1,721,089 research outputs found
Allostery Frustrates the Experimentalist
Full text linkProteins interact with other proteins, with nucleic acids, lipids, carbohydrates and various small molecules in the living cell. These interactions have been quantified and structurally characterized in numerous stud-ies such that we today have a comprehensive picture of protein structure and function. However, proteins are dynamic and even folded proteins are likely more heterogeneous than they appear in most descrip-tions. One property of proteins that relies on dynamics and heterogeneity is allostery, the ability of a pro-tein to change structure and function upon ligand binding to an allosteric site. Over the last decades the concept of allostery was broadened to embrace all types of long-range interactions across a protein including purely entropic changes without a conformational change in single protein domains. But with this re-definition came a problem: How do we measure allostery? In this opinion, we discuss some caveats arising from the quantitative description of single-domain allostery from an experimental perspective and how the limitations cannot be separated from the definition of allostery per se. Furthermore, we attempt to tie together allostery with the concept of frustration in an effort to investigate the links between these two complex, and yet general, properties of proteins. We arrive at the conclusion that the sensitivity to perturbation of allosteric networks in single protein domains is too large for the networks to be of sig-nificant biological relevance
How fast is protein– ligand association?
No full textThere is increasing interest in studying protein interactions and their role in cell biology using kinetics. However, there is confusion about the proper terminology in terms of the distinction between rates and rate constants. We recommend a more stringent use of the words speed, fast, slow, rate, and rate constant
Dissecting Inter-domain Cooperativity in the Folding of a Multi Domain Protein
Full text linkCorrect protein folding underlies all cellular functions. While there are detailed descriptions and a good understanding of protein folding pathways for single globular domains there is a paucity of quantitative data regarding folding of multidomain proteins. We have here investigated the folding of a three-domain supramodule from the protein PSD-95, consisting of one PDZ domain, one SH3 domain and one guanylate kinase-like (GK) domain. This supramodule has previously been shown to work as one functional unit with regard to ligand binding. We used equilibrium and kinetic folding experiments to demonstrate that the PDZ domain folds faster and independently from the SH3-GK tandem, which folds as one cooperative unit. However, concurrent folding of the PDZ domain slows down folding of SH3-GK by non-native interactions, resulting in an off-pathway folding intermediate. Our data contribute to an emerging description of multidomain protein folding in which individual domains cannot a priori be viewed as separate folding units.</p
Templated folding of intrinsically disordered proteins
No full textMuch of our current knowledge of
biological chemistry is founded in the
structure-function relationship, whereby
sequence determines structure that
determines function. Thus, the discovery
that a large fraction of the proteome is
intrinsically disordered, while being
functional,
has
revolutionized
our
understanding of proteins and raised new
and
interesting
questions.
Many
intrinsically disordered proteins (IDPs)
have been determined to undergo a
disorder to order transition when
recognizing their physiological partners,
suggesting their mechanisms of folding are
intrinsically different from those observed
in globular proteins. However, IDPs also
follow some of the classic paradigms
established for globular proteins, pointing
to important similarities in their behavior.
In this review, we compare and contrast the
folding mechanisms of globular proteins
with the emerging features of binding-
induced folding of intrinsically disordered
order transitions of intrinsically disordered
proteins appear to follow rules of globular
protein folding such as the cooperative
nature of the reaction, their folding
pathways are remarkably more malleable,
due to the heterogeneous nature of their
folding nuclei, as probed by analysis of
linear free energy relationship plots. These
insights have led to a new model for the
disorder-to-order transition in IDPs termed
‘templated folding’, whereby the binding
partner dictates distinct structural
transitions en route to product, while
ensuring a co-operative folding
Protein binding and folding through an evolutionary lens
No full textProtein-protein associations are often mediated by an intrinsically disordered protein region interacting with a folded domain in a coupled binding and folding reaction. Classic physical organic chemistry approaches together with structural biology have shed light on mechanistic aspects of such reactions. Further insight into general principles may be obtained by interpreting the results through an evolutionary lens. This review attempts to provide an overview on how the analysis of binding and folding reactions can benefit from an evolutionary approach, and is aimed at protein scientists without a background in evolution. Evolution constantly reshapes existing proteins by sampling more or less fit variants. Most new variants are weeded out as generations and new species come and go over hundreds to hundreds of millions of years. The huge ongoing genome sequencing efforts have provided us with a snapshot of existing adapted fit-for-purpose protein homologs in thousands of different organisms. Comparison of present-day orthologs and paralogs highlights general principles of the evolution of coupled binding and folding reactions and demonstrate a great potential for evolution to operate on disordered regions and modulate affinity and specificity of the interactions
Double Mutant Cycles as a Tool to Address Folding, Binding, and Allostery
Full text linkQuantitative measurement of intramolecular and intermolecular interactions in protein structure is an elusive task, not easy to address experimentally. The phenomenon denoted 'energetic coupling' describes short- and long-range interactions between two residues in a protein system. A powerful method to identify and quantitatively characterize long-range interactions and allosteric networks in proteins or protein-ligand complexes is called double-mutant cycles analysis. In this review we describe the thermodynamic principles and basic equations that underlie the double mutant cycle methodology, its fields of application and latest employments, and caveats and pitfalls that the experimentalists must consider. In particular, we show how double mutant cycles can be a powerful tool to investigate allosteric mechanisms in protein binding reactions as well as elusive states in protein folding pathways
Biosynthetic oligosaccharide libraries for identification of protein-binding heparan sulfate motifs - Exploring the structural diversity by screening for fibroblast growth factor (FGF) 1 and FGF2 binding
No full text8 p.-5 fig.-1 sch.Heparan sulfate is crucial for vital reactions in the body because of its ability to bind various proteins. The identification of protein-binding heparan sulfate sequences is essential to our understanding of heparan sulfate biology and raises the possibility to develop drugs against diseases such as cancer and inflammatory conditions. We present proof-of-principle that in vitro generated heparan sulfate oligosaccharide libraries can be used to explore interactions between heparan sulfate and proteins, and that the libraries expand the available heparan sulfate sequence space. Oligosaccharide libraries mimicking highly 6-O-sulfated domains of heparan sulfate were constructed by enzymatic O-sulfation of O-desulfated, end-group H-3-labeled heparin octasaccharides. Acceptor oligosaccharides that were 6-O-desulfated but only partially 2O-desulfated yielded oligosaccharide arrays with increased ratio of iduronyl 2-O-sulfate/glucosaminyl 6-O-sulfate. The products were probed by affinity chromatography on immobilized growth factors, fibroblast growth factor-1 (FGF1) and FGF2, followed by sequence analysis of trapped oligosaccharides. An N-sulfated octasaccharide, devoid of 2-O-sulfate but with three 6-O-sulfate groups, was unexpectedly found to bind FGF1 as well as FGF2 at physiological ionic strength. However, a single 2-O-sulfate group in the absence of 6-O-sulfation gave higher affinity for FGF2. FGF1 binding was also augmented by 2-O-sulfation, preferentially in combination with an adjacent upstream 6-O-sulfate group. These results demonstrate the potential of the enzymatically generated oligosaccharide libraries.This work was supported by European Commission Grants QLK-CT-1999.00536 (Program “Biologically Active Novel Glycosaminoglycans”) and BIO4-CT98-0538 (Program “Heparan Sulfate Sequencing Demonstration”), by Swedish Research Council Grant 13401, and by a grant from Polysackaridforskning AB.Peer reviewe
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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