Target highlights from the first post‐PSI CASP experiment (CASP12, May–August 2016)

Kryshtafovych, Andriy; Albrecht, R.; Baslé, Arnaud; Bule, Pedro; Caputo, Alessandro T.; Carvalho, Ana Luı́sa; Chao, Kinlin; Diskin, Ron; Fidelis, Krzysztof; Fontes, Carlos M. G. A.; Fredslund, Folmer; Gilbert, Harry J.; Goulding, Celia W.; Hartmann, M.D.; Hayes, Christopher S.; Herzberg, Osnat; Hill, Johan C.; Joachimiak, A.; Kohring, Gert‐Wieland; Koning, Roman I.; Leggio, Leila Lo; Mangiagalli, Marco; Michalska, K.; Moult, John; Najmudin, Shabir; Nardini, M.; Nardone, Valentina; Ndeh, Didier; Nguyen, Thanh H.; Pintacuda, Guido; Postel, Sandra; Raaij, Mark J. van; Roversi, Pietro; Shimon, Amir; Singh, Abhimanyu; Sundberg, Eric J.; Tars, K.; Zitzmann, Nicole; Schwede, Torsten

doi:10.1002/prot.25392

Cited by 13 publications

(19 citation statements)

References 121 publications

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“…About 34 experimental structure determination groups provided modeling targets (see the CASP12 Targets Highlights paper for details of some of these). About 82 structures were selected by the CASP organizers, resulting in a total of 90 CASP12 targets (T0859 to T0948).…”

Section: Introductionmentioning

confidence: 99%

Critical assessment of methods of protein structure prediction (CASP)—Round XII

et al. 2017

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This article reports the outcome of the 12th round of Critical Assessment of Structure Prediction (CASP12), held in 2016. CASP is a community experiment to determine the state of the art in modeling protein structure from amino acid sequence. Participants are provided sequence information and in turn provide protein structure models and related information. Analysis of the submitted structures by independent assessors provides a comprehensive picture of the capabilities of current methods, and allows progress to be identified. This was again an exciting round of CASP, with significant advances in 4 areas: (i) The use of new methods for predicting three-dimensional contacts led to a two-fold improvement in contact accuracy. (ii) As a consequence, model accuracy for proteins where no template was available improved dramatically. (iii) Models based on a structural template showed overall improvement in accuracy. (iv) Methods for estimating the accuracy of a model continued to improve. CASP continued to develop new areas: (i) Assessing methods for building quaternary structure models, including an expansion of the collaboration between CASP and CAPRI. (ii) Modeling with the aid of experimental data was extended to include SAXS data, as well as again using chemical cross-linking information. (iii) A team of assessors evaluated the suitability of models for a range of applications, including mutation interpretation, analysis of ligand binding properties, and identification of interfaces. This article describes the experiment and summarizes the results. The rest of this special issue of PROTEINS contains papers describing CASP12 results and assessments in more detail.

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Section: Introductionmentioning

confidence: 99%

Critical assessment of methods of protein structure prediction (CASP)—Round XII

et al. 2017

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“…This fold has an extra four-helical subdomain capping one side of a thioredoxin domain βαβ-αββα ( Kozlov and Gehring, 2020 ). The UGGT-TRXL1 domain has a slightly altered and unique topology, with the four-helical subdomain inserted before the thioredoxin one: αααα-βαβ-αββα ( Kryshtafovych et al., 2018 ). The wild-type protein crystallized in three different conformations, called “closed” (PDB: 5N2J , Figure 1 A, and gray with purple TRXL2 and TRXL3 domains in Figure 1 C), “open” (PDB: 5MZO , Figure 1 B and gray with green TRXL2 and TRXL3 domains in Figure 1 C), and “intermediate” (PDB: 5MU1 , gray with yellow TRXL2 and TRXL3 domains in Figure 1 C) ( Roversi et al., 2017 ).…”

Section: Resultsmentioning

confidence: 99%

Clamping, bending, and twisting inter-domain motions in the misfold-recognizing portion of UDP-glucose: Glycoprotein glucosyltransferase

et al. 2021

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Summary UDP-glucose:glycoprotein glucosyltransferase (UGGT) flags misfolded glycoproteins for ER retention. We report crystal structures of full-length Chaetomium thermophilum UGGT ( Ct UGGT), two Ct UGGT double-cysteine mutants, and its TRXL2 domain truncation ( Ct UGGT-ΔTRXL2). Ct UGGT molecular dynamics (MD) simulations capture extended conformations and reveal clamping, bending, and twisting inter-domain movements. We name “Parodi limit” the maximum distance on the same glycoprotein between a site of misfolding and an N-linked glycan that can be reglucosylated by monomeric UGGT in vitro , in response to recognition of misfold at that site. Based on the MD simulations, we estimate the Parodi limit as around 70–80 Å. Frequency distributions of distances between glycoprotein residues and their closest N-linked glycosylation sites in glycoprotein crystal structures suggests relevance of the Parodi limit to UGGT activity in vivo . Our data support a “one-size-fits-all adjustable spanner” UGGT substrate recognition model, with an essential role for the UGGT TRXL2 domain.

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“…This fold has an extra four-helical subdomain capping one side of a thioredoxin domain bab-abba (Kozlov and Gehring, 2020). The UGGT-TRXL1 domain has a slightly altered and unique topology, with the four-helical subdomain inserted before the thioredoxin one: aaaa-bab-abba (Kryshtafovych et al, 2018). The wild-type protein crystallized in three different conformations, called ''closed'' (PDB: 5N2J, Figure 1A, and gray with purple TRXL2 and TRXL3 domains in Figure 1C), ''open'' (PDB: 5MZO, Figure 1B and gray with green TRXL2 and TRXL3 domains in Figure 1C), and ''intermediate'' (PDB: 5MU1, gray with yellow TRXL2 and TRXL3 domains in Figure 1C) (Roversi et al, 2017).…”

Section: Resultsmentioning

confidence: 99%