Time-resolved observation of protein allosteric communication

Buchenberg, Sebastian; Sittel, Florian; Stock, Gerhard

doi:10.1073/pnas.1707694114

Cited by 69 publications

(96 citation statements)

References 71 publications

(100 reference statements)

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“…In this way, despite the short timescale, it can be speculated that F508del delays the transmission of energy after hydrolysis, which could account for the increased closed times observed in electrophysiology assays. Additionally, it is plausible that F508del affects the propagation of the conformational changes after hydrolysis, via allosteric mechanisms, in a similar way as photoswitchable systems, whose simulations, revealed a similar behavior, in which, after an induced perturbation, there is an elastic response in the timespan of 0.1 ns …”

Section: Resultsmentioning

confidence: 93%

“…Additionally, it is plausible that F508del affects the propagation of the conformational changes after hydrolysis, via allosteric mechanisms, in a similar way as photoswitchable systems, whose simulations, revealed a similar behavior, in which, after an induced perturbation, there is an elastic response in the timespan of 0.1 ns. 78…”

Section: Does F508del Affect Short-term Conformational Changes Aftementioning

confidence: 99%

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F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis

et al. 2019

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The cystic fibrosis transmembrane conductance regulator (CFTR) channel is an ion channel responsible for chloride transport in epithelia and it belongs to the class of ABC transporters. The deletion of phenylalanine 508 (F508del) in CFTR is the most common mutation responsible for cystic fibrosis. Little is known about the effect of the mutation in the isolated nucleotide binding domains (NBDs), on dimer dynamics, ATP hydrolysis and even on nucleotide binding. Using molecular dynamics simulations of the human CFTR NBD dimer, we showed that F508del increases, in the prehydrolysis state, the inter‐motif distance in both ATP binding sites (ABP) when ATP is bound. Additionally, a decrease in the number of catalytically competent conformations was observed in the presence of F508del. We used the subtraction technique to study the first 300 ps after ATP hydrolysis in the catalytic competent site and found that the F508del dimer evidences lower conformational changes than the wild type. Using longer simulation times, the magnitude of the conformational changes in both forms increases. Nonetheless, the F508del dimer shows lower C‐α RMS values in comparison to the wild‐type, on the F508del loop, on the residues surrounding the catalytic site and the portion of NBD2 adjacent to ABP1. These results provide evidence that F508del interferes with the NBD dynamics before and after ATP hydrolysis. These findings shed a new light on the effect of F508del on NBD dynamics and reveal a novel mechanism for the influence of F508del on CFTR.

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Section: Resultsmentioning

confidence: 93%

Section: Does F508del Affect Short-term Conformational Changes Aftementioning

confidence: 99%

F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis

et al. 2019

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“…We need to add that the missing convergence to state B-associated distances implies that the reported structural changes are only the start of a full transfer from state A to the proposed state B. Indeed, already the relaxation of small proteins from nonequilibrium states involves time-scales of tens of microseconds and beyond, 11 and thus are outside of the scope of current unbiased MD simulation techniques.…”

Section: Resultsmentioning

confidence: 99%

“…[1][2][3] In spite of its importance as elementary process of cell signalling, there is surprisingly little known about the underlying dynamical process and the timescales of allosteric communication. [4][5][6][7][8][9][10][11] Understanding of the molecular mechanisms of allostery is crucial to, e.g., elucidate the effects of point mutations in cancer development 12 and exploit it for the design of small molecule drugs. 13 In this work, we investigate allostery within the structure of the yeast molecular chaperone heat shock protein 90 (Hsp90).…”

Section: Introductionmentioning

confidence: 99%

Hierarchical coupling between ATP hydrolysis and Hsp90’s client binding site

Wolf

Sohmen

Hellenkamp

et al. 2020

Preprint

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I.ABSTRACTSeveral indicators for a signal propagation from a binding site to a distant functional site have been found in the Hsp90 dimer. Here we determined a time-resolved pathway from ATP hydrolysis to changes in a distant folding substrate binding site. This was possible by combining single-molecule fluorescence-based methods with extensive atomistic nonequilibrium molecular dynamics simulations. We find that hydrolysis of one ATP effects a structural asymmetry in the full Hsp90 dimer that leads to the collapse of a central folding substrate binding site. Arg380 is the major mediator in transferring structural information from the nucleotide to the substrate binding site. This allosteric process occurs via hierarchical dynamics that involve timescales from picoto milliseconds and length scales from Ångstroms to several nanometers. We presume that similar hierarchical mechanisms are fundamental for information transfer through many other proteins.

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“…5 and 6), which are peripheral to SyH7's core epitope. Deprotection of these peptides could be the result of relaxation of the structure through stress created by the primary antibody binding site (61).…”

Section: Hx-ms Analysis Of Rivax Bound To Cluster I Mabs (Pb10 R70 mentioning

confidence: 99%

High-Definition Mapping of Four Spatially Distinct Neutralizing Epitope Clusters on RiVax, a Candidate Ricin Toxin Subunit Vaccine

Toth

Angalakurthi

Slyke

et al. 2017

Clin Vaccine Immunol

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RiVax is a promising recombinant ricin toxin A subunit (RTA) vaccine antigen that has been shown to be safe and immunogenic in humans and effective at protecting rhesus macaques against lethal-dose aerosolized toxin exposure. We previously used a panel of RTA-specific monoclonal antibodies (MAbs) to demonstrate, by competition enzyme-linked immunosorbent assay (ELISA), that RiVax elicits similar serum antibody profiles in humans and macaques. However, the MAb binding sites on RiVax have yet to be defined. In this study, we employed hydrogen exchange-mass spectrometry (HX-MS) to localize the epitopes on RiVax recognized by nine toxin-neutralizing MAbs and one nonneutralizing MAb. Based on strong protection from hydrogen exchange, the nine MAbs grouped into four spatially distinct epitope clusters (namely, clusters I to IV). Cluster I MAbs protected RiVax's ␣-helix B (residues 94 to 107), a protruding immunodominant secondary structure element known to be a target of potent toxin-neutralizing antibodies. Cluster II consisted of two subclusters located on the "back side" (relative to the active site pocket) of RiVax. One subcluster involved ␣-helix A (residues 14 to 24) and ␣-helices F-G (residues 184 to 207); the other encompassed ␤-strand d (residues 62 to 69) and parts of ␣-helices D-E (154 to 164) and the intervening loop. Cluster III involved ␣-helices C and G on the front side of RiVax, while cluster IV formed a sash from the front to back of RiVax, spanning strands b, c, and d (residues 35 to 59). Having a highresolution B cell epitope map of RiVax will enable the development and optimization of competitive serum profiling assays to examine vaccine-induced antibody responses across species.KEYWORDS antibody, biodefense, epitope, mass spectrometry, toxin, vaccine R icin is one of a small group of plant and bacterial toxins that are classified at the domestic and international levels as potential agents of bioterrorism (1, 2). Ricin is a product of castor beans (Ricinus communis), which are cultivated globally for their oils that are used in industrial lubricants, cosmetics, and biofuels. The toxin itself is an ϳ65-kDa glycoprotein that makes up ϳ5% of the dry weight of a castor bean. The toxin can be purified by relatively simple affinity chromatography (3, 4). On a cellular level, ricin exerts its cytotoxic effects through ribosome inactivation and triggering of programmed cell death (5). Ricin's binding subunit, ricin toxin B subunit (RTB), is a galactose/N-acetyl galactosamine (Gal/GalNAc)-specific lectin that promotes toxin entry into mammalian cells, while ricin's enzymatic subunit, RTA, is an RNA N-glycosidase (EC 3.2.2.22) that, when successfully delivered into the cytoplasm, cleaves the sarcin-ricin

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Time-resolved observation of protein allosteric communication

Cited by 69 publications

References 71 publications

F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis

F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis

Hierarchical coupling between ATP hydrolysis and Hsp90’s client binding site

High-Definition Mapping of Four Spatially Distinct Neutralizing Epitope Clusters on RiVax, a Candidate Ricin Toxin Subunit Vaccine

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