scispace - formally typeset
Search or ask a question
Topic

Structural biology

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


Papers
More filters
Journal ArticleDOI
24 Oct 2006-Proteins
TL;DR: This work identifies all direct folding route trees to the native state and allows us to construct a simple model of the folding process, which provides an account for the fact that folding rates depend only on the topology of thenative state but not on sequence composition.
Abstract: An important puzzle in structural biology is the question of how proteins are able to fold so quickly into their unique native structures. There is much evidence that protein folding is hierarchic. In that case, folding routes are not linear, but have a tree structure. Trees are commonly used to represent the grammatical structure of natural language sentences, and chart parsing algorithms efficiently search the space of all possible trees for a given input string. Here we show that one such method, the CKY algorithm, can be useful both for providing novel insight into the physical protein folding process, and for computational protein structure prediction. As proof of concept, we apply this algorithm to the HP lattice model of proteins. Our algorithm identifies all direct folding route trees to the native state and allows us to construct a simple model of the folding process. Despite its simplicity, our model provides an account for the fact that folding rates depend only on the topology of the native state but not on sequence composition. Proteins 2007. © 2006 Wiley-Liss, Inc.

33 citations

Journal ArticleDOI
TL;DR: An insight into protein structure and the underlying chemistry and physics that is used to uncover protein structure is given and the variety of methods biochemists use to uncover the structure and properties of proteins are described.
Abstract: Structural biology is the study of the molecular arrangement and dynamics of biological macromolecules, particularly proteins. The resulting structures are then used to help explain how proteins function. This article gives the reader an insight into protein structure and the underlying chemistry and physics that is used to uncover protein structure. We start with the chemistry of amino acids and how they interact within, and between proteins, we also explore the four levels of protein structure and how proteins fold into discrete domains. We consider the thermodynamics of protein folding and why proteins misfold. We look at protein dynamics and how proteins can take on a range of conformations and states. In the second part of this review, we describe the variety of methods biochemists use to uncover the structure and properties of proteins that were described in the first part. Protein structural biology is a relatively new and exciting field that promises to provide atomic-level detail to more and more of the molecules that are fundamental to life processes.

33 citations

Journal ArticleDOI
TL;DR: An electron microscopy 3D reconstruction of ligand-induced dimers of intact receptor tyrosine kinase, KIT is presented and it is observed that KIT protomers form close contacts throughout the entire structure of lig and-bound receptor dimers, and that the dimeric receptors adopt multiple, defined conformational states.
Abstract: Using electron microscopy and fitting of crystal structures, we present the 3D reconstruction of ligand-induced dimers of intact receptor tyrosine kinase, KIT. We observe that KIT protomers form close contacts throughout the entire structure of ligand-bound receptor dimers, and that the dimeric receptors adopt multiple, defined conformational states. Interestingly, the homotypic interactions in the membrane proximal Ig-like domain of the extracellular region differ from those observed in the crystal structure of the unconstrained extracellular regions. We observe two prevalent conformations in which the tyrosine kinase domains interact asymmetrically. The asymmetric arrangement of the cytoplasmic regions may represent snapshots of molecular interactions occurring during trans autophosphorylation. Moreover, the asymmetric arrangements may facilitate specific intermolecular interactions necessary for trans phosphorylation of different KIT autophosphorylation sites that are required for stimulation of kinase activity and recruitment of signaling proteins by activated KIT.

33 citations

Book ChapterDOI
TL;DR: Advances in the past several years have shed light on structural basis for integrin regulation and signaling, especially how the large-scale reorientations of the ectodomain are related to the inter-domain and intra-domain shape shifting that changes ligand-binding affinity.
Abstract: Integrins are cell adhesion molecules that play important roles in many biological processes including hemostasis, immune responses, development, and cancer. Their adhesiveness is dynamically regulated through a process termed inside-out signaling. In addition, ligand binding transduces outside-in signals from the extracellular domain to the cytoplasm. Advances in the past several years have shed light on structural basis for integrin regulation and signaling, especially how the large-scale reorientations of the ectodomain are related to the inter-domain and intra-domain shape shifting that changes ligand-binding affinity. Experiments have also shown how the conformational changes of the ectodomain are linked to changes in the α- and β-subunit transmembrane and cytoplasmic domains.

33 citations

Journal ArticleDOI
TL;DR: For the experimental model system of mechanosensitive ion channels, the approach predicts how directional elastic interactions affect the molecular structure, organization, and biological function of proteins in crowded membranes.
Abstract: While modern structural biology has provided us with a rich and diverse picture of membrane proteins, the biological function of membrane proteins is often influenced by the mechanical properties of the surrounding lipid bilayer. Here we explore the relation between the shape of membrane proteins and the cooperative function of membrane proteins induced by membrane-mediated elastic interactions. For the experimental model system of mechanosensitive ion channels we find that the sign and strength of elastic interactions depend on the protein shape, yielding distinct cooperative gating curves for distinct protein orientations. Our approach predicts how directional elastic interactions affect the molecular structure, organization, and biological function of proteins in crowded membranes.

33 citations


Network Information
Related Topics (5)
Protein structure
42.3K papers, 3M citations
92% related
Transcription (biology)
56.5K papers, 2.9M citations
85% related
RNA
111.6K papers, 5.4M citations
85% related
Peptide sequence
84.1K papers, 4.3M citations
84% related
Chromatin
50.7K papers, 2.7M citations
84% related
Performance
Metrics
No. of papers in the topic in previous years
YearPapers
202335
202272
2021149
2020154
2019152
2018140