Molecular basis for the allosteric activation mechanism of the heterodimeric imidazole glycerol phosphate synthase complex

Wurm, Jan Philip; Sung, Sihyun; Kneuttinger, Andrea Christa; Hupfeld, Enrico; Sterner, Reinhard; Wilmanns, Matthias; Sprangers, Remco

doi:10.1038/s41467-021-22968-6

Cited by 31 publications

(79 citation statements)

References 62 publications

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“…This conformation, characterized by the alignment of h α1 and f α3 helices, is transiently populated in the substrate-free simulations and resembles the substrate-bound X-ray closed state of the catalytically inactive h C84A IGPS. 32 Our simulations indicate that a closed state of the HisF:HisH interface can be attained in solution, even in the absence of l -Gln or PRFAR. These results are consistent with the idea that productive HisF:HisH closure is key for efficient catalysis and for retaining the substrate during glutamine hydrolysis and preventing the loss of the produced ammonia to the media.…”

Section: Discussionmentioning

confidence: 66%

“…The ability of l -Gln to bind only the inactive-OxH conformation in the presence of PRFAR is in line with recent solution NMR experiments of the h C84S IGPS variant. 32 …”

Section: Resultsmentioning

confidence: 99%

“…More importantly, this active-OxH conformation of wt IGPS revealed by means of extensive aMD simulations presents significant similarities with the recently obtained allosterically activated h C84A IGPS X-ray structure ( Figure S29 ). 32 Altogether, μs-aMD simulations unraveled, without using a priori information of the active state, the catalytically competent pose corresponding to the allosterically active ternary complex of wt IGPS.…”

Section: Resultsmentioning

confidence: 99%

“… 26 , 29 , 30 However, the rapid turnover observed in wt IGPS and the instability of the effector PRFAR prevented the experimental detection of the allosterically active state in the wild-type enzyme, which still remains elusive. 32 The millisecond allosteric activation of IGPS challenges the computational elucidation of these functionally relevant states and the characterization of the time evolution of the conformational ensemble upon ternary complex formation. In this work, a computational strategy tailored to reconstruct millisecond time scale events was devised to describe, step by step, the allosteric activation of IGPS at the molecular level, from the inactive substrate-free form to the active ternary complex.…”

Section: Discussionmentioning

confidence: 99%

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Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase

et al. 2022

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Deciphering the molecular mechanisms of enzymatic allosteric regulation requires the structural characterization of functional states and also their time evolution toward the formation of the allosterically activated ternary complex. The transient nature and usually slow millisecond time scale interconversion between these functional states hamper their experimental and computational characterization. Here, we combine extensive molecular dynamics simulations, enhanced sampling techniques, and dynamical networks to describe the allosteric activation of imidazole glycerol phosphate synthase (IGPS) from the substrate-free form to the active ternary complex. IGPS is a heterodimeric bienzyme complex whose HisH subunit is responsible for hydrolyzing glutamine and delivering ammonia for the cyclase activity in HisF. Despite significant advances in understanding the underlying allosteric mechanism, essential molecular details of the long-range millisecond allosteric activation of IGPS remain hidden. Without using a priori information of the active state, our simulations uncover how IGPS, with the allosteric effector bound in HisF, spontaneously captures glutamine in a catalytically inactive HisH conformation, subsequently attains a closed HisF:HisH interface, and finally forms the oxyanion hole in HisH for efficient glutamine hydrolysis. We show that the combined effector and substrate binding dramatically decreases the conformational barrier associated with oxyanion hole formation, in line with the experimentally observed 4500-fold activity increase in glutamine hydrolysis. The allosteric activation is controlled by correlated time-evolving dynamic networks connecting the effector and substrate binding sites. This computational strategy tailored to describe millisecond events can be used to rationalize the effect of mutations on the allosteric regulation and guide IGPS engineering efforts.

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Section: Discussionmentioning

confidence: 66%

“…The ability of l -Gln to bind only the inactive-OxH conformation in the presence of PRFAR is in line with recent solution NMR experiments of the h C84S IGPS variant. 32 …”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase

et al. 2022

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“…However, often the functionality of these molecules depends on their ability to exchange between different conformational states. Thus, quantifying the interconversion between these states is an important first step towards understanding how these biomolecules work (Yang et al 2003;Karplus and Kuriyan 2005;Boehr et al 2006;Henzler-Wildman and Kern 2007;Faust et al 2020;Xie et al 2020;Wurm et al 2021). When conformational exchange is present, there is often one major populated state, the ground state, and a set of transiently low-populated states that, despite their low populations and short lifetimes, often play crucial roles for function.…”

Section: Introductionmentioning

confidence: 99%

Towards autonomous analysis of chemical exchange saturation transfer experiments using deep neural networks

et al. 2022

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Macromolecules often exchange between functional states on timescales that can be accessed with NMR spectroscopy and many NMR tools have been developed to characterise the kinetics and thermodynamics of the exchange processes, as well as the structure of the conformers that are involved. However, analysis of the NMR data that report on exchanging macromolecules often hinges on complex least-squares fitting procedures as well as human experience and intuition, which, in some cases, limits the widespread use of the methods. The applications of deep neural networks (DNNs) and artificial intelligence have increased significantly in the sciences, and recently, specifically, within the field of biomolecular NMR, where DNNs are now available for tasks such as the reconstruction of sparsely sampled spectra, peak picking, and virtual decoupling. Here we present a DNN for the analysis of chemical exchange saturation transfer (CEST) data reporting on two- or three-site chemical exchange involving sparse state lifetimes of between approximately 3–60 ms, the range most frequently observed via experiment. The work presented here focuses on the 1H CEST class of methods that are further complicated, in relation to applications to other nuclei, by anti-phase features. The developed DNNs accurately predict the chemical shifts of nuclei in the exchanging species directly from anti-phase 1HN CEST profiles, along with an uncertainty associated with the predictions. The performance of the DNN was quantitatively assessed using both synthetic and experimental anti-phase CEST profiles. The assessments show that the DNN accurately determines chemical shifts and their associated uncertainties. The DNNs developed here do not contain any parameters for the end-user to adjust and the method therefore allows for autonomous analysis of complex NMR data that report on conformational exchange.

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Stimulus‐Responsive Amino Acids Behind In Situ Assembled Bioactive Peptide Materials

et al. 2022

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In situ self-assembly of peptides into well-defined nanostructures represents one of versatile strategies for creation of bioactive materials within living cells with great potential in disease diagnosis and treatment. The intimate relationship between amino acid sequences and the assembling propensity of peptides has been thoroughly elucidated over the past few decades. This has inspired development of various controllable self-assembling peptide systems based on stimuli-responsive naturally occurring or non-canonical amino acids, including redox-, pH-, photo-, enzyme-responsive amino acids. This review attempts to summarize the recent progress achieved in manipulating in situ self-assembly of peptides by controllable reactions occurring to amino acids. We will highlight the systems containing non-canonical amino acids developed in our laboratory during the past few years, primarily including acid/enzyme-responsive 4-aminoproline, redox-responsive (seleno)methionine, and enzyme-responsive 2-nitroimidazolyl alanine. Utilization of the stimuli-responsive assembling systems in creation of bioactive materials will be specifically introduced to emphasize their advantages for addressing the concerns lying in disease theranostics. Eventually, we will provide the perspectives for the further development of stimulus-responsive amino acids and thereby demonstrating their great potential in development of next-generation biomaterials.

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Molecular basis for the allosteric activation mechanism of the heterodimeric imidazole glycerol phosphate synthase complex

Cited by 31 publications

References 62 publications

Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase

Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase

Towards autonomous analysis of chemical exchange saturation transfer experiments using deep neural networks

Stimulus‐Responsive Amino Acids Behind In Situ Assembled Bioactive Peptide Materials

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