We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy.

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Proteins were detected in channels of commercial starches of normal maize, waxy maize, sorghum, and wheat through labeling with a protein‐specific dye and examination using confocal laser scanning microscopy (CLSM). The dye, specifically 3‐(4‐carboxybenzoyl)quinoline‐2‐carboxaldehyde (CBQCA), fluoresces only after it reacts with primary amines in proteins, and CLSM detects fluorescence‐labeled protein distribution in an optical section of a starch granule while it is still in an intact state. Starch granules in thin sections of maize kernels also had channel proteins, indicating that proteins are native to the channels and not artifacts of isolation. Incubation of maize starch with protease (thermolysin) removed channel proteins, showing that channels are open to the external environment. SDS‐PAGE analysis of total protein from gelatinized commercial waxy maize starch revealed two major proteins of about Mr 38,000 and 40,000, both of which disappeared after thermolysin digestion of raw starch. Commercial waxy maize starch granule surface and channel proteins were extracted by SDS‐PAGE sample buffer without gelatinization of the granules. The major Mr 40,000 band was identified by MALDI‐TOF‐MS and N‐terminal sequence analysis as brittle‐1 (bt1) protein.

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A low glycemic index starch was developed by partial alpha-amylase treatment, and its fine structure responsible for slowly digestible and resistant properties was investigated. Different digestion rates were obtained for gelatinized, retrograded starch by varying the enzyme dosage and reaction time. Analysis by high performance size-exclusion chromatography (HPSEC) coupled with multiangle laser-light scattering indicated that the molecular weighs of amylopectin and amylose were reduced during the digestion, to less than 100 kDa. A debranched chain length study using high performance anion-exchange chromatography equipped with an amyloglucosidase reactor and a pulsed amperometric detector and HPSEC revealed that short chains of amylopectin and noncrystalline amylose were rapidly digested, while DPn 121 chains showed resistance, followed by DPn 46 chains. X-ray diffraction analysis revealed that the crystalline structure in the treated starches survived cooking. These starches not only have slowly digestible and resistant character, but also retain some branched structure for adequate functionality.