000189385 001__ 189385
000189385 005__ 20181203023253.0
000189385 0247_ $$2doi$$a10.1088/1478-3975/10/4/045006
000189385 022__ $$a1478-3967
000189385 02470 $$2ISI$$a000322701100008
000189385 037__ $$aARTICLE
000189385 245__ $$aAll-atom simulations of crowding effects on ubiquitin dynamics
000189385 260__ $$aBristol$$bIop Publishing Ltd$$c2013
000189385 269__ $$a2013
000189385 300__ $$a8
000189385 336__ $$aJournal Articles
000189385 520__ $$aIt is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to probe experimentally. Here we report on a simulation study aimed at evaluating the effects of crowding on internal protein dynamics, based on fully all-atom descriptions of the protein, the solvent and the crowder. Our model system consists of ubiquitin, a protein whose dynamic features are closely related to its ability to bind to multiple partners, in a 325 g L-1 solution of glucose in water, a condition widely employed in in vitro studies of crowding effects. We observe a slight reduction in loop flexibility accompanied by a dramatic restriction of the conformational space explored in the timescale of the simulations (similar to 0.5 mu s), indicating that crowding slows down collective motions and the rate of exploration of the conformational space. This effect is attributed to the extensive and long-lasting interactions observed between protein residues and glucose molecules throughout the entire protein surface. Potential implications of the observed effects are discussed.
000189385 700__ $$aAbriata, Luciano A.
000189385 700__ $$0244240$$aSpiga, Enrico$$g188104
000189385 700__ $$0243887$$aDal Peraro, Matteo$$g182443
000189385 773__ $$j10$$k4$$tPhysical Biology
000189385 909C0 $$0252070$$pUPDALPE$$xU11830
000189385 909CO $$ooai:infoscience.tind.io:189385$$pSV$$particle
000189385 937__ $$aEPFL-ARTICLE-189385
000189385 973__ $$aEPFL$$rREVIEWED$$sPUBLISHED
000189385 980__ $$aARTICLE