@article {2030,
	title = {Direct observation of Markovian behavior of the mechanical unfolding of individual proteins},
	journal = {Biophysical Journal},
	volume = {95},
	number = {2},
	year = {2008},
	note = {ISI Document Delivery No.: 318WGTimes Cited: 8Cited Reference Count: 20Cao, Yi Kuske, Rachel Li, Hongbin},
	month = {Jul},
	pages = {782-788},
	type = {Article},
	abstract = {Single-molecule force-clamp spectroscopy is a valuable tool to analyze unfolding kinetics of proteins. Previous force-clamp spectroscopy experiments have demonstrated that the mechanical unfolding of ubiquitin deviates from the generally assumed Markovian behavior and involves the features of glassy dynamics. Here we use single molecule force-clamp spectroscopy to study the unfolding kinetics of a computationally designed fast-folding mutant of the small protein GB1, which shares a similar beta-grasp fold as ubiquitin. By treating the mechanical unfolding of polyproteins as the superposition of multiple identical Poisson processes, we developed a simple stochastic analysis approach to analyze the dwell time distribution of individual unfolding events in polyprotein unfolding trajectories. Our results unambiguously demonstrate that the mechanical unfolding of NuG2 fulfills all criteria of a memoryless Markovian process. This result, in contrast with the complex mechanical unfolding behaviors observed for ubiquitin, serves as a direct experimental demonstration of the Markovian behavior for the mechanical unfolding of a protein and reveals the complexity of the unfolding dynamics among structurally similar proteins. Furthermore, we extended our method into a robust and efficient pseudo-dwell-time analysis method, which allows one to make full use of all the unfolding events obtained in force-clamp experiments without categorizing the unfolding events. This method enabled us to measure the key parameters characterizing the mechanical unfolding energy landscape of NuG2 with improved precision. We anticipate that the methods demonstrated here will find broad applications in single-molecule force-clamp spectroscopy studies for a wide range of proteins.},
	keywords = {ADHESION, BONDS, FORCE-CLAMP SPECTROSCOPY, MICROSCOPE, REVEALS, SINGLE-MOLECULE, UBIQUITIN},
	isbn = {0006-3495},
	url = {<Go to ISI>://000257122900033},
	author = {Cao, Y. and Kuske, R. and Li, H. B.}
}
@article {2247,
	title = {Stabilization provided by neighboring strands is critical for the mechanical stability of proteins},
	journal = {Biophysical Journal},
	volume = {95},
	number = {8},
	year = {2008},
	note = {ISI Document Delivery No.: 352NMTimes Cited: 5Cited Reference Count: 37Sharma, Deepak Feng, Gang Khor, Dingyue Genchev, Georgi Z. Lu, Hui Li, Hongbin},
	month = {Oct},
	pages = {3935-3942},
	type = {Article},
	abstract = {Single-molecule force spectroscopy studies and steered molecular dynamics simulations have revealed that protein topology and pulling geometry play important roles in determining the mechanical stability of proteins. Most studies have focused on local interactions that are associated with the force-bearing beta-strands. Interactions mediated by neighboring strands are often overlooked. Here we use Top7 and barstar as model systems to illustrate the critical importance of the stabilization effect provided by neighboring beta-strands on the mechanical stability. Using single-molecule atomic force microscopy, we showed that Top7 and barstar, which have similar topology in their force-bearing region, exhibit vastly different mechanical-stability characteristics. Top7 is mechanically stable and unfolds at similar to 150 pN, whereas barstar is mechanically labile and unfolds largely below 50 pN. Steered molecular dynamics simulations revealed that stretching force peels one force-bearing strand away from barstar to trigger unfolding, whereas Top7 unfolds via a substructure-sliding mechanism. This previously overlooked stabilization effect from neighboring beta-strands is likely to be a general mechanism in protein mechanics and can serve as a guideline for the de novo design of proteins with significant mechanical stability and novel protein topology.},
	keywords = {BARSTAR, DYNAMICS SIMULATIONS, IMMUNOGLOBULIN DOMAINS, MICROSCOPE, MOLECULE FORCE SPECTROSCOPY, resistance, SINGLE PROTEIN, TITIN, TOPOLOGY, UBIQUITIN},
	isbn = {0006-3495},
	url = {<Go to ISI>://000259503900036},
	author = {Sharma, D. and Feng, G. and Khor, D. and Genchev, G. Z. and Lu, H. and Li, H. B.}
}
