Advances in the REDCAT software package

Schmidt, C. C.; Irausquin, Stephanie; Valafar, Homayoun

doi:10.1186/1471-2105-14-302

Cited by 15 publications

(14 citation statements)

References 82 publications

(97 reference statements)

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“…loop regions as identified from the crystal structures and low correlation time regions). The REDCAT software package was used, along with the 2GK2 and 4QXW monomer structures, to solve for the best set of order parameters describing the extent, anisotropy, and direction of alignment (41,42). These parameters were used to backcalculate RDCs for comparison to experimental data.…”

Section: Resultsmentioning

confidence: 99%

Glycosylation Alters Dimerization Properties of a Cell-surface Signaling Protein, Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1)

Zhuo

Yang

Moremen

et al. 2016

Journal of Biological Chemistry

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Human carcinoembryonic antigen-related cell adhesion molecule 1 (C?/Au: EACAM1) is a cell-surface signaling molecule involved in cell adhesion, proliferation, and immune response. It is also implicated in cancer angiogenesis, progression, and metastasis. This diverse set of effects likely arises as a result of the numerous homophilic and heterophilic interactions that CEACAM1 can have with itself and other molecules. Its N-terminal Ig variable (Ig V ) domain has been suggested to be a principal player in these interactions. Previous crystal structures of the ␤-sandwich-like Ig V domain have been produced using Escherichia coli-expressed material, which lacks native glycosylation. These have led to distinctly different proposals for dimer interfaces, one involving interactions of ABED ␤-strands and the other involving GFCCC؆ ␤-strands, with the former burying one prominent glycosylation site. These structures raise ques- The human carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) 2 is involved in cell adhesion, proliferation, and immune response (1, 2). It also is implicated in cancer angiogenesis, progression, and metastasis (3). More specifically, it is known that CEACAM1 is a negative-regulator of cell proliferation and is down-regulated in some tumor cells (4 -10). Yet, CEACAM1 expression is reported to protect tumor cells from killing by immune cells (11)(12)(13)(14) and it has been found that the high expression level is associated with a number of other cancers (15)(16)(17)(18)(19). It is likely that this complex set of effects arises as a result of the numerous homophilic and heterophilic interactions that CEACAM1 can have with itself and other members of the CEACAM superfamily. The N-terminal Ig variable (Ig V ) domain of CEACAM1 has been suggested to be the basis of cis and trans homo-dimer formation (20), as well as interactions with other molecules (21-24). There are crystal structures of the Ig V domain expressed in Escherichia coli, which have led to the suggestion of two distinct dimerization interfaces (24, 25). However, examination of the interfaces suggests that the extensive glycosylation found in native material would inhibit dimer formation in one of these cases. This raises questions about the actual type of dimer found in solution, with and without glycosylation. Here, we use NMR methods to examine dimer structures in solution using a non-glycosylated form expressed in E. coli, and several glycosylated variants expressed in HEK293 cells.Dimerization of cell surface molecules is a well accepted mechanism for transmitting signals from the cell surface to the interior (26). In the case of CEACAM1 it is believed that modulation of intercellular adhesion as well as transmission of signals to the cell interior involves switching between cis and trans dimerization interactions. The full-length CEACAM1 molecule is large, sharing a topology with many other cell-surface signaling molecules; the extracellular domain is composed of one Ig V -like domain and typically 3 Ig C2 -like dom...

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Section: Resultsmentioning

confidence: 99%

Glycosylation Alters Dimerization Properties of a Cell-surface Signaling Protein, Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1)

Zhuo

Yang

Moremen

et al. 2016

Journal of Biological Chemistry

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“…The software package REDCAT used this formalism to simulate 15 N‐ 1 H N RDCs for the target proteins. REDCAT uses the protein structure and an order tensor S to calculate RDCs using Equations (2)‐(4).…”

Section: Resultsmentioning

confidence: 99%

Protein structure prediction assisted with sparse NMR data in CASP13

et al. 2019

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CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and 15N‐1H residual dipolar coupling data, typical of that obtained for 15N,13C‐enriched, perdeuterated proteins up to about 40 kDa, were simulated for 11 CASP13 targets ranging in size from 80 to 326 residues. For several targets, two prediction groups generated models that are more accurate than those produced using baseline methods. Real NMR data collected for a de novo designed protein were also provided to predictors, including one data set in which only backbone resonance assignments were available. Some NMR‐assisted prediction groups also did very well with these data. CASP13 also assessed whether incorporation of sparse NMR data improves the accuracy of protein structure prediction relative to nonassisted regular methods. In most cases, incorporation of sparse, noisy NMR data results in models with higher accuracy. The best NMR‐assisted models were also compared with the best regular predictions of any CASP13 group for the same target. For six of 13 targets, the most accurate model provided by any NMR‐assisted prediction group was more accurate than the most accurate model provided by any regular prediction group; however, for the remaining seven targets, one or more regular prediction method provided a more accurate model than even the best NMR‐assisted model. These results suggest a novel approach for protein structure determination, in which advanced prediction methods are first used to generate structural models, and sparse NMR data is then used to validate and/or refine these models.

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“…Our evaluation of REDCRAFT’s improved decimation routine proceeded in three main steps. During the first step, the known structure of 1A1Z was used to generate simulated RDC data using typical order tensors previously used in several studies [ 25 , 48 ] and the software package REDCAT [ 49 ]. The RDC set simulated included the four of the previously available RDC vectors as well as two new vectors ([H ⍺ -C ⍺ , N-C ⍺ ]) that were previously unusable in REDCRAFT.…”

Section: Methodsmentioning

confidence: 99%

Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package

et al. 2020

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Background Traditional approaches to elucidation of protein structures by Nuclear Magnetic Resonance spectroscopy (NMR) rely on distance restraints also known as Nuclear Overhauser effects (NOEs). The use of NOEs as the primary source of structure determination by NMR spectroscopy is time consuming and expensive. Residual Dipolar Couplings (RDCs) have become an alternate approach for structure calculation by NMR spectroscopy. In previous works, the software package REDCRAFT has been presented as a means of harnessing the information containing in RDCs for structure calculation of proteins. However, to meet its full potential, several improvements to REDCRAFT must be made. Results In this work, we present improvements to REDCRAFT that include increased usability, better interoperability, and a more robust core algorithm. We have demonstrated the impact of the improved core algorithm in the successful folding of the protein 1A1Z with as high as ±4 Hz of added error. The REDCRAFT computed structure from the highly corrupted data exhibited less than 1.0 Å with respect to the X-ray structure. We have also demonstrated the interoperability of REDCRAFT in a few instances including with PDBMine to reduce the amount of required data in successful folding of proteins to unprecedented levels. Here we have demonstrated the successful folding of the protein 1D3Z (to within 2.4 Å of the X-ray structure) using only N-H RDCs from one alignment medium. Conclusions The additional GUI features of REDCRAFT combined with the NEF compliance have significantly increased the flexibility and usability of this software package. The improvements of the core algorithm have substantially improved the robustness of REDCRAFT in utilizing less experimental data both in quality and quantity.

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Advances in the REDCAT software package

Cited by 15 publications

References 82 publications

Glycosylation Alters Dimerization Properties of a Cell-surface Signaling Protein, Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1)

Glycosylation Alters Dimerization Properties of a Cell-surface Signaling Protein, Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1)

Protein structure prediction assisted with sparse NMR data in CASP13

Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package

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