pipath: An optimized algorithm for generating α-helical structures from PISEMA data

Asbury, T.; Quine, J. R.; Achuthan, Srisairam; Hu, Jun; Chapman, Michael S.; Cross, Timothy A.; Bertram, Richard

doi:10.1016/j.jmr.2006.07.020

Cited by 14 publications

(20 citation statements)

References 20 publications

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“…The degeneracies associated with a diplane have been incorporated into equations for torsion angles, and the continuity conditions were rewritten so that they could be used with the torsion angle formulas. These formulas are in a convenient form for algorithms such as PIPATH [25] which derive plausible protein structures directly from PISEMA data. The formulas in fact form an essential aspect of the PIPATH algorithm in the process of deriving protein structures from uniformly labelled two-dimensional ssNMR data.…”

Section: Discussionmentioning

confidence: 99%

“…The molecular backbone structure can be determined by gluing together the consecutive diplanes, as in the PIPATH algorithm [25]. The multiplicities in torsion angles translate to multiplicities in diplane orientations.…”

Section: Introductionmentioning

confidence: 99%

“…The shotgun approach [18] for determining α-helical membrane protein structures is an example of the gluing method. Another example is the PIPATH algorithm [25] which builds an atomic model of a protein by gluing together the diplanes. The PIPATH algorithm was used in the determination of the atomic structure of the amantadine-blocked transmembrane domain of the M2 proton channel from Influenza A virus [29].…”

Section: Introductionmentioning

confidence: 99%

“…The primary goal of this paper is to rewrite the torsion angle formulas from Cross et al [22] so that they incorporate a rule, which we call the continuity condition, that ensures the proper gluing of overlapping diplanes. This makes it much simpler to build structures using gluing, and is a key element of the PIPATH algorithm [25] for building structures using uniformly labelled two-dimensional ssNMR data. The torsion angle formulas can provide an initial model, but further refinement of the model is needed [20] using both stereochemical restraints and the NMR data.…”

Section: Introductionmentioning

confidence: 99%

“…We rewrite the torsion angle formulas from [22] so that they automatically satisfy the continuity conditions. The reformulated torsion angle formulas have been applied recently in the PIPATH algorithm [25] and will be helpful in other applications in which diplane gluing is used to construct a protein backbone model. …”

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confidence: 99%

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Continuity conditions and torsion angles from ssNMR orientational restraints

Achuthan¹,

Asbury²,

Hu³

et al. 2008

Journal of Magnetic Resonance

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The backbone torsion angle pair (φ, ψ) at each amino acid of a polypeptide is a descriptor of its conformation. One can use chemical shift and dipolar coupling data from solid-state NMR PISEMA experiments to directly calculate the torsion angles for the membrane-spanning portion of a protein.However, degeneracies inherent in the data give rise to multiple potential torsion angles between two adjacent peptide planes (a diplane). The molecular backbone structure can be determined by gluing together the consecutive diplanes, as in the PIPATH algorithm [25]. The multiplicities in torsion angles translate to multiplicities in diplane orientations. In this paper, we show that adjacent diplanes can be glued together to form a permissible structure only if they satisfy continuity conditions, described quantitatively here. These restrict the number of potential torsion angle pairs. We rewrite the torsion angle formulas from [22] so that they automatically satisfy the continuity conditions. The reformulated torsion angle formulas have been applied recently in the PIPATH algorithm [25] and will be helpful in other applications in which diplane gluing is used to construct a protein backbone model.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

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Continuity conditions and torsion angles from ssNMR orientational restraints

Achuthan¹,

Asbury²,

Hu³

et al. 2008

Journal of Magnetic Resonance

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Concurrent lobular neoplasia increases the risk of ipsilateral breast cancer recurrence in patients with ductal carcinoma in situ treated with breast‐conserving therapy

Rudloff

Brogi

Brockway

et al. 2009

Cancer

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BACKGROUND:Multiple clinicopathologic factors have been analyzed for their association with an increased risk of ipsilateral breast tumor recurrence (IBTR) after women receive breast‐conserving treatment (BCT) for ductal carcinoma in situ (DCIS). The reported incidence of proliferative lesions, such as atypical ductal hyperplasia (ADH), columnar cell changes (CCC), and lobular neoplasia associated with breast cancer, has been as high as 23%; however, the relevance of these lesions on the natural history of DCIS and the risk of IBTR remains unknown.METHODS:Two hundred ninety‐four patients with DCIS who received BCT between 1991 and 1995 were identified from the authors' institutional database. Slides were reviewed by a dedicated breast pathologist with particular attention to the presence of lobular neoplasia, ADH, and CCC. The actuarial 5‐, 10‐, and 15‐year IBTR rates were calculated using the Kaplan‐Meier method and were compared using the log‐rank test.RESULTS:Concurrent lobular neoplasia was present in 41 of 294 patients (14%), ADH was present in 37 of 294 patients (13%), and CCC was present in 71 of 294 patients (24%). The median follow‐up was 11 years. IBTR occurred in 40 of 227 patients without lobular neoplasia (18%) versus 15 of 41 patients with lobular neoplasia (37%; P=.005; hazard ratio [HR], 2.49). The 5‐, 10‐, and 15‐year cumulative incidence rates of IBTR were twice as high in women who had DCIS and lobular neoplasia compared with women who had DCIS alone (P=.002). Concomitant ADH (HR, 1.53) and CCC (HR, 1.24) were not associated significantly with IBTR (P=.20 and P=.44, respectively).CONCLUSIONS:Concurrent lobular neoplasia is associated with a significantly higher risk of IBTR in women with DCIS who received BCT. Women with coexisting DCIS and lobular neoplasia who receive BCT should consider using additional risk‐reducing strategies. Cancer 2009. © 2009 American Cancer Society.

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Membrane orientation of the Na,K-ATPase regulatory membrane protein CHIF determined by solid-state NMR

Franzin¹,

Teriete²,

Marassi³

2007

Magn. Reson. Chem.

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Corticosteroid hormone-induced factor (CHIF) is a major regulatory subunit of the Na,K-ATPase, and a member of an evolutionarily conserved family of membrane proteins that regulate the function of the enzyme complex in a tissue-specific and physiological-state-specific manner. Here we present the structure of CHIF oriented in the membrane, determined by solid-state NMR orientation-dependent restraints. Because CHIF adopts a similar structure in lipid micelles and bilayers, it is possible to assign the solid-state NMR spectrum measured for (15)N-labeled CHIF in oriented bilayers from the structure determined in micelles, to obtain the global orientation of the protein in the membrane.

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pipath: An optimized algorithm for generating α-helical structures from PISEMA data

Cited by 14 publications

References 20 publications

Continuity conditions and torsion angles from ssNMR orientational restraints

Continuity conditions and torsion angles from ssNMR orientational restraints

Concurrent lobular neoplasia increases the risk of ipsilateral breast cancer recurrence in patients with ductal carcinoma in situ treated with breast‐conserving therapy

Membrane orientation of the Na,K-ATPase regulatory membrane protein CHIF determined by solid-state NMR

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