Local frustration around enzyme active sites

Freiberger, María I.; Guzovsky, A. Brenda; Wolynes, Peter G.; Parra, R. Gonzalo; Ferreiro, Diego U.

doi:10.1073/pnas.1819859116

Cited by 64 publications

(73 citation statements)

References 27 publications

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“…We show that this chemical specificity derives from a unique energetic landscape dictated by the protein matrix, which dictates the spectrum of posttranslational modifications by minimizing local structural frustration, while exploiting steric hindrance and low nucleophilicity. This work illustrates how the “minimal frustration principle” previously applied to allosteric communication 43,44 and enzymatic activity 45 dictates chemical specificity when supramolecular chemistry determined by the protein structure is critical to understand biological outcomes.…”

Section: Figurementioning

confidence: 78%

“…The conformational frustration patterns were calculated using the protein Frustratometer software (www.frustratometer.tk/) 45,53 . This software that has been described in more detail elsewhere 45,53 and has been extensively used to classify energetic frustration in different folded proteins 44,45,53,54 . It determines the local frustration by evaluating how favorable a specific contact is relative to the set of all possible contacts in that location.…”

Section: Methodsmentioning

confidence: 99%

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Structural determinants of persulfide-sensing specificity in a dithiol-based transcriptional regulator

Capdevila¹,

Walsh²,

Zhang³

et al. 2020

Preprint

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1Cysteine thiol-based transcriptional regulators orchestrate coordinated regulation of redox homeostasis 2 and other cellular processes by "sensing" or detecting a specific redox-active molecule, which in turn 3 activates the transcription of a specific detoxification pathway. The extent to which these sensors are 4 truly specific in cells for a singular class of reactive small molecule stressors, e.g., reactive oxygen or 5 sulfur species, is largely unknown. Here we report novel structural and mechanistic insights into a thiol-6 based transcriptional repressor SqrR, that reacts exclusively with organic and inorganic oxidized sulfur 7 species, e.g., persulfides, to yield a unique tetrasulfide bridge that allosterically inhibits DNA operator-8 promoter binding. Evaluation of five crystallographic structures of SqrR in various derivatized states, 9 coupled with the results of a mass spectrometry-based kinetic profiling strategy, suggest that persulfide 1 0 selectivity is determined by structural frustration of the disulfide form. This energetic roadblock 1 1 effectively decreases the reactivity toward major oxidants to kinetically favor formation of the 1 2 tetrasulfide product. These findings lead to the identification of an uncharacterized repressor from the 1 3 increasingly antibiotic-resistant bacterial pathogen, Acinetobacter baumannii, as a persulfide sensor, 1 4illustrating the predictive power of this work and potential applications to bacterial infectious disease. 1 5 1 6Regulatory posttranslational modifications on thiol groups of redox-active and allosterically important 1 cysteines are a critical component of signaling and redox regulation in cells 1-3 . The successful 2 adaptation of microorganisms to an ever-changing microenvironment depends, to a considerable degree, 3 on the specificity of the regulation of the expression of needed repair enzymes 4-6 . Understanding the 4 extent to which transcriptional regulation is specific to a particular redox-active small molecule(s) is 5 complicated by cross-talk or interconversion among these species in cells 7,8 and the difficulties 6 associated with identifying a posttranslational modification that is biologically meaningful at cell-7 appropriate concentrations that induce a cellular response 9 . Prominent exceptions to this are a handful 8 of transcriptional regulators that employ a metallated cofactor, such as a mononuclear iron 10,11 , an iron-9 sulfur cluster 12,13 or a heme-based sensing moeity 14 ; here, the local inorganic chemistry alone is 1 0 typically sufficient to explain the specificity of these switches toward their inducer 15 . In fact, it remains 1 1 unclear if and how a non-metallated, dithiol-based transcriptional regulator achieves a similar level of 1 2 specificity toward different cellular oxidants.

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Section: Figurementioning

confidence: 78%

Section: Methodsmentioning

confidence: 99%

Structural determinants of persulfide-sensing specificity in a dithiol-based transcriptional regulator

Capdevila¹,

Walsh²,

Zhang³

et al. 2020

Preprint

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“…the higher mutational robustness of the surface of small proteins compared to the surface of longer proteins, can be explained by the larger fraction of functional residues. These residues are known to be well optimized for function but poorly for stability [20,37]. Therefore, their substitutions are likely to be stabilizing, which confers a higher mutational robustness to the surface of small proteins.…”

Section: Protein Lengthmentioning

confidence: 99%

Large-scalein silicomutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness

Schwersensky

Rooman

Pucci

2020

Preprint

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The question of how natural evolution acts on DNA and protein sequences to ensure mutational robustness and evolvability has been asked for decades without definitive answer. We tackled this issue through a structurome-scale computational investigation, in which we estimated the change in folding free energy upon all possible single-site mutations introduced in more than 20,000 protein structures. The validity of our results are supported by a very good agreement with experimental mutagenesis data. At the amino acid level, we found the protein surface to be more robust to mutations than the core, in a protein length-dependent manner. About 4% of all mutations were shown to be stabilizing, and a majority of mutations on the surface and in the core to be neutral and destabilizing, respectively. At the nucleobase level, single base substitutions were shown to yield on average less destabilizing amino acid mutations than multiple base substitutions. More precisely, the smallest average destabilization occurs for substitutions of base III in the codon, followed by base I, bases I+III, and base II. This ranking highly anticorrelates with the frequency of codon-anticodon mispairing, and suggests that the standard genetic code is optimized more to limit translation errors than the impact of random mutations. Moreover, the codon usage also appears to be optimized for minimizing the errors at the protein level, especially for surface residues that evolve faster and have therefore been under stronger selection, and for biased codons, suggesting that the codon usage bias also partly aims to optimize protein mutational robustness.

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“…However, characterization of the relationship between HLA polymorphism and pMHC stability as well as TCR/KIR/PLC interactions requires the modeling of the whole complex and the use of proper methods for identifying residue-level effects on stability and protein interactions. To this end, quantification of local frustration in the structure can be utilized [45–49]. Local frustration analysis has already been applied successfully to perform similar sequence-structure-function studies on calmodulin [50,51], repeat proteins [5,52], and TEM beta-lactamases [6].…”

Section: Introductionmentioning

confidence: 99%

Sequence-structure-function relationships in class I MHC: a local frustration perspective

Serçinoğlu

Ozbek

2019

Preprint

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12 Class I Major Histocompatibility Complex (MHC) binds short antigenic peptides with the 13 help of Peptide Loading Complex (PLC), and presents them to T-cell Receptors 14 (TCRs) of cytotoxic T-cells and Killer-cell Immunglobulin-like Receptors (KIRs) of 15 Natural Killer (NK) cells. With more than 10000 alleles, the Human Leukocyte Antigen 16 (HLA) chain of MHC is the most polymorphic protein in humans. This allelic diversity 17 provides a wide coverage of peptide sequence space, yet does not affect the three-18 dimensional structure of the complex. Moreover, TCRs mostly interact with pMHC in a 19 common diagonal binding mode, and KIR-pMHC interaction is allele-dependent. With 20 the aim of establishing a framework for understanding the relationships between 21 polymorphism (sequence), structure (conserved fold) and function (protein interactions) 22 of the MHC, we performed here a local frustration analysis on pMHC homology models 23 covering 1436 HLA I alleles. An analysis of local frustration profiles indicated that (1) 24 variations in MHC fold are unlikely due to minimally-frustrated and relatively conserved 25 residues within the HLA peptide-binding groove, (2) high frustration patches on HLA 26 helices are either involved in or near interaction sites of MHC with the TCR, KIR, or 27 Tapasin of the PLC, and (3) peptide ligands mainly stabilize the F-pocket of HLA 28 binding groove. 29 Author Summary30 A protein complex called the Major Histocompatibility Complex (MHC) plays a critical 31 role in our fight against pathogens via presentation of antigenic peptides to receptor 32 molecules of our immune system cells. Our knowledge on genetics, structure and 33 protein interactions of MHC revealed that the peptide-binding groove of Human 3 34 Leukocyte Chain (HLA I) of this complex is highly polymorphic and interacts with 35 different proteins for peptide-binding and presentation over the course of its lifetime.36 Although the relationship between polymorphism and peptide-binding is well-known, 37 we still lack a proper framework to understand how this polymorphism affects the 38 overall MHC structure and protein interactions. Here, we used computational 39 biophysics methods to generate structural models of 1436 HLA I alleles, and quantified 40 local frustration within the HLA I, which indicates energetic optimization levels of 41 contacts between amino acids. We identified a group of minimally frustrated and 42 conserved positions which may be responsible for the conserved MHC structure, and 43 detected high frustration patches on HLA surface positions taking part in interactions 44 with other immune system proteins. Our results provide a biophysical basis for 45 relationships between sequence, structure, and function of MHC I. 46 4 47 48The sequence-structure-function paradigm plays a central role in structural 49 biology: the primary structure (i.e. amino acid sequence) of a protein dictates the three-50 dimensional structure (fold), which in turn influences the function [1-3]. The close 51 relationship bet...

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Local frustration around enzyme active sites

Cited by 64 publications

References 27 publications

Structural determinants of persulfide-sensing specificity in a dithiol-based transcriptional regulator

Structural determinants of persulfide-sensing specificity in a dithiol-based transcriptional regulator

Large-scalein silicomutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness

Sequence-structure-function relationships in class I MHC: a local frustration perspective

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