Dataset Information

Redesigning symmetry-related "mini-core" regions of FGF-1 to increase primary structure symmetry: thermodynamic and functional consequences of structural symmetry.

ABSTRACT: Previous reports detailing mutational effects within the hydrophobic core of human acidic fibroblast growth factor (FGF-1) have shown that a symmetric primary structure constraint is compatible with a stably folded protein. In the present report, we investigate symmetrically related pairs of buried hydrophobic residues in FGF-1 (termed "mini-cores") that are not part of the central core. The effect upon the stability and function of FGF-1 mutations designed to increase primary structure symmetry within these "mini-core" regions was evaluated. At symmetry-related positions 22, 64, and 108, the wild-type protein contains either Tyr or Phe side chains. The results show that either residue can be readily accommodated at these positions. At symmetry-related positions 42, 83, and 130, the wild-type protein contains either Cys or Ile side chains. While positions 42 and 130 can readily accommodate either Cys or Ile side chains, position 83 is substantially destabilized by substitution by Ile. Tertiary structure asymmetry in the vicinity of position 83 appears responsible for the inability to accommodate an Ile side chain at this position, and is known to contribute to functional half-life. A mutant form of FGF-1 with enforced primary structure symmetry at positions 22, 64, and 108 (all Tyr) and 42, 83, and 130 (all Cys) is shown to be more stable than the reference FGF-1 protein. The results support the hypothesis that a symmetric primary structure within a symmetric protein superfold represents a solution to achieving a foldable, stable polypeptide, and highlight the role that function may play in the evolution of asymmetry within symmetric superfolds.

SUBMITTER: Dubey VK

PROVIDER: S-EPMC2253474 | biostudies-literature | 2005 Sep

REPOSITORIES: biostudies-literature

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Redesigning symmetry-related "mini-core" regions of FGF-1 to increase primary structure symmetry: thermodynamic and functional consequences of structural symmetry.

Dubey Vikash Kumar VK Lee Jihun J Blaber Michael M

Protein science : a publication of the Protein Society 20050804 9

Previous reports detailing mutational effects within the hydrophobic core of human acidic fibroblast growth factor (FGF-1) have shown that a symmetric primary structure constraint is compatible with a stably folded protein. In the present report, we investigate symmetrically related pairs of buried hydrophobic residues in FGF-1 (termed "mini-cores") that are not part of the central core. The effect upon the stability and function of FGF-1 mutations designed to increase primary structure symmetry ...[more]

PMID: 16081654

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Project description:BackgroundAflatoxin contamination caused by Aspergillus fungi has been a serious factor affecting food safety of peanut (Arachis hypogaea L.) because aflatoxins are highly harmful for human and animal health. As three mechanisms of resistance to aflatoxin in peanut including shell infection resistance, seed infection resistance and aflatoxin production resistance exist among naturally evolved germplasm stocks, it is highly crucial to pyramid these three resistances for promoting peanut industry development and protecting consumers' health. However, less research effort has been made yet to investigate the differentiation and genetic relationship among the three resistances in diversified peanut germplasm collections.ResultsIn this study, the Chinese peanut mini-mini core collection selected from a large basic collection was systematically evaluated for the three resistances against A. flavus for the first time. The research revealed a wide variation among the diversified peanut accessions for all the three resistances. Totally, 14 resistant accessions were identified, including three with shell infection resistance, seven with seed infection resistance and five with aflatoxin production resistance. A special accession, Zh.h1312, was identified with both seed infection and aflatoxin production resistance. Among the five botanic types of A. hypogaea, the var. vulgaris (Spanish type) belonging to subspecies fastigiata is the only one which possessed all the three resistances. There was no close correlation between shell infection resistance and other two resistances, while there was a significant positive correlation between seed infection and toxin production resistance. All the three resistances had a significant negative correlation with pod or seed size. A total of 16 SNPs/InDels associated with the three resistances were identified through genome-wide association study (GWAS). Through comparative analysis, Zh.h1312 with seed infection resistance and aflatoxin production resistance was also revealed to possess all the resistance alleles of associated loci for seed infection index and aflatoxin content.ConclusionsThis study provided the first comprehensive understanding of differentiation of aflatoxin resistance in diversified peanut germplasm collection, and would further contribute to the genetic enhancement for resistance to aflatoxin contamination.

Project description:BackgroundClinical trials that assess the benefits and harms of an intervention do so by measuring and reporting outcomes. Inconsistent selection and diversity in the choice of outcomes make it challenging to directly compare interventions. To achieve an agreed core set of outcomes, a consensus methodology is recommended, comprising a web-based Delphi survey and a face-to-face consensus meeting. However, UK government regulations to control the pandemic prohibited plans for a face-to-face consensus meeting as part of the Core Rehabilitation Outcome Set for Single-Sided Deafness (CROSSSD) study.ObjectiveThis study aims to evaluate the modifications made by the CROSSSD study team to achieve consensus using web-based methods, but with minimal deviation from the original study protocol.MethodsThe study team worked with health care users and professionals to translate the planned face-to-face consensus meeting in a web-based format, preserving the key elements of the nominal group technique. A follow-up survey gathered evaluation feedback on the experiences of the 22 participating members. Feedback covered premeeting preparation, the process of facilitated discussions and voting, ability to contribute, and perceived fairness of the outcome.ResultsOverall, 98% (53/54) of feedback responses agreed or strongly agreed with the statements given, indicating that the web-based meeting achieved its original goals of open discussion, debate, and voting to agree with a core outcome set for single-sided deafness. Hearing-impaired participants were fully engaged, but there were some methodological challenges. For the participants, challenges included building rapport, understanding, and delivering the tasks in hand. For the study team, challenges included the need for thorough preparation and management of the unpredictability of tasks on the day.ConclusionsSharing our experiences and lessons learned can benefit future core outcome set developers. Overcoming the challenges of delivering a web-based consensus exercise in the face of the pandemic can be applied more generally to maximize inclusiveness, enhance geographical access, and reduce research costs.

Dataset Information

Redesigning symmetry-related "mini-core" regions of FGF-1 to increase primary structure symmetry: thermodynamic and functional consequences of structural symmetry.

Publications

Redesigning symmetry-related "mini-core" regions of FGF-1 to increase primary structure symmetry: thermodynamic and functional consequences of structural symmetry.

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