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      Mechanistic studies of the biogenesis and folding of outer membrane proteins in vitro and in vivo: What have we learned to date?

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          Abstract

          Highlights

          • Summary of key concepts in protein folding from the study of water-soluble proteins.

          • Discussion of the complexity of studying folding of outer membrane proteins (OMPs).

          • Role of periplasmic chaperones and the BAM complex in the folding of OMPs in vivo.

          • Examples of the application of biophysical methods to study OMP folding in vitro.

          • Comparisons of the folding of water-soluble proteins and OMPs.

          Abstract

          Research into the mechanisms by which proteins fold into their native structures has been on-going since the work of Anfinsen in the 1960s. Since that time, the folding mechanisms of small, water-soluble proteins have been well characterised. By contrast, progress in understanding the biogenesis and folding mechanisms of integral membrane proteins has lagged significantly because of the need to create a membrane mimetic environment for folding studies in vitro and the difficulties in finding suitable conditions in which reversible folding can be achieved. Improved knowledge of the factors that promote membrane protein folding and disfavour aggregation now allows studies of folding into lipid bilayers in vitro to be performed. Consequently, mechanistic details and structural information about membrane protein folding are now emerging at an ever increasing pace. Using the panoply of methods developed for studies of the folding of water-soluble proteins. This review summarises current knowledge of the mechanisms of outer membrane protein biogenesis and folding into lipid bilayers in vivo and in vitro and discusses the experimental techniques utilised to gain this information. The emerging knowledge is beginning to allow comparisons to be made between the folding of membrane proteins with current understanding of the mechanisms of folding of water-soluble proteins.

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          Most cited references242

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          Principles that govern the folding of protein chains.

          C ANFINSEN (1973)
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            How fast-folding proteins fold.

            An outstanding challenge in the field of molecular biology has been to understand the process by which proteins fold into their characteristic three-dimensional structures. Here, we report the results of atomic-level molecular dynamics simulations, over periods ranging between 100 μs and 1 ms, that reveal a set of common principles underlying the folding of 12 structurally diverse proteins. In simulations conducted with a single physics-based energy function, the proteins, representing all three major structural classes, spontaneously and repeatedly fold to their experimentally determined native structures. Early in the folding process, the protein backbone adopts a nativelike topology while certain secondary structure elements and a small number of nonlocal contacts form. In most cases, folding follows a single dominant route in which elements of the native structure appear in an order highly correlated with their propensity to form in the unfolded state.
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              Funnels, pathways, and the energy landscape of protein folding: a synthesis.

              The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation, that is, to the energy landscape. The statistical energy landscape approach explains when and why unique behaviors, such as specific folding pathways, occur in some proteins and more generally explains the distinction between folding processes common to all sequences and those peculiar to individual sequences. This approach also gives new, quantitative insights into the interpretation of experiments and simulations of protein folding thermodynamics and kinetics. Specifically, the picture provides simple explanations for folding as a two-state first-order phase transition, for the origin of metastable collapsed unfolded states and for the curved Arrhenius plots observed in both laboratory experiments and discrete lattice simulations. The relation of these quantitative ideas to folding pathways, to uniexponential vs. multiexponential behavior in protein folding experiments and to the effect of mutations on folding is also discussed. The success of energy landscape ideas in protein structure prediction is also described. The use of the energy landscape approach for analyzing data is illustrated with a quantitative analysis of some recent simulations, and a qualitative analysis of experiments on the folding of three proteins. The work unifies several previously proposed ideas concerning the mechanism protein folding and delimits the regions of validity of these ideas under different thermodynamic conditions.
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                Author and article information

                Contributors
                Journal
                Arch Biochem Biophys
                Arch. Biochem. Biophys
                Archives of Biochemistry and Biophysics
                Academic Press
                0003-9861
                1096-0384
                15 December 2014
                15 December 2014
                : 564
                : 265-280
                Affiliations
                Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
                School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
                Author notes
                [* ]Corresponding author at: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK. s.e.radford@ 123456leeds.ac.uk
                Article
                S0003-9861(14)00076-9
                10.1016/j.abb.2014.02.011
                4262575
                24613287
                fe6c1995-271b-4d65-84a0-77fb9c142736
                © 2014 The Authors. Published by Elsevier Inc.
                History
                : 10 January 2014
                : 16 February 2014
                : 20 February 2014
                Categories
                Review

                Biochemistry
                protein folding,outer membrane protein,periplasmic chaperone,bam complex,φ-value analysis,protein stability

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