybkeabiugta

Introduction to protein crystallization

Alexander McPherson, Jose A. Gavira
2013 Acta Crystallographica Section F Structural Biology Communications  
The crystallization of proteins, nucleic acids and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule but exhibits conditions  ...  Protein crystallization was discovered by chance about 150 years ago and was developed in the late 19th century as a powerful purification tool and as a demonstration of chemical purity.  ...  In these cases the antibody fragment enhanced the solubility of the otherwise insoluble protein and provided additional lattice contacts in the resultant crystals.  ... 
doi:10.1107/s2053230x13033141 pmid:24419610 pmcid:PMC3943105 fatcat:r5oxmbkjazgljbqmu6zaouk43y

What's in a Drop? Correlating Observations and Outcomes to Guide Macromolecular Crystallization Experiments

Joseph R. Luft, Jennifer R. Wolfley, Edward H. Snell
2011 Crystal Growth & Design  
The methods and rationale are broadly and generally applicable in any crystallization laboratory.  ...  Through a combination of incomplete factorial sampling of crystallization cocktails, standard outcome classifications, visualization of outcomes as they relate chemically, and application of a simple phase  ...  J.R.L. and E.H.S. would like to acknowledge NIH for funding support through U54 GM074899 and  ... 
doi:10.1021/cg1013945 pmid:21643490 pmcid:PMC3106348 fatcat:qxxvpzd575a5dlielz7isgdrmi

Modeling Complex Liquid Crystals Mixtures: From Polymer Dispersed Mesophase to Nematic Nanocolloids [article]

Ezequiel R. Soule, Alejandro D. Rey
2013 arXiv   pre-print
and order fluctuations, (v) the formation of novel material architectures such as colloidal crystals, (vi) the particle rich phase behaviour in liquid crystal nanocomposites, (vii) the use of topological  ...  The novelties of incorporating mesophases into blends, solutions, dispersions and mixtures is revealed by using theory, modelling, computation, and visualization.  ...  Acknoeldegements This work is based on the research performed by A.  ... 
arXiv:1310.8645v1 fatcat:e7lecb5ou5efvo4af7y57646wq

Crystal Quartz Microbalance for Protein Adsorption Measurement [chapter]

Osvaldo N. Oliveira, Diogo Volpati
2016 Encyclopedia of Membranes  
Despite wide applications, cadmium is known to be a toxic element, and the occupational exposure is by inhalation of fumes and ingestion of soluble cadmium compounds.  ...  Cadmium separation by liquid membranes: Cadmium occurs as a minor component in the zinc ores. It has many common industrial applications.  ...  In the case of crystallization of proteins, ligands and cofactors can be exploited to stabilize the protein or to increase its conformational purity.  ... 
doi:10.1007/978-3-662-44324-8_1524 fatcat:jbqz25jxtjgsljzy5v63uagiee

Photonic crystal enhanced microscopy for imaging of live cell adhesion

Weili Chen, Kenneth D. Long, Meng Lu, Vikram Chaudhery, Hojeong Yu, Ji Sun Choi, James Polans, Yue Zhuo, Brendan A. C. Harley, Brian T. Cunningham
2013 The Analyst  
A form of microscopy based on the unique optical properties of a photonic crystal (PC) biosensor provides both label-free (LF) and enhanced fluorescence (EF) imaging modalities for the study of cell-surface  ...  The imaging system utilizes an angle-tunable illumination source, either LED or laser, to achieve highly efficient coupling of  ...  PC biosensors are fabricated from inexpensive materials and require only low intensity illumination from beneath the sensor, so no electrical or physical contact between the sensor and the detection system  ... 
doi:10.1039/c3an01541f pmid:23971078 fatcat:alb5lwrbzzduhbo6wyyytfj33e

Quantitative imaging of cell membrane-associated effective mass density using Photonic Crystal Enhanced Microscopy (PCEM)

Yue Zhuo, Ji Sun Choi, Thibault Marin, Hojeong Yu, Brendan A. Harley, Brian T. Cunningham
2016 Progress in Quantum Electronics  
fabricated the PC sensors; B.C. and B.H. provided guidance and edited the manuscript.  ...  It is followed by the redistribution of cellular materials at the cell membrane or at the cell-surface interface for cells interacting with surfaces, such as basement membranes.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the NSF and NIH. Porcine adipose derived stem cells were a gift from Dr.  ... 
doi:10.1016/j.pquantelec.2016.10.001 pmid:28649149 pmcid:PMC5479321 fatcat:6e5q7xe5hfh7leub7l6psakoau

Science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems

Andrea C Ferrari, Francesco Bonaccorso, Vladimir Fal'ko, Konstantin S Novoselov, Stephan Roche, Peter Bøggild, Stefano Borini, Frank H L Koppens, Vincenzo Palermo, Nicola Pugno, José A Garrido, Roman Sordan (+52 others)
2015 Nanoscale  
We present the science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems, targeting an evolution in technology, that might lead to impacts and benefits reaching  ...  This roadmap was developed within the framework of the European Graphene Flagship and outlines the main targets and research areas as best understood at the start of this ambitious project.  ...  , and the understanding of the interfacial electronic structure of such contacts.  ... 
doi:10.1039/c4nr01600a pmid:25707682 fatcat:hzfkhollfbbunbdroujkvqzxke

Fabrication of Massive Sheets of Single Layer Patterned Arrays Using Lipid Directed Reengineered Phi29 Motor Dodecamer

Feng Xiao, Jinchuan Sun, Oana Coban, Peter Schoen, Joseph Che-Yen Wang, R. Holland Cheng, Peixuan Guo
2008 ACS Nano  
Green from University of California at Davis for his technical assistance and valuable comments, as well as the preparation of Figures 1D and 2 .  ...  The structural and conformational complexity of biological molecules brings about new avenues and challenges to experimental approaches at the bio/nano interface. 1,4,33Ϫ36 For instance, fabrication  ...  The arrangement of the individual dodecamers is dictated by the intermolecular protein contacts and proteinϪ surface interactions.  ... 
doi:10.1021/nn800409a pmid:19206255 pmcid:PMC2651733 fatcat:kxregblrb5a3pll6xhrelwqdvi

Biosensors and Biochips for Nanomedical Applications: a Review

Sarmishtha GHOSHAL, Debasis MITRA, Sudip ROY, Dwijesh DUTTA MAJUMDER
2010 Sensors & Transducers  
In the last few decades, a tremendous growth in the field of nanotechnology has been witnessed and its applications to various disciplines are being continuously explored.  ...  as an interface mechanism, are also reviewed.  ...  The biological events like, antibody/ DNA binding, oxidation/reduction, etc., need to be transduced into a format understandable by a computer (voltage, light, intensity, mass, etc.), for analyzing and  ... 
doaj:659d1e73fafd474fb7b784b61854140e fatcat:at4vqgiz25czzn4xa4mtkd27fu

Biomineralization Forming Process and Bio-inspired Nanomaterials for Biomedical Application: A Review

Yuanyuan Chen, Yanmin Feng, John Gregory Deveaux, Mohamed Ahmed Masoud, Felix Sunata Chandra, Huawei Chen, Deyuan Zhang, Lin Feng
2019 Minerals  
The artificially introducing and utilization of biomineralization, the bio-inspired synthesis of nanomaterials, in biomedical fields was further discussed, mainly in five potential fields: drug and cell-therapy  ...  In this review, the regulating roles of temperature, pH, and organics in biominerals forming process were reviewed.  ...  Acknowledgments: The authors gratefully acknowledge the financial support from the Natural Science Foundation of Beijing Municipality (Grant No. 17L20128) and Beihang University (No.  ... 
doi:10.3390/min9020068 fatcat:4c62uxckkrbs5lundpf5tqcnia

Opportunities in theoretical and computational polymeric materials and soft matter

Andrea J. Liu, Gary S. Grest, M. Cristina Marchetti, Gregory M. Grason, Mark O. Robbins, Glenn H. Fredrickson, Michael Rubinstein, Monica Olvera de la Cruz
2015 Soft Matter  
CHALLENGES The convergence of new methods for materials synthesis and fabrication, rapidly expanding computational capabilities, and emerging conceptual frameworks for understanding multi---length scale  ...  An important part of this challenge is to standardize and validate the methods used to couple models at interfaces between different computational zones.  ...  Participant check---in All participants 9:00 - 9:30am Introduction/charge from organizers All participants 9:30---10:20am Introduction Combined session β All participants 5:30pm Dinner and close of day  ... 
doi:10.1039/c4sm02344g pmid:25711605 fatcat:4smqrcruhzgs7gl7y4cdxsa3zi

Computational Issues in Biomedical Nanometrics and Nano-Materials

Heng Huang, Li Shen, James Ford, Yu Hang Wang, Yu Rong Xu
2008 Journal of Nano Research  
It is widely recognized as one of the most potentially beneficial applications of nanotechnology to industry and society to date.  ...  computational methods are helping to generate remarkable new insights into how biological systems function, how metabolic processes interrelate, and how new molecular scale machines can operate.  ...  Understanding of biological processes on the nano-scale level is a strong driving force behind development of nanotechnology [34] .  ... 
doi:10.4028/www.scientific.net/jnanor.1.50 fatcat:prlk2t7dhbdifgdfsp76i7kmim
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