BL19U2:Small-angle X-ray scattering beamline for biological macromolecules in solution at SSRF

The BL19U2 at the Shanghai Synchrotron Radiation Facility is a small-angle X-ray scattering beamline dedicated to structural studies pertaining to biological macromolecules in solution.The beamline has been officially opened to users in March 2015,and since then,a series of technological innovations has been developed to optimize beamline performance,thereby significantly improving the data collection efficiency and broadening the application scope of biological small-angle X-ray scattering.BL19U2 is ideal for the high-throughput screening of weakly scattered proteins,protein assemblies,nucleic acids,inorganic nanomaterials,and organic drug molecules.This paper describes the design and overview of the BL19U2 beamline.Versatile sample environments at the experimental station and some recent scientific highlights are presented.

Encoding of Primary Structures of Biological Macromolecules Within a Data Mining Perspective

An encoding method has a direct effect on the quality and the representationof the discovered knowledge in data mining systems. Biological macromolecules are encoded by stringsof characters, called primary structures. Knowing that data mining systems usually use relationaltables to encode data, we have then to re-encode these strings and transform them into relationaltables. In this paper, we do a comparative study of the existing static encoding methods, that arebased on the Biologist know-how, and our new dynamic encoding one, that is based on the constructionof Discriminant and Minimal Substrings (DMS). Different classification methods are used to do thisstudy. The experimental results show that our dynamic encoding method is more efficient than thestatic ones, to encode biological macromolecules within a data mining perspective.

Microorganism-derived biological macromolecules for tissue engineering

According to literature,certain microorganism productions mediate biological effects.However,their beneficial characteristics remain unclear.Nowadays,scientists concentrate on obtaining natural materials from live creatures as new sources to produce innovative smart biomaterials for increasing tissue reconstruction in tissue engineering and regenerative medicine.The present review aims to introduce microorganism-derived biological macromolecules,such as pullulan,alginate,dextran,curdlan,and hyaluronic acid,and their available sources for tissue engineering.Growing evidence indicates that these materials can be used as biological material in scaffolds to enhance regeneration in damaged tissues and contribute to cosmetic and dermatological applications.These natural-based materials are attractive in pharmaceutical,regenerative medicine,and biomedical applications.This study provides a detailed overview of natural-based biomaterials,their chemical and physical properties,and new directions for future research and therapeutic applications.

PDBlocal:A web-based tool for local inspectionof biological macromolecular 3D structures

Functional research on biological macromolecules must fcus on specific loca regions.PDBlocal is aweb-based tool developed to overcome the limitations of traditional molecular visualization tools forthre-dimensional(3D)inspection of local regions.PDBlocal provides an intuitive and easy-to-manipulate web page interface and some new useful functions.It can kep loca regions flashing,display sequence text that is dynamically consistent with the 3D structure in local appearance undermultiple local manipulations,use two scenes to help users inspect the same local region withdifferent statuses,list all historical manipulation statuses with a tree structure,llow users toannotate regions ofinterest,and save ll historical statuses and other data to a web server for futureresearch.PDBlocal has met expectations and shown satisfactory performance for both expert andnovice users.This tool is available at http:/labsystem.scuec.edu.cn/pdblocal/.

On the stochastic dynamics of molecular conformation

An important functioning mechanism of biological macromolecules is the transition between different conformed states due to thermal fluctuation. In the present paper, a biological macromolecule is modeled as two strands with side chains facing each other, and its stochastic dynamics including the statistics of stationary motion and the statistics of conformational transition is studied by using the stochastic averaging method for quasi Hamikonian systems. The theoretical results are confirmed with the results from Monte Carlo simulation.