CiteULike: cactus's structural_change

Multiple Conformations of E. coli Hsp90 in Solution: Insights into the Conformational Dynamics of Hsp90

Kristin Krukenberg — 2008-05-21T07:01:18-00:00

Structure, Vol. 16, No. 5. (7 May 2008), pp. 755-765.

Summary Hsp90, an essential eukaryotic chaperone, depends upon its intrinsic ATPase activity for function. Crystal structures of the bacterial Hsp90 homolog, HtpG, and the yeast Hsp90 reveal large domain rearrangements between the nucleotide-free and the nucleotide-bound forms. We used small-angle X-ray scattering and recently developed molecular modeling methods to characterize the solution structure of HtpG and demonstrate how it differs from known Hsp90 conformations. In addition to this HtpG conformation, we demonstrate that under physiologically relevant conditions, multiple conformations coexist in equilibrium. In solution, nucleotide-free HtpG adopts a more extended conformation than observed in the crystal, and upon the addition of AMPPNP, HtpG is in equilibrium between this open state and a closed state that is in good agreement with the yeast AMPPNP crystal structure. These studies provide a unique view of Hsp90 conformational dynamics and provide a model for the role of nucleotide in effecting conformational change.

The lattice as allosteric effector: Structural studies of alphabeta- and gamma-tubulin clarify the role of GTP in microtubule assembly

Luke Rice — 2008-05-02T10:24:15-00:00

Proceedings of the National Academy of Sciences, Vol. 105, No. 14. (8 April 2008), pp. 5378-5383.

GTP-dependent microtubule polymerization dynamics are required for cell division and are accompanied by domain rearrangements in the polymerizing subunit, alpha-tubulin. Two opposing models describe the role of GTP and its relationship to conformational change in alpha-tubulin. The allosteric model posits that unpolymerized alpha-tubulin adopts a more polymerization-competent conformation upon GTP binding. The lattice model posits that conformational changes occur only upon recruitment into the growing lattice. Published data support a lattice model, but are largely indirect and so the allosteric model has prevailed. We present two independent solution probes of the conformation of alpha-tubulin, the 2.3 A crystal structure of gamma-tubulin bound to GDP, and kinetic simulations to interpret the functional consequences of the structural data. These results (with our previous gamma-tubulin:GTPgammaS structure) support the lattice model by demonstrating that major domain rearrangements do not occur in eukaryotic tubulins in response to GTP binding, and that the unpolymerized conformation of alpha-tubulin differs significantly from the polymerized one. Thus, geometric constraints of lateral self-assembly must drive alpha-tubulin conformational changes, whereas GTP plays a secondary role to tune the strength of longitudinal contacts within the microtubule lattice. alpha-Tubulin behaves like a bent spring, resisting straightening until forced to do so by GTP-mediated interactions with the growing microtubule. Kinetic simulations demonstrate that resistance to straightening opposes microtubule initiation by specifically destabilizing early assembly intermediates that are especially sensitive to the strength of lateral interactions. These data provide new insights into the molecular origins of dynamic microtubule behavior. 10.1073/pnas.0801155105

Interconversion between two unrelated protein folds in the lymphotactin native state

Robbyn Tuinstra — 2008-04-02T09:10:15-00:00

Proceedings of the National Academy of Sciences, Vol. 105, No. 13. (1 April 2008), pp. 5057-5062.

Proteins often have multiple functional states, which might not always be accommodated by a single fold. Lymphotactin (Ltn) adopts two distinct structures in equilibrium, one corresponding to the canonical chemokine fold consisting of a monomeric three-stranded -sheet and carboxyl-terminal helix. The second Ltn structure solved by NMR reveals a dimeric all--sheet arrangement with no similarity to other known proteins. In physiological solution conditions, both structures are significantly populated and interconvert rapidly. Interconversion replaces long-range interactions that stabilize the chemokine fold with an entirely new set of tertiary and quaternary contacts. The chemokine-like Ltn conformation is a functional XCR1 agonist, but fails to bind heparin. In contrast, the alternative structure binds glycosaminoglycans with high affinity but fails to activate XCR1. Because each structural species displays only one of the two functional properties essential for activity in vivo, the conformational equilibrium is likely to be essential for the biological activity of lymphotactin. These results demonstrate that the functional repertoire and regulation of a single naturally occurring amino acid sequence can be expanded by access to a set of highly dissimilar native-state structures. 10.1073/pnas.0709518105

Targeted molecular dynamics: A new approach for searching pathways of conformational transitions

J Schlitter — 2008-02-13T09:56:33-00:00

Journal of Molecular Graphics, Vol. 12, No. 2. (June 1994), pp. 84-89.

Molecular dynamics simulations have proven to be a valuable tool to investigate the dynamic behavior of stable macromolecules at finite temperatures. However, considerable conformational transitions take place during a simulation only accidentally or at exceptionally high temperatures far from the range of experimental conditions. Targeted molecular dynamics (TMD) is a method to induce a conformational change to a known target structure at ordinary temperature by applying a time-dependent, purely geometrical constraint. The transition is enforced independently of the height of energy barriers, while the dynamics of the molecule is only minimally influenced by the constraint. Simulations of decaalanine and insulin show the ability of the method to explore the configurational space for pathways accessible at a given temperature. The transitions studied at insulin comprise unfolding of an [alpha]-helical portion and, in the reverse direction, refolding from an extended conformation. A possible application of TMD is the search for energy barriers and stable intermediates from rather local changes up to protein denaturation.

Myosin VI Walks "Wiggly" on Actin with Large and Variable Tilting

Yujie Sun — 2008-01-17T11:43:52-00:00

Molecular Cell, Vol. 28, No. 6. (28 December 2007), pp. 954-964.

Summary Myosin VI is an unconventional motor protein with unusual motility properties such as its direction of motion and path on actin and a large stride relative to its short lever arms. To understand these features, the rotational dynamics of the lever arm were studied by single-molecule polarized total internal reflection fluorescence (polTIRF) microscopy during processive motility of myosin VI along actin. The axial angle is distributed in two peaks, consistent with the hand-over-hand model. The changes in lever arm angles during discrete steps suggest that it exhibits large and variable tilting in the plane of actin and to the sides. These motions imply that, in addition to the previously suggested flexible tail domain, there is a compliant region between the motor domain and lever arm that allows myosin VI to accommodate the helical position of binding sites while taking variable step sizes along the actin filament.

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

Katherine Henzler-Wildman — 2007-11-19T21:02:56-00:00

Nature (18 November 2007)

Intrinsic motions along an enzymatic reaction trajectory

Katherine Henzler-Wildman — 2007-11-19T21:02:56-00:00

Nature (18 November 2007)

How kinesin waits between steps

Teppei Mori — 2007-11-15T08:53:49-00:00

Nature (14 November 2007)

Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

Karunesh Arora — 2007-11-14T04:42:00-00:00

Proceedings of the National Academy of Sciences (13 November 2007), 0706443104.

Large-scale conformational changes in proteins are often associated with the binding of a substrate. Because conformational changes may be related to the function of an enzyme, understanding the kinetics and energetics of these motions is very important. We have delineated the atomically detailed conformational transition pathway of the phosphotransferase enzyme adenylate kinase (AdK) in the absence and presence of an inhibitor. The computed free energy profiles associated with conformational transitions offer detailed mechanistic insights into, as well as kinetic information on, the ligand binding mechanism. Specifically, potential of mean force calculations reveal that in the ligand-free state, there is no significant barrier separating the open and closed conformations of AdK. The enzyme samples near closed conformations, even in the absence of its substrate. The ligand binding event occurs late, toward the closed state, and transforms the free energy landscape. In the ligand-bound state, the closed conformation is energetically most favored with a large barrier to opening. These results emphasize the underlying dynamic nature of the enzyme and indicate that the conformational transitions in AdK are more intricate than a mere two-state jump between the crystal-bound and -unbound states. Based on the existence of the multiple conformations of the enzyme in the open and closed states, a different viewpoint of ligand binding is presented. Our estimated activation energy barrier for the conformational transition is also in reasonable accord with the experimental findings. 10.1073/pnas.0706443104

Mutations as trapdoors to two competing native conformations of the Rop-dimer

Alexander Schug — 2007-11-22T09:15:02-00:00

Proceedings of the National Academy of Sciences, Vol. 104, No. 45. (6 November 2007), pp. 17674-17679.

Conformational transitions play a central role in regulating protein function. Structure-based models with multiple basins have been used to understand the mechanisms governing these transitions. A model able to accommodate multiple folding basins is proposed to explore the mutational effects in the folding of the Rop-dimer (Rop). In experiments, Rop mutants show unusually strong increases in folding rates with marginal effects on stability. We investigate the possibility of two competing conformations representing a parallel (P) and the wild-type antiparallel (AP) arrangement of the monomers as possible native conformations. We observe occupation of both distinct states and characterize the transition pathways. An interesting observation from the simulations is that, for equivalent energetic bias, the transition to the P basin (non-wild-type basin) shows a lower free-energy barrier. Thus, the rapid kinetics observed in experiments appear to be the result of two competing states with different kinetic behavior, triggered upon mutation by the opening of a trapdoor arising from Rop's symmetric structure. The general concept of having competing conformations for the native state goes beyond explaining Rop's mutational behaviors and can be applied to other systems. A switch between competing native structures might be triggered by external factors to allow, for example, allosteric control or signaling. 10.1073/pnas.0706077104

Fluorescence polarization from isomers of tetramethylrhodamine at SH-1 in rabbit psoas muscle fibers.

CL Berger — 2007-11-20T09:14:33-00:00

Biophys J, Vol. 68, No. 4 Suppl. (April 1995)

We have used fluorescence polarization to examine orientational changes of the 5- and 6-isomers of acetamidotetramethylrhodamine (ATR) covalently bound to SH-1 (Cys-707 of the myosin heavy chain) in single, skinned fibers from rabbit psoas muscle after rapid length steps or photolysis of caged nucleotides. Similar results were obtained with both the 5- and 6-isomers of ATR. After the photolysis of caged ATP, large and rapid changes in the fluorescence polarization signals were observed and were complete well before appreciable force had been generated. Changes in the fluorescence polarization signals after the photolysis of caged ADP were similar to those after the photolysis of caged ATP, despite an almost negligible change in force. The fluorescence polarization signals remained almost constant after rapid length steps in both rigor and active muscle fibers. These results suggest that structural changes at SH-1 monitored by 5- or 6-ATR are not associated directly with the force-generating event of muscle contraction, but may be involved in the communication pathway between the nucleotide and actin-binding sites of myosin.

Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR

Chun Tang — 2007-10-25T05:11:27-00:00

Nature, Vol. 449, No. 7165., pp. 1078-1082.

Polymorphism in the intermediates and products of amyloid assembly.

Ravindra Kodali — 2007-02-14T17:21:39-00:00

Curr Opin Struct Biol (22 January 2007)

Amyloid formation reactions exhibit two classes of polymorphisms: the metastable intermediates commonly observed during amyloid formation and the range of conformationally distinct mature fibrils often seen at the reaction endpoint. Although recent data suggest that spherical oligomers and protofibrils in most cases are not obligate intermediates of amyloid assembly, oligomeric states might sometimes serve as on-pathway intermediates. Mature amyloid polymorphs self-propagate as a result of the normally very high fidelity of amyloid elongation, giving rise to strain behavior and species barriers in prion phenomena. Oligomers, protofibrils and various polymorphic forms of mature amyloid fibrils seem to be distinguished by differences in atomic structure that give rise to differences in observed morphologies.

Crystal structure of the human prion protein reveals a mechanism for oligomerization

Karen Knaus — 2007-10-18T04:44:23-00:00

Nat Struct Mol Biol, Vol. 8, No. 9. (2001), pp. 770-774.

Conformational switching and fibrillogenesis in the amyloidogenic fragment of apolipoprotein a-I.

A Andreola — 2007-10-15T16:11:46-00:00

J Biol Chem, Vol. 278, No. 4. (24 January 2003), pp. 2444-2451.

The N-terminal portion of apolipoprotein A-I corresponding to the first 93 residues has been identified as the main component of apolipoprotein A-I fibrils in a form of systemic amyloidosis. We have been able to characterize the process of conformational switching and fibrillogenesis in this fragment of apolipoprotein A-I purified directly from ex vivo amyloid material. The peptide exists in an unstructured form in aqueous solution at neutral pH. The acidification of the solution provokes a collapse into a more compact, intermediate state and the transient appearance of a helical conformation that rapidly converts to a stable, mainly beta-structure in the fibrils. The transition from helical to sheet structure occurs concomitantly with peptide self-aggregation, and fibrils are detected after 72 h. The alpha-helical conformation is induced by the addition of trifluoroethanol and phospholipids. Interaction of the amyloidogenic polypeptide with phospholipids prevents the switching from helical to beta-sheet form and inhibits fibril formation. The secondary structure propensity of the apolipoprotein A-I fragment appears poised between helix and the beta-sheet. These findings reinforce the idea of a delicate balance between natively stabilizing interactions and fatally stabilizing interactions and stress the importance of cellular localization and environment in the maintenance of protein conformation.

The Structural Coupling between ATPase Activation and Recovery Stroke in the Myosin II Motor

Sampath Koppole — 2007-08-08T10:21:07-00:00

Structure, Vol. 15, No. 7. (18 July 2007), pp. 825-837.

Summary Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates ~65[degree sign]. Simultaneous with this "recovery stroke," myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 A-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transition at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.