Protein dynamics

Jardetzky, Oleg; Lefèvre, Jean‐François

doi:10.1016/0014-5793(94)80277-7

Cited by 23 publications

(25 citation statements)

References 45 publications

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“…The core ␤-barrel and the two helices of N-TIMP-2 were all found to be comparatively rigid on a picosecond to nanosecond time scale. This picture of N-TIMP-2 is consistent with that seen for other proteins, where in general the highest flexibility of the protein backbone is found in surface loop regions (29). The rapid motion found for the AB ␤-hairpin confirms our earlier suggestion that this region is flexible and able to move through a relatively large conformational space (17).…”

Section: Backbone Mobility Of N-timp-2supporting

confidence: 88%

The Effect of Matrix Metalloproteinase Complex Formation on the Conformational Mobility of Tissue Inhibitor of Metalloproteinases-2 (TIMP-2)

Williamson

Muskett

Howard

et al. 1999

Journal of Biological Chemistry

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The backbone mobility of the N-terminal domain of tissue inhibitor of metalloproteinases-2 (N-TIMP-2) was determined both for the free protein and when bound to the catalytic domain of matrix metalloproteinase-3 (N-MMP-3). Regions of the protein with internal motion were identified by comparison of the T 1 and T 2 relaxation times and 1 H-15 N nuclear Overhauser effect values for the backbone amide 15 N signals for each residue in the sequence. This analysis revealed rapid internal motion on the picosecond to nanosecond time scale for several regions of free N-TIMP-2, including the extended ␤-hairpin between ␤-strands A and B, which forms part of the MMP binding site. Evidence of relatively slow motion indicative of exchange between two or more local conformations on a microsecond to millisecond time scale was also found in the free protein, including two other regions of the MMP binding site (the CD and EF loops). On formation of a tight N-TIMP-2⅐N-MMP-3 complex, the rapid internal motion of the AB ␤-hairpin was largely abolished, a change consistent with tight binding of this region to the MMP-3 catalytic domain. The extended AB ␤-hairpin is not a feature of all members of the TIMP family; therefore, the binding of this highly mobile region to a site distant from the catalytic cleft of the MMPs suggests a key role in TIMP-2 binding specificity.Breakdown of the extracellular matrix is an important event in many normal and pathological processes, such as growth, wound repair, tumor metastasis, and arthritis (1-3). A large family of zinc-dependent proteinases, the matrix metalloproteinases (MMPs), 1 are thought to be primarily responsible for this matrix catabolism. The activities of the MMP family in the extracellular matrix are highly regulated by transcriptional control, zymogen activation, and inhibition by a family of specific protein inhibitors, the tissue inhibitors of metalloproteinases or TIMPs (4). The TIMPs bind tightly to the active proteinases to form an inactive TIMP⅐MMP complex (5). Four mammalian TIMP proteins have now been identified (TIMP-1 to -4) (6 -9), and their high degree of sequence similarity and conservation of 12 Cys residues suggests that each consists of the same basic fold but with some variations in loop structures and glycosylation. The location of the MMP inhibitory site on the TIMP molecule has been shown to reside predominantly in the N-terminal two-thirds of the protein, defined by the first three disulfide bonds. This domain (N-TIMP) can be expressed independently to generate a fully folded, stable, and active inhibitor (10, 11).High resolution three-dimensional structures are now available for both the active N-terminal domain of TIMP-2 (12) and for the full-length inhibitor (13). Crystal structures have also been published for full-length TIMP-1 and TIMP-2 in complexes with the catalytic domains of MMP-3 (N-MMP-3) and MT1-MMP, respectively (14, 15). The structures of the TIMP⅐MMP complexes, together with NMR data on chemical shift perturbation seen for N-TIMP-2 on complex fo...

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Section: Backbone Mobility Of N-timp-2supporting

confidence: 88%

The Effect of Matrix Metalloproteinase Complex Formation on the Conformational Mobility of Tissue Inhibitor of Metalloproteinases-2 (TIMP-2)

Williamson

Muskett

Howard

et al. 1999

Journal of Biological Chemistry

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“…For a bisubstrate or multisubstrate enzyme, additional liganded forms, such as binary and ternary substrate complexes and product complexes, must be assumed, so as to undergo some additional conformational transitions between them. While ample evidence has indicated that, in a two-state equilibrium, an unbound enzyme can assume a bound as well as an unbound conformation, which is the current focus of experimental and computational studies; however, in a more complex situation for a bisubstrate or multisubstrate enzyme, it remains largely unknown whether one liganded form, such as binary or ternary substrate complexes, can assume multiple conformations that an enzyme must adopt throughout its catalytic cycle. − …”

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confidence: 99%

A Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Binary Complex of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase with MgATP

2016

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6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the first reaction in the folate biosynthetic pathway. Comparison of its X-ray and nuclear magnetic resonance structures suggests that the enzyme undergoes significant conformational change upon binding to its substrates, especially in three catalytic loops. Experimental research has shown that, in its binary form, even bound by analogues of MgATP, loops 2 and 3 remain rather flexible; this raises questions about the putative large-scale induced-fit conformational change of the HPPK-MgATP binary complex. In this work, long-time all-atomic molecular dynamics simulations were conducted to investigate the loop dynamics in this complex. Our simulations show that, with loop 3 closed, multiple conformations of loop 2, including the open, semiopen, and closed forms, are all accessible to the binary complex. These results provide valuable structural insights into the details of conformational changes upon 6-hydroxymethyl-7,8-dihydropterin (HP) binding and biological activities of HPPK. Conformational network analysis and principal component analysis related to the loops are also discussed.

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“…There is no simple relationship between protein flexibility and the average structure, observable by x-ray crystallography (5-7), or necessarily the thermal fluctuations about the average structure as determined by NMR spectroscopy (8)(9)(10). The most pertinent information is available from crystallographic DebyeWaller factors (11) or from NMR order parameters (10).…”

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confidence: 99%

Flexibility and molecular recognition in the immune system

Jimenez

Salazar

Baldridge

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

109

108

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Photon echo spectroscopy has been used to measure the response of three antibody-binding sites to perturbation from electronic excitation of a bound antigen, fluorescein. The three antibodies show motions that range in time scale from tens of femtoseconds to nanoseconds. Relative to the others, one antibody, 4-4-20, possesses a rigid binding site that likely results from a short and inflexible heavy chain complementarity-determining region 3 (HCDR3) loop and a critical Tyr that acts as a ''molecular splint,'' rigidifying the antigen across its most flexible internal degree of freedom. The remaining two antibodies, 34F10 and 40G4, despite being generated against the same antigen, possess binding sites that are considerably more flexible. The more flexible combining sites likely result from longer HCDR3 loops and a deletion in the light chain complementarity-determining region 1 (LCDR1) that removes the critical Tyr residue. The binding site flexibilities may result in varying mechanisms of antigen recognition including lock-and-key, induced-fit, and conformational selection.T he optimization of protein-based molecular recognition may require significant conformational adjustments of the participating proteins, ligands, or substrates. Several models of molecular recognition have been proposed that are differentiated by the role of flexibility. The ''lock-and-key'' model, where no structural optimization of the binding partners is required, presumes that the molecules have a geometry appropriate for tight binding (1). However, there is a growing consensus that protein flexibility may be required for optimal molecular recognition. As a result, two alternatives to the lock-and-key mechanism explicitly consider molecular flexibility. The original model that evoked flexibility, known as ''induced fit,'' posits that after the initial formation of an unoptimized complex, the molecules structurally reorganize to optimize binding interactions (2). A related model, ''conformational selection,'' hypothesizes that a small fraction of molecules exists transiently in appropriate geometries before binding (3). Although induced-fit and conformational selection evoke fluctuations that occur before or after initial complex formation, they both are differentiated from the lock-and-key model by the important role played by protein flexibility. Flexibility may also play an important role in binding specificity, because structurally distinct protein conformations are expected to facilitate the binding of structurally distinct molecules. The importance of flexibility in the affinity and specificity of molecular interactions is nowhere more obvious than in the humoral immune system, where a limited set of proteins (antibodies, Abs) must bind a virtually unlimited range of foreign molecules (i.e., small-molecule antigens, Ags). It has been suggested that the immune system may accomplish this task by using a limited set of flexible Abs that may bind a wide range of Ags (4, 5). Experiments that measure Ab and Ag flexibility would be interes...

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Protein dynamics

Cited by 23 publications

References 45 publications

The Effect of Matrix Metalloproteinase Complex Formation on the Conformational Mobility of Tissue Inhibitor of Metalloproteinases-2 (TIMP-2)

The Effect of Matrix Metalloproteinase Complex Formation on the Conformational Mobility of Tissue Inhibitor of Metalloproteinases-2 (TIMP-2)

A Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Binary Complex of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase with MgATP

Flexibility and molecular recognition in the immune system

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