@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 {2120,
	title = {Identification and structural characterization of a CBP/p300-binding domain from the ETS family transcription factor GABP alpha},
	journal = {Journal of Molecular Biology},
	volume = {377},
	number = {3},
	year = {2008},
	note = {ISI Document Delivery No.: 293ZPTimes Cited: 5Cited Reference Count: 60Kang, Hyun-Seo Nelson, Mary L. Mackereth, Cameron D. Scharpf, Manuela Graves, Barbara J. McIntosh, Lawrence P.},
	month = {Mar},
	pages = {636-646},
	type = {Article},
	abstract = {Using NMR spectroscopy, we identified and characterized a previously unrecognized structured domain near the N-terminus (residues 35-121) of the ETS family transcription factor GABP alpha. The monomeric domain folds as a five-stranded beta-sheet crossed by a distorted helix. Although globally resembling ubiquitin, the GABP(x fragment differs in its secondary structure topology and thus appears to represent a new protein fold that we term the OST (On-SighT) domain. The surface of the GABP alpha OST domain contains two predominant clusters of negatively-charged residues suggestive of electrostatically driven interactions with positively-charged partner proteins. Following a best-candidate approach to identify such a partner, we demonstrated through NMR-monitored titrations and glutathione S-transferase pulldown assays that the OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300. This provides a direct structural link between GABP and a central component of the transcriptional machinery. (C) 2008 Elsevier Ltd. All rights reserved.},
	keywords = {BACKBONE DYNAMICS, C-13-LABELED PROTEINS, CREB-BINDING-PROTEIN, ESCHERICHIA-COLI, HIGH-RESOLUTION, HYPOXIA-INDUCIBLE FACTOR-1-ALPHA, LARGER PROTEINS, NEUROMUSCULAR-JUNCTION, NMR, NMR EXPERIMENTS, protein-protein interaction, RESIDUAL DIPOLAR COUPLINGS, SPECTROSCOPY, TRANSCRIPTION FACTOR, UBIQUITIN},
	isbn = {0022-2836},
	url = {<Go to ISI>://000255374200006},
	author = {Kang, H. S. and Nelson, M. L. and Mackereth, C. D. and Scharpf, M. and Graves, B. J. and McIntosh, L. P.}
}
@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.}
}
@article {1618,
	title = {Sub-angstrom conformational changes of a single molecule captured by AFM variance analysis},
	journal = {Biophysical Journal},
	volume = {90},
	number = {10},
	year = {2006},
	note = {ISI Document Delivery No.: 034CETimes Cited: 20Cited Reference Count: 34},
	month = {May},
	pages = {3806-3812},
	type = {Article},
	abstract = {A system{\textquoteright}s equilibrium variance can be analyzed to probe its underlying dynamics at higher resolution. Here, using single-molecule atomic-force microscope techniques, we show how the variance in the length of a single dextran molecule can be used to establish thermodynamic equilibrium and to detect conformational changes not directly observable with other methods. Dextran is comprised of a chain of pyranose rings that each undergoes an Angstrom-scale transition from a chair to boat conformation under a stretching force. Our analysis of the variance of the molecule{\textquoteright}s fluctuations verifies equilibrium throughout the force-extension curve, consistent with the expected thermodynamic ensemble. This validates further analysis of the variance in the transition region, which reveals an intermediate conformation between the chair and the boat on the sub-Angstrom scale. Our test of thermal equilibrium as well as our variance analysis can be readily extended to a wide variety of molecules, including proteins.},
	keywords = {ATOMIC-FORCE MICROSCOPE, CHAIR-BOAT TRANSITIONS, HIGH-RESOLUTION, LIQUIDS, MECHANICAL FORCE, POLYSACCHARIDES, PROTEIN, RNA MOLECULES, SPECTROSCOPY, UBIQUITIN},
	isbn = {0006-3495},
	url = {<Go to ISI>://000236901400043},
	author = {Walther, K. A. and Brujic, J. and Li, H. B. and Fernandez, J. M.}
}
@article {1621,
	title = {The unfolding and folding dynamics of TNfnALL probed by single molecule force-ramp spectroscopy},
	journal = {Polymer},
	volume = {47},
	number = {7},
	year = {2006},
	note = {ISI Document Delivery No.: 030JETimes Cited: 10Cited Reference Count: 53},
	month = {Mar},
	pages = {2548-2554},
	type = {Article},
	abstract = {Tenascin, an important extracellular matrix protein, is subject to stretching force under physiological conditions and plays important roles in regulating the cell-matrix interactions. Using the recently developed single molecule force-ramp spectroscopy, we investigated the unfolding-folding kinetics of a recombinant tenascin fragment TNfnALL. Our results showed that all the 15 FnIII domains in TNfnALL have similar spontaneous unfolding rate constant at zero force, but show great difference in their folding rate constants. Our results demonstrated that single molecule force-ramp spectroscopy is a powerful tool for accurate determination of the kinetic parameters that characterize the unfolding and folding reactions. We anticipate that single molecule force-ramp spectroscopy will become a versatile addition to the single molecule manipulation tool box and greatly expand the scope of single molecule force spectroscopy. (c) 2006 Elsevier Ltd. All rights reserved.},
	keywords = {ADHESION, DOMAIN, EXPRESSION, III, IMMUNOGLOBULIN, MATRIX PROTEINS, MECHANICAL STABILITY, microscopy, MUSCLE PROTEIN TITIN, tenascin, UBIQUITIN},
	isbn = {0032-3861},
	url = {<Go to ISI>://000236629900037},
	author = {Wang, M. J. and Cao, Y. and Li, H. B.}
}
@article {932,
	title = {Structural and dynamic independence of isopeptide-linked RanGAP1 and SUMO-1},
	journal = {Journal of Biological Chemistry},
	volume = {279},
	number = {47},
	year = {2004},
	note = {ISI Document Delivery No.: 870ZPTimes Cited: 14Cited Reference Count: 46},
	month = {Nov},
	pages = {49131-49137},
	type = {Article},
	abstract = {Although sumoylation regulates a diverse and growing number of recognized biological processes, the molecular mechanisms by which the covalent attachment of the ubiquitin-like protein SUMO can alter the properties of a target protein remain to be established. To address this question, we have used NMR spectroscopy to characterize the complex of mature SUMO-1 with the C-terminal domain of human RanGAP1. Based on amide chemical shift and N-15 relaxation measurements, we show that the C terminus of SUMO-1 and the loop containing the consensus sumoylation site in RanGAP1 are both conformationally flexible. Furthermore, the overall structure and backbone dynamics of each protein remain unchanged upon the covalent linkage of Lys(524) in RanGAP1 to the C-terminal Gly(97) of SUMO-1. Therefore, SUMO-1 and RanGAP1 behave as "beads-on-a-string," connected by a flexible isopeptide tether. Accordingly, the sumoylation-dependent interaction of RanGAP1 with the nucleoporin RanBP2 may arise through the bipartite recognition of both RanGAP1 and SUMO-1 rather than through a new binding surface induced in either individual protein upon their covalent linkage. We hypothesize that this conformational flexibility may be a general feature contributing to the recognition of ubiquitin-like modified proteins by their downstream effector machineries.},
	keywords = {BACKBONE DYNAMICS, BINDING, CONJUGATION, CRYSTAL-STRUCTURE, GTPASE-ACTIVATING PROTEIN, IN-VIVO, MOLYBDOPTERIN, NUCLEAR-PORE COMPLEX, SYNTHASE, UBC9, UBIQUITIN},
	isbn = {0021-9258},
	url = {<Go to ISI>://000225098100078},
	author = {Macauley, M. S. and Errington, W. J. and Okon, M. and Scharpf, M. and Mackereth, C. D. and Schulman, B. A. and McIntosh, L. P.}
}
@article {4313,
	title = {Unfolding of proteins monitored by electrospray ionization mass spectrometry: A comparison of positive and negative ion modes},
	journal = {Journal of the American Society for Mass Spectrometry},
	volume = {9},
	number = {12},
	year = {1998},
	note = {ISI Document Delivery No.: 141FPTimes Cited: 72Cited Reference Count: 56},
	month = {Dec},
	pages = {1248-1254},
	type = {Article},
	abstract = {Electrospray ionization (ESI) mass spectrometry (MS) in both the positive and negative ion mode has been used to study protein unfolding transitions of lysozyme, cytochrome c (cyt c), and ubiquitin in solution. As expected, ESI of unfolded lysozyme leads to the formation of substantially higher charge states than the tightly folded protein in both modes of operation. Surprisingly, the acid-induced unfolding of cyt c as well as the acid and the base-induced unfolding of ubiquitin show different behavior: In these three cases protein unfolding only leads to marginal changes in the negative ion charge state distributions, whereas in the positive ion mode pronounced shifts to higher charge states are observed. This shows that ESI MS in the negative ion mode as a method for probing conformational changes of proteins in solution should be treated with caution. The data presented in this work provide further evidence that the conformation of a protein in solution not its charge state is the predominant factor for determining the ESI charge slate distribution in the positive ion mode. Furthermore, these data support the hypothesis of a recent study (Konermann and Douglas, Biochemistry 1997, 36, 12296-12302) which suggested that ESI in the positive ion mode is not sensitive to changes in the secondary structure of proteins but only to changes in the tertiary structure. (C) 1998 American Society for Mass Spectrometry.},
	keywords = {A-STATE, BINDING, CIRCULAR-DICHROISM, CYTOCHROME-C, HYDROGEN-DEUTERIUM EXCHANGE, INDUCED CONFORMATIONAL-CHANGES, MYOGLOBIN, NUCLEAR-MAGNETIC-RESONANCE, SITES, SPECTRA, UBIQUITIN},
	isbn = {1044-0305},
	url = {<Go to ISI>://000077132600002},
	author = {Konermann, L. and Douglas, D. J.}
}
