Correlated Inter-Domain Motions in Adenylate Kinase

Esteban‐Martín, Santiago; Fenwick, R. Bryn; Ådén, Jörgen; Cossins, Benjamin P.; Bertoncini, Carlos W.; Guallar, Vı́ctor; Wolf‐Watz, Magnus; Salvatella, Xavier

doi:10.1371/journal.pcbi.1003721

Cited by 21 publications

(31 citation statements)

References 44 publications

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“…5). This observation is consistent with Esteban-Martin et al's work (67) in the case of the unbound state. To experimentally verify this order of domain closure, one may do site mutations at helixes a6 and a7 to restrict their cracking motion.…”

Section: Rate-limiting Step and Domain-transition Order In Adksupporting

confidence: 93%

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Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case

Liu

2015

Biophysical Journal

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Conformational transition describes the essential dynamics and mechanism of enzymes in pursuing their various functions. The fundamental and practical challenge to researchers is to quantitatively describe the roles of large-scale dynamic transitions for regulating the catalytic processes. In this study, we tackled this challenge by exploring the pathways and free energy landscape of conformational changes in adenylate kinase (AdK), a key ubiquitous enzyme for cellular energy homeostasis. Using explicit long-timescale (up to microseconds) molecular dynamics and bias-exchange metadynamics simulations, we determined at the atomistic level the intermediate conformational states and mapped the transition pathways of AdK in the presence and absence of ligands. There is clearly chronological operation of the functional domains of AdK. Specifically in the ligand-free AdK, there is no significant energy barrier in the free energy landscape separating the open and closed states. Instead there are multiple intermediate conformational states, which facilitate the rapid transitions of AdK. In the ligand-bound AdK, the closed conformation is energetically most favored with a large energy barrier to open it up, and the conformational population prefers to shift to the closed form coupled with transitions. The results suggest a perspective for a hybrid of conformational selection and induced fit operations of ligand binding to AdK. These observations, depicted in the most comprehensive and quantitative way to date, to our knowledge, emphasize the underlying intrinsic dynamics of AdK and reveal the sophisticated conformational transitions of AdK in fulfilling its enzymatic functions. The developed methodology can also apply to other proteins and biomolecular systems.

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Section: Rate-limiting Step and Domain-transition Order In Adksupporting

confidence: 93%

“…AdK mainly follows the pathway in which LID closes first and then NMP closes afterward, which is consistent with Esteban-Martin et al's experimental work (67). It also explains our observation in LT-MD simulations that AdK mainly follows this pathway (see Figs.…”

Section: Biophysical Journal 109(3) 647-660supporting

confidence: 93%

Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case

Liu

2015

Biophysical Journal

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“…Propagating signals by domain-domain interactions may be essential (30,54). Some of the NMR methods used here, RDCs, for example, are well suited to the investigation of domain-domain interactions (55). As all of these domains are heavily glycosylated, it will be important to study these constructs with defined glycosylation patterns.…”

Section: Discussionmentioning

confidence: 99%

Glycosylation Alters Dimerization Properties of a Cell-surface Signaling Protein, Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1)

Zhuo

Yang

Moremen

et al. 2016

Journal of Biological Chemistry

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Human carcinoembryonic antigen-related cell adhesion molecule 1 (C?/Au: EACAM1) is a cell-surface signaling molecule involved in cell adhesion, proliferation, and immune response. It is also implicated in cancer angiogenesis, progression, and metastasis. This diverse set of effects likely arises as a result of the numerous homophilic and heterophilic interactions that CEACAM1 can have with itself and other molecules. Its N-terminal Ig variable (Ig V ) domain has been suggested to be a principal player in these interactions. Previous crystal structures of the ␤-sandwich-like Ig V domain have been produced using Escherichia coli-expressed material, which lacks native glycosylation. These have led to distinctly different proposals for dimer interfaces, one involving interactions of ABED ␤-strands and the other involving GFCCC؆ ␤-strands, with the former burying one prominent glycosylation site. These structures raise ques- The human carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) 2 is involved in cell adhesion, proliferation, and immune response (1, 2). It also is implicated in cancer angiogenesis, progression, and metastasis (3). More specifically, it is known that CEACAM1 is a negative-regulator of cell proliferation and is down-regulated in some tumor cells (4 -10). Yet, CEACAM1 expression is reported to protect tumor cells from killing by immune cells (11)(12)(13)(14) and it has been found that the high expression level is associated with a number of other cancers (15)(16)(17)(18)(19). It is likely that this complex set of effects arises as a result of the numerous homophilic and heterophilic interactions that CEACAM1 can have with itself and other members of the CEACAM superfamily. The N-terminal Ig variable (Ig V ) domain of CEACAM1 has been suggested to be the basis of cis and trans homo-dimer formation (20), as well as interactions with other molecules (21-24). There are crystal structures of the Ig V domain expressed in Escherichia coli, which have led to the suggestion of two distinct dimerization interfaces (24, 25). However, examination of the interfaces suggests that the extensive glycosylation found in native material would inhibit dimer formation in one of these cases. This raises questions about the actual type of dimer found in solution, with and without glycosylation. Here, we use NMR methods to examine dimer structures in solution using a non-glycosylated form expressed in E. coli, and several glycosylated variants expressed in HEK293 cells.Dimerization of cell surface molecules is a well accepted mechanism for transmitting signals from the cell surface to the interior (26). In the case of CEACAM1 it is believed that modulation of intercellular adhesion as well as transmission of signals to the cell interior involves switching between cis and trans dimerization interactions. The full-length CEACAM1 molecule is large, sharing a topology with many other cell-surface signaling molecules; the extracellular domain is composed of one Ig V -like domain and typically 3 Ig C2 -like dom...

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“…1–5 Further, for enzymes in which the active site is formed from multiple domains, concerted domain motions can greatly influence the positioning of catalytic residues and thus regulate catalytic activity. 3 In another example, the modular structure of a protein can serve to form a binding surface across domains so that variation in domain structure is the basis for regulating the interaction with binding partners. 1,6 …”

Section: Introductionmentioning

confidence: 99%

Analysis of Multidomain Protein Dynamics

Roy

Hua²,

Post³

2015

J. Chem. Theory Comput.

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Proteins with a modular architecture of multiple domains connected by linkers often exhibit diversity in the relative positions of domains while the domain tertiary structure remains unchanged. The biological function of these modular proteins, or the regulation of their activity depends on the variation in domain orientation and separation. Accordingly, careful characterization of inter-domain motion and correlated fluctuations of multi-domain systems is relevant for understanding the functional behavior of modular proteins. Molecular dynamics (MD) simulations provides a powerful approach to study these motions in atomic detail. Nevertheless, the common procedure for analyzing fluctuations from MD simulations after overall rigid-body alignment fails for multi-domain proteins; it greatly overestimates correlated positional fluctuations in the presence of relative domain motion. We show here that expressing the atomic motions of a multi-domain protein as a combination of displacement within the domain reference frame and motion of the relative domains correctly separates the internal motions to allow a useful description of correlated fluctuations. We illustrate the methodology of separating the domain fluctuations and local fluctuations by application to the tandem SH2 domains of human Syk protein kinase and by characterizing an effect of phosphorylation on the dynamics. Correlated motions are assessed from a distance covariance rather than the more common vector-coordinate covariance. The approach makes it possible to calculate the proper correlations in fluctuations internal to a domain as well as between domains.

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Correlated Inter-Domain Motions in Adenylate Kinase

Cited by 21 publications

References 44 publications

Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case

Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case

Glycosylation Alters Dimerization Properties of a Cell-surface Signaling Protein, Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1)

Analysis of Multidomain Protein Dynamics

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