Biochemistry - Metamorphic proteins

MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK.
Science (Impact Factor: 31.48). 07/2008; 320(5884):1725-6. DOI: 10.1126/science.1158868
Source: PubMed
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    ABSTRACT: The three-dimensional structures of proteins are often considered fundamental for understanding their function. Yet, because of the complexity of protein structure, extracting specific functional information from structures can be a considerable challenge. Here, we present selected approaches and tools that we have developed to study and connect protein sequence, structure, and function spaces. First, we consider a global perspective of structure space and view the protein data bank (PDB) as a database. We highlight challenges in searching protein structure space and in using the PDB as the starting point for computational structural studies. Then we describe a function-oriented view and show examples of how multiple protein structures can be used to extract insights about the function and specificity of proteins at the family level.
    Israel Journal of Chemistry (Online) 04/2013; 53(3‐4). DOI:10.1002/ijch.201200078 · 2.56 Impact Factor
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    ABSTRACT: Molecular plasticity controls enzymatic activity: the native fold of a protein in a given environment is normally unique and at a global free-energy minimum. Some proteins, however, spontaneously undergo substantial fold switching to reversibly transit between defined conformers, the “metamorphic” proteins. Here, we present a minimal metamorphic, selective, and specific caseinolytic metallopeptidase, selecase, which reversibly transits between several different states of defined three-dimensional structure, which are associated with loss of enzymatic activity due to autoinhibition. The latter is triggered by sequestering the competent conformation in incompetent but structured dimers, tetramers, and octamers. This system, which is compatible with a discrete multifunnel energy landscape, affords a switch that provides a reversible mechanism of control of catalytic activity unique in nature.
    Angewandte Chemie International Edition 09/2014; 53(40). DOI:10.1002/anie.201405727 · 11.34 Impact Factor
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    ABSTRACT: Metamorphic proteins, including proteins with high levels of sequence identity but different folds, are exceptions to the long-standing rule-of-thumb that proteins with as little as 30% sequence identity adopt the same fold. Which topologies can be bridged by these highly identical sequences remains an open question. Here we bridge two 3-α-helix bundle proteins with two radically different folds. Using a straightforward approach, we engineered the sequences of one subdomain within maltose binding protein (MBP, α/β/α-sandwich) and another within outer surface protein A (OspA, β-sheet) to have high sequence identity (80 and 77%, respectively) with engineered variants of protein G (GA, 3-α-helix bundle). Circular dichroism and nuclear magnetic resonance spectra of all engineered variants demonstrate that they maintain their native conformations despite substantial sequence modification. Furthermore, the MBP variant (80% identical to GA) remained active. Thermodynamic analysis of numerous GA and MBP variants suggests that the key to our approach involved stabilizing the modified MBP and OspA subdomains via external interactions with neighboring substructures, indicating that subdomain interactions can stabilize alternative folds over a broad range of sequence variation. These findings suggest that it is possible to bridge one fold with many other topologies, which has implications for protein folding, evolution, and misfolding diseases. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.
    Biophysical Journal 01/2015; 108(1):154-62. DOI:10.1016/j.bpj.2014.10.073 · 3.83 Impact Factor