On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

Brokaw, Jason; Chu, Jhih‐Wei

doi:10.1016/j.bpj.2010.09.040

Cited by 48 publications

(74 citation statements)

References 74 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In our simulations, cracking was indeed observed in the vicinity of the hinge region linking the N and C lobes; this led to highly extended conformations, which the kinase visited while interconverting between its active and Srclike inactive conformations. These simulations are among the few examples thus far of spontaneous cracking being directly observed in unbiased atomistic simulations (22). Importantly, the simulations suggest that a protein may need to significantly deviate from its relatively compact native-like conformation in the process of a conformational change.…”

Section: Discussionmentioning

confidence: 68%

“…They argued that cracking may lower the freeenergy barrier of the conformational change and that the entropic gain resulting from the greater number of accessible conformations may overcome the enthalpic loss due to the disruption of favorable contacts that results from unfolding. Various models were subsequently developed to demonstrate the cracking mechanism (20,21), but cracking has only rarely been observed in fully atomistic simulations of protein conformational changes without using artificial biasing forces (22).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Transitions to catalytically inactive conformations in EGFR kinase

Shan

Arkhipov

Kim

et al. 2013

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

190

216

View full text Add to dashboard Cite

The epidermal growth factor receptor (EGFR) is a key protein in cellular signaling, and its kinase domain (EGFR kinase) is an intensely pursued target of small-molecule drugs. Although both catalytically active and inactive conformations of EGFR kinase have been resolved crystallographically, experimental characterization of the transitions between these conformations remains difficult. Using unbiased, all-atom molecular dynamics simulations, we observed EGFR kinase spontaneously transition from the active to the socalled "Src-like inactive" conformation by way of two sets of intermediate conformations: One corresponds to a previously identified locally disordered state and the other to previously undescribed "extended" conformations, marked by the opening of the ATP-binding site between the two lobes of the kinase domain. We also simulated the protonation-dependent transition of EGFR kinase to another ["Asp-Phe-Gly-out" ("DFG-out")] inactive conformation and observed similar intermediate conformations. A key element observed in the simulated transitions is local unfolding, or "cracking," which supports a prediction of energy landscape theory. We used hydrogen-deuterium (H/D) exchange measurements to corroborate our simulations and found that the simulated intermediate conformations correlate better with the H/D exchange data than existing active or inactive EGFR kinase crystal structures. The intermediate conformations revealed by our simulations of the transition process differ significantly from the existing crystal structures and may provide unique possibilities for structure-based drug discovery.molten globule intermediate state | hinge unfolding | high-entropy transition state | activation loop conformations E pidermal growth factor receptor (EGFR, also known as ErbB1/Her1) kinase, the cytoplasmic kinase domain of the cell-surface receptor EGFR (1), is a widely studied protein domain and the target of a number of small-molecule drugs used to treat a variety of cancers (2). Crystal structures reveal that the active state of EGFR kinase shares characteristics common to almost all active protein kinases (3). Two inactive conformations of EGFR kinase have also been obtained from crystal structures (4, 5), one resembling the "Src-like inactive" state and one the "Asp-Phe-Gly-out" ("DFG-out") state, each of which is observed in many other protein kinases (6).Despite these structural findings, the transition pathways between the active and inactive states of EGFR kinase remain unclear. Like many other protein domains, EGFR kinase presumably adopts a multitude of intermediate conformations; identifying such conformations is crucial to a comprehensive, molecular-level understanding of the protein's dynamic behavior in solution. It is also possible that such intermediate conformations could be captured and stabilized by suitable small molecules, offering unique opportunities for drug discovery. Intermediate conformations of EGFR kinase, however, have not been directly observed experimentally. Molecular dynamics (MD)...

show abstract

Section: Discussionmentioning

confidence: 68%

mentioning

confidence: 99%

Transitions to catalytically inactive conformations in EGFR kinase

Shan

Arkhipov

Kim

et al. 2013

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

190

216

View full text Add to dashboard Cite

show abstract

“…On the other hand, four studies find the free energy of the open state to be lower than the closed state for unligated AdK [24,61,66,74] with several others indirectly supporting this result, having found their simulations to have a preference for the open confor-mation. [8,23,72] Across all studies, there are large discrepancies in the estimated free energy differences between the two states, and at present the source of the discrepancy is not obvious.…”

Section: Conformational Equilibrium Between Open and Closed Statesmentioning

confidence: 99%

“…Other order parameter pairs to characterize 2D motions include the RMSD to/from the final and/or initial structure(s) [23,59,61,62], essential variables from PCA or NMA [8,23,43,65,69,70], and fractions of native contacts relative to the initial and final structures [16,59]. Lou and Cukier [71], Brokaw and Chu [72], and Pontiggia et al [73] all measure NMP-CORE separation with the distance between residues 55 and 169, but each, respectively, monitor LID-CORE variation differently: LID-CORE mass-center distance [71], C α distance between residues 127 and 194 [72], and LID-CORE angle [73]. Progress along one dimension (e.g., plotting the potential of mean force) was captured using domain mass-center distances [24,58,69,74], RMSD to and/or from crystal structures [15,61,67,75], and indices or distances along a computed reaction coordinate pathway [24,47,48,66,76,77].…”

Section: Collective Variables Describing the Adk Transitionmentioning

confidence: 99%

“…Comparison of such distances with the thermodynamic free energy landscape derived from MD simulations [31] showed that the distance between residues A55-V169 (NMP-CORE, Sinev et al [37]) and A127-A194 (LID-CORE, Hanson et al [39]) track the major conformational changes in apo-AdK in an almost orthogonal manner. A 2D space spanned by these two observables can serve to study the conformational dynamics of AdK at the level of individual domain motions Collective variables/Order parameters References 1D LID/NMP-CORE MCD [24,58,61,69,74] RMSD (to an end structure) [15,61,67,75] Indices along Rxn Coordinate [24,47,48,66,76,77] 2D LID/NMP-CORE MCD [24,58,[61][62][63][64][65][66] LID/NMP-CORE angle [15,31,59,67,68] RMSD (to end structures) [23,59,62] Essential Variables [8,23,43,65,69,70] Fraction of Native Contacts [16,59] Other [71][72]…”

Section: Experimental Fret Distances As Collective Variablesmentioning

confidence: 99%

See 1 more Smart Citation

Sampling large conformational transitions: adenylate kinase as a testing ground

Seyler

Beckstein

2014

Molecular Simulation

View full text Add to dashboard Cite

A fundamental problem in computational biophysics is to deduce the function of a protein from the structure. Many biological macromolecules such as enzymes, molecular motors, or membrane transport proteins perform their function by cycling between multiple conformational states. Understanding such conformational transitions, which typically occur on the millisecond to second time scale, is central to understanding protein function. Molecular dynamics (MD) computer simulations have become an important tool to connect molecular structure to function but equilibrium MD simulations are rarely able to sample on time scales longer than a few microseconds-orders of magnitudes shorter than the time scales of interest. A range of different simulation methods have been proposed to overcome this time-scale limitation. These include calculations of the free energy landscape and path sampling methods to directly sample transitions between known conformations. All these methods solve the problem to sample infrequently occupied but important regions of configuration space. Many path-sampling algorithms have been applied to the closed ↔ open transition of the enzyme adenylate kinase (AdK), which undergoes a large, clamshell-like conformational transition between an open and a closed state. Here we review approaches to sample macromolecular transitions through the lens of AdK. We focus our main discussion on the current state of knowledge-both from simulations and experiments-about the transition pathways of ligand-free AdK, its energy landscape, transition rates, and interactions with substrates. We conclude with a comparison of the discussed approaches with a view towards quantitative evaluation of path-sampling methods.

show abstract

How Simulations Reveal Dynamics, Disorder, and the Energy Landscapes of Biomolecular Function

Noel

Whitford

2014

Israel Journal of Chemistry

View full text Add to dashboard Cite

Over the last 40 years, the area of computational molecular biophysics has grown and developed to the point where simulations can now provide detailed mechanistic insights, suggest theoretical principles that underpin function, and provide frameworks for understanding and interpreting experimental measurements. The success of molecular simulations has been the result of the unrelenting development of novel theoretical models, exponential growth in computational resources, and advances in structural biology techniques. Through the continued refinement and application of diverse classes of models, general themes in biomolecular dynamics are beginning to surface. In particular, molecular simulations are highlighting the pervasive role that orderdisorder events play in molecular biology. These dynamic modes of function are transforming our perspective on the role that entropy has in many large‐scale biological processes.

show abstract

On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

Cited by 48 publications

References 74 publications

Transitions to catalytically inactive conformations in EGFR kinase

Transitions to catalytically inactive conformations in EGFR kinase

Sampling large conformational transitions: adenylate kinase as a testing ground

How Simulations Reveal Dynamics, Disorder, and the Energy Landscapes of Biomolecular Function

Contact Info

Product

Resources

About