Protein Conformational Relaxation and Ligand Migration in Myoglobin:  A Nanosecond to Millisecond Molecular Movie from Time-Resolved Laue X-ray Diffraction

Srajer,; Ren, Zhi-An; Ty, Teng; Schmidt, Marius; Ursby, Thomas; Bourgeois, Dominique; Pradervand, Claude; Schildkamp, W.; Wulff, Michaël; Moffat, Keith

doi:10.1021/bi010715u

Cited by 323 publications

(397 citation statements)

References 50 publications

(106 reference statements)

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“…Each class controls a different aspect of the binding of small ligands such as CO or O 2 to Mb. We still do not have a complete understanding of binding, but crucial features have become clear through a combination of kinetic (1,41) and x-ray studies (42)(43)(44). A CO, after entering Mb, spends some time in the pocket denoted as Xe1 in Fig.…”

Section: Fluctuations and Function In Mbmentioning

confidence: 99%

Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions

Fenimore

Frauenfelder²,

McMahon³

et al. 2004

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

498

504

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The concept that proteins exist in numerous different conformations or conformational substates, described by an energy landscape, is now accepted, but the dynamics is incompletely explored. We have previously shown that large-scale protein motions, such as the exit of a ligand from the protein interior, follow the dielectric fluctuations in the bulk solvent. Here, we demonstrate, by using mean-square displacements (msd) from Mö ssbauer and neutron P roteins are the molecules that perform most biological functions, from storage of dioxygen (O 2 ) to enzyme catalysis. A central goal of protein science is to relate structure, dynamics, and function. Although investigations of protein structures and functions are well organized industries, protein dynamics is still in its infancy. Dynamics studies are best performed on proteins whose structures and functions are well known, e.g., myoglobin (Mb), the protein that gives muscles their red color. A hybrid picture of Mb is shown in Fig. 1. The lower part displays a piece of the protein backbone, namely, three ␣-helices. The upper part presents a space-filling view of the protein atoms. The active center, a heme group with a central iron atom, is red. Two cavities are also shown, Xe1 and the heme cavity. The protein is surrounded by the hydration shell, one to two layers of water, and is embedded in the bulk solvent. In Mb's role as an oxygenstorage protein, O 2 enters the protein, stays some time in Xe1, then binds at the heme iron (1). CO follows a similar path through the protein. The structure of Mb shows no permanent channel that leads from the outside to either Xe1 or the heme pocket or from Xe1 to the heme pocket. Thus, structural fluctuations are necessary for function (2).Fluctuations imply that Mb possesses numerous different conformations, called conformational substates (CS) (3). The different CS can be described by an energy landscape (EL) (4), the central concept in the folding (5), dynamics, and function of proteins. The EL is a construct in Ϸ3N dimensions, where N is the number of atoms forming the protein and the hydration shell. A substate is a point in this hyperspace, and structural fluctuations are represented by jumps between points. Initially, we assumed that protein conformations could be organized into a simple, rough EL (1). Experiments showed, however, that there are wells within wells within wells, and an organization of the EL with several tiers of decreasing free-energy barriers ensued (6). The top tier, denoted by CS0, contains a small number of CS with different structures that can have different functions: in A 0 Mb is involved in NO enzymatics; in A 1 it acts as an oxygen-storage system (7). Each of the CS0 substates can assume a very large number of CS1, called statistical substates. They perform the same function but with different rates. Here, we will show that the statistical substates comprise two tiers, CS1␣ and CS1␤. Fluctuations between CS1␣ substates are slaved to the solvent motions and involve sizeable structural changes (8). ...

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Section: Fluctuations and Function In Mbmentioning

confidence: 99%

Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions

Fenimore

Frauenfelder²,

McMahon³

et al. 2004

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

498

504

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“…Although static structures of alternate states are available for a number of allosteric proteins, information about the kinetic pathway between such functionally important states is limited. Time-resolved crystallographic analysis (1)(2)(3)(4)(5)(6)(7)(8)(9) provides the unique opportunity to obtain direct, time-dependent structural information at high resolution on the entire protein molecule as it undergoes structural change.…”

Section: Allosteric Protein Transitions ͉ Intersubunit Communication mentioning

confidence: 99%

Allosteric action in real time: Time-resolved crystallographic studies of a cooperative dimeric hemoglobin

Knapp

Pahl²,

Šrajer

et al. 2006

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

Self Cite

111

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Protein allostery provides mechanisms for regulation of biological function at the molecular level. We present here an investigation of global, ligand-induced allosteric transition in a protein by time-resolved x-ray diffraction. The study provides a view of structural changes in single crystals of Scapharca dimeric hemoglobin as they proceed in real time, from 5 ns to 80 s after ligand photodissociation. A tertiary intermediate structure forms rapidly (<5 ns) as the protein responds to the presence of an unliganded heme within each R-state protein subunit, with key structural changes observed in the heme groups, neighboring residues, and interface water molecules. This intermediate lays a foundation for the concerted tertiary and quaternary structural changes that occur on a microsecond time scale and are associated with the transition to a low-affinity T-state structure. Reversal of these changes shows a considerable lag as a T-like structure persists well after ligand rebinding, suggesting a slow T-to-R transition.allosteric protein transitions ͉ intersubunit communication ͉ kinetics A fundamental goal in biology is to understand how organisms respond to environmental signals. Central to this process are allosteric proteins that undergo structural transitions between alternate states in response to stimuli such as ligand binding. Although static structures of alternate states are available for a number of allosteric proteins, information about the kinetic pathway between such functionally important states is limited. Time-resolved crystallographic analysis (1-9) provides the unique opportunity to obtain direct, time-dependent structural information at high resolution on the entire protein molecule as it undergoes structural change.Much of our understanding of allosteric protein function has come from investigations into mammalian hemoglobins. Evidence of substantial structural changes accompanying ligand binding dates back to the 1930s with the observation that unliganded, high-salt, hemoglobin crystals exposed to oxygen shatter (10), foreshadowing the discovery of large quaternary changes that are linked to oxygen binding (11). Unliganded crystals of human hemoglobin grown under certain low-salt conditions can maintain their integrity upon oxygen binding; however, oxygen binding in this case is noncooperative (12). Although the ability to follow allosteric transitions in the crystalline state is limited when such large quaternary structural changes accompany cooperative ligand binding, spectroscopic investigations of hemoglobin solutions have revealed some aspects of the kinetic pathway of allosteric structural transitions (13-15). Results to date suggest a multistep pathway, with key tertiary structural transitions taking place within a few microseconds and quaternary rearrangements occurring in the range of tens of microseconds. In addition to providing structural information on high-affinity R and low-affinity T quaternary forms at the atomic level (16-18), crystallographic experiments have also succeeded...

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“…38,43,44 The studies also suggest that small ligands can move through the bulky regions of the protein governed by thermal fluctuations of the protein and that ligand migration follows defined routes through the protein matrix. 42,[45][46][47][48][49][50][51][52][53][54][55][56][57][58][59][60] Multiple pathways and active migration make a kinetic analysis of the ligand dynamics particularly relevant in view of the different time scales involved.…”

Section: Introductionmentioning

confidence: 99%

A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks

Cazade

Zheng

Prada‐Gracia

et al. 2015

The Journal of Chemical Physics

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The ligand migration network for O2–diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k–means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is found that all three methods agree well in their geometrical definition of the most important docking site, and all experimentally known docking sites are recovered by all three methods. Also, for most of the states, their population coincides quite favourably, whereas the kinetics of and between the states differs. One of the major differences between k–means and MCL clustering on the one hand and LSDMap on the other is that the latter finds one large primary cluster containing the Xe1a, IS1, and ENT states. This is related to the fact that the motion within the state occurs on similar time scales, whereas structurally the state is found to be quite diverse. In agreement with previous explicit atomistic simulations, the Xe3 pocket is found to be a highly dynamical site which points to its potential role as a hub in the network. This is also highlighted in the fact that LSDMap cannot identify this state. First passage time distributions from MCL clusterings using a one- (ligand-position) and two-dimensional (ligand-position and protein-structure) descriptor suggest that ligand- and protein-motions are coupled. The benefits and drawbacks of the three methods are discussed in a comparative fashion and highlight that depending on the questions at hand the best-performing method for a particular data set may differ.

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Protein Conformational Relaxation and Ligand Migration in Myoglobin: A Nanosecond to Millisecond Molecular Movie from Time-Resolved Laue X-ray Diffraction

Cited by 323 publications

References 50 publications

Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions

Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions

Allosteric action in real time: Time-resolved crystallographic studies of a cooperative dimeric hemoglobin

A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks

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