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Structural biology

About: Structural biology is a research topic. Over the lifetime, 2206 publications have been published within this topic receiving 126070 citations.


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Journal ArticleDOI
TL;DR: It is shown that domain-selective perdeuteration combined with contrast-matched small-angle neutron scattering (SANS), SAXS and computational modeling provides valuable information to precisely define relative domain arrangements in RBP TIA-1.
Abstract: Multi-domain proteins play critical roles in fine-tuning essential processes in cellular signaling and gene regulation. Typically, multiple globular domains that are connected by flexible linkers undergo dynamic re-arrangements upon binding to protein, DNA or RNA ligands. RNA binding proteins (RBPs) represent an important class of multi-domain proteins, which regulate gene expression by recognizing linear or structured RNA sequence motifs. Here, we employ segmental perdeuteration of the three RNA recognition motif (RRM) domains in the RBP TIA-1 using Sortase A-mediated protein ligation. We show that domain-selective perdeuteration combined with contrast-matched small-angle neutron scattering (SANS), SAXS and computational modelling provides valuable information to precisely define relative domain arrangements. The approach is generally applicable to study conformational arrangements of individual domains in multi-domain proteins and changes induced by ligand binding.

50 citations

Journal ArticleDOI
TL;DR: G protein-coupled receptors represent the largest family of human membrane proteins, as well as drug targets, and a wealth of single point mutants has accumulated in literature and public databases.

50 citations

Book ChapterDOI
TL;DR: Detailed molecular understanding of BH3-only protein action has aided the development of novel chemical entities that initiate cell death by mimicking the properties of B H3- only proteins.
Abstract: B-cell lymphoma-2 (Bcl-2) homology-3 (BH3)-only proteins are considered members of the Bcl-2 family, though they bear little sequence or structural identity with the multi-BH motif prosurvival or proapoptotic Bcl-2 proteins like Bcl-2 or Bax. They are better considered a separate phylogenetic entity. In combination, results from biophysical, biochemical, cell biological, and animal studies in conjunction with structural investigations have elucidated the function and mechanism of action of these proteins. Either by antagonizing prosurvival Bcl-2 proteins or directly activating proapoptotic Bcl-2 proteins (Bax or Bak) they initiate apoptosis. BH3-only proteins are intrinsically disordered and fold and bind into a groove provided by their cognate receptor Bcl-2 family proteins. Our detailed molecular understanding of BH3-only protein action has aided the development of novel chemical entities that initiate cell death by mimicking the properties of BH3-only proteins.

50 citations

Journal ArticleDOI
TL;DR: General protocols aimed at protecting protein structure upon the removal of bulk solvent will undoubtedly enable biomolecular structure characterization through gas-phase structural biology approaches, like IM-MS.
Abstract: Mass spectrometry (MS) has revealed the composition, stoichiometry, connectivity, and dynamics of many multiprotein complexes that remain challenging for other structural biology tools.[1] More recently, ion mobility (IM), a gas-phase separation technology that operates to resolve protein ions according to their size and charge,[2] coupled with MS (IM-MS) has been used to generate 3D structure information from such samples.[3] Information from many such gas-phase technologies[4] can be combined to overcome challenging aspects of protein structure characterization. Even though such methods are proving to be useful, their development is not devoid of experimental challenges. Chief among these is establishing a general correlation between gas-phase measurements and protein structures in solution. Several reports have observed significant rearrangements of protein structure upon desolvation and ionization,[5] although recent data suggest that these examples may be in the minority.[6] Despite this, general protocols aimed at protecting protein structure upon the removal of bulk solvent will undoubtedly enable biomolecular structure characterization through gas-phase structural biology approaches, like IM-MS.

50 citations

Proceedings ArticleDOI
01 Dec 1998
TL;DR: An algorithm to identify the maximum match sequence at each position with a calculation cost of O(N log N) and memory space of O(-N) is proposed and applied to some sequences, it was found unexpectedly large palindromes and repeats in DNA.
Abstract: Genomic science and structural biology meet in the relationship between the sequence and the structure of nucleic acids. The structure that supports each function is preserved in the process of evolution as specific sequences. Particularly, the same sequence which appears in a different place such as a palindromic or repetitive sequence has biophysical meaning: recognition site of dimers, forming stem-loops, and contributions to global structure of nucleic acids. Also, the genetic network, transduction pathway, and tissue specificity largely depend on these. Although the relationship between them can be found experimentally, there is increasing demand for automated analysis. Especially, it is desirable to extract the same character sequences of arbitrary length (especially, very long ones) which co-occur at an arbitrary separation. We propose an algorithm to identify the maximum match sequence at each position with a calculation cost of O(N log N) and memory space of O(N). Applying it to some sequences, we found unexpectedly large palindromes and repeats in DNA.

50 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
202335
202272
2021149
2020154
2019152
2018140