Critical Residues In Proteins Research Articles

Base-editing mutagenesis maps alleles to tune human T cell functions.

CRISPR-enabled screening is a powerful tool for the discovery of genes that control T cell function and has nominated candidate targets for immunotherapies1-6. However, new approaches are required to probe specific nucleotide sequences within key genes. Systematic mutagenesis in primary human T cells could reveal alleles that tune specific phenotypes. DNA base editors are powerful tools for introducing targeted mutations with high efficiency7,8. Here we develop a large-scale base-editing mutagenesis platform with the goal of pinpointing nucleotides that encode amino acid residues that tune primary human T cell activation responses. We generated a library of around 117,000 single guide RNA molecules targeting base editors to protein-coding sites across 385 genes implicated in T cell function and systematically identified protein domains and specific amino acid residues that regulate T cell activation and cytokine production. We found a broad spectrum of alleles with variants encoding critical residues in proteins including PIK3CD, VAV1, LCP2, PLCG1 and DGKZ, including both gain-of-function and loss-of-function mutations. We validated the functional effects of many alleles and further demonstrated that base-editing hits could positively and negatively tune T cell cytotoxic function. Finally, higher-resolution screening using a base editor with relaxed protospacer-adjacent motif requirements9 (NG versus NGG) revealed specific structural domains and protein-protein interaction sites that can be targeted to tune T cell functions. Base-editing screens in primary immune cells thus provide biochemical insights with thepotential to accelerate immunotherapy design.

Global computational mutagenesis provides a critical stability framework in protein structures.

A protein’s amino acid sequence dictates the folds and final structure the macromolecule will form. We propose that by identifying critical residues in a protein’s atomic structure, we can select a critical stability framework within the protein structure essential to proper protein folding. We use global computational mutagenesis based on the unfolding mutation screen to test the effect of every possible missense mutation on the protein structure to identify the residues that cannot tolerate a substitution without causing protein misfolding. This method was tested using molecular dynamics to simulate the stability effects of mutating critical residues in proteins involved in inherited disease, such as myoglobin, p53, and the 15th sushi domain of complement factor H. In addition we prove that when the critical residues are in place, other residues may be changed within the structure without a stability loss. We validate that critical residues are conserved using myoglobin to show that critical residues are the same for crystal structures of 6 different species and comparing conservation indices to critical residues in 9 eye disease-related proteins. Our studies demonstrate that by using a selection of critical elements in a protein structure we can identify a critical protein stability framework. The frame of critical residues can be used in genetic engineering to improve small molecule binding for drug studies, identify loss-of-function disease-causing missense mutations in genetics studies, and aide in identifying templates for homology modeling.

Methods for Detecting Critical Residues in Proteins.

In proteins, certain amino acids may play a critical role in determining their structure and function. Examples include flexible regions, which allow domain motions, and highly conserved residues on functional interfaces, which play a role in binding and interaction with other proteins. Detecting these regions facilitates the analysis and simulation of protein rigidity and conformational changes, and aids in characterizing protein-protein binding. We present a protocol that combines graph-theory rigidity analysis and machine-learning-based methods for predicting critical residues in proteins. Our approach combines amino-acid specific information and data obtained by two complementary methods. One method, KINARI, performs graph-based analysis to find rigid clusters of amino acids in a protein, while the other method relies on evolutionary conservation scores to find functional interfaces in proteins. Our machine learning model combines both methods, in addition to amino acid type and solvent-accessible surface area.

A conservation and rigidity based method for detecting critical protein residues

BackgroundCertain amino acids in proteins play a critical role in determining their structural stability and function. Examples include flexible regions such as hinges which allow domain motion, and highly conserved residues on functional interfaces which allow interactions with other proteins. Detecting these regions can aid in the analysis and simulation of protein rigidity and conformational changes, and helps characterizing protein binding and docking. We present an analysis of critical residues in proteins using a combination of two complementary techniques. One method performs in-silico mutations and analyzes the protein's rigidity to infer the role of a point substitution to Glycine or Alanine. The other method uses evolutionary conservation to find functional interfaces in proteins.ResultsWe applied the two methods to a dataset of proteins, including biomolecules with experimentally known critical residues as determined by the free energy of unfolding. Our results show that the combination of the two methods can detect the vast majority of critical residues in tested proteins.ConclusionsOur results show that the combination of the two methods has the potential to detect more information than each method separately. Future work will provide a confidence level for the criticalness of a residue to improve the accuracy of our method and eliminate false positives. Once the combined methods are integrated into one scoring function, it can be applied to other domains such as estimating functional interfaces.

Site-specific AGE modifications in the extracellular matrix: a role for glyoxal in protein damage in diabetes

Non-enzymatic modification of proteins in hyperglycemia is a major proposed mechanism of diabetic complications. Specifically, advanced glycation end products (AGEs) derived from hyperglycemia-induced reactive carbonyl species (RCS) can have pathogenic consequences when they target functionally critical protein residues. Modification of a small number of these critical residues, often undetectable by the methodologies relying on measurements of total AGE levels, can cause significant functional damage. Therefore, detection of specific sites of protein damage in diabetes is central to understanding the molecular basis of diabetic complications and for identification of biomarkers which are mechanistically linked to the disease. The current paradigm of RCS-derived protein damage places a major focus on methylglyoxal (MGO), an intermediate of cellular glycolysis. We propose that glyoxal (GO) is a major contributor to extracellular matrix (ECM) damage in diabetes. Here, we review the current knowledge and provide new data about GO-derived site-specific ECM modification in experimental diabetes.

The 6th Computational Structural Bioinformatics Workshop

The rapid accumulation of macromolecular structures presents a unique set of challenges and opportunities in the analysis, comparison, modeling, and prediction of macromolecular structures and interactions. The 6th Computational Structural Bioinformatics Workshop (CSBW) was held in Philadelphia on October 4, 2012. This issue includes eleven papers selected from the work presented at the CSBW of 2012. In "Four-body atomic potential for modeling protein-ligand binding affinity: application to enzyme-inhibitor binding energy prediction", a predictive model of free-energy was built to evaluate the binding between a protein and a ligand. In "Unbiased, scalable sampling of protein loop conformations from probabilistic priors", a new Markov chain Monte Carlo algorithm was proposed to generate unbiased conformations of closed protein loops from probabilistic priors. In "Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce", authors demonstrate an enhanced method by cutting a long RNA sequence into smaller chunks at strategically selected points, and distributing the tasks to multiple processors. In "A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction", the authors present an evolutionary search algorithm to obtain a discrete representation of the protein energy surface in terms of an ensemble of conformations representing local energy minima. In "Estimating loop length from Cryo-EM images at medium resolutions", the authors developed a computational geometry method to simplify the points along the skeleton to measure loop length in 3D images. The paper "A conservation and rigidity based method for detecting critical protein residues" presents a method that combines the rigidity and the evolutionary conservation in detection of the critical residues. In "A conservation and biophysics guided stochastic approach to refining docked multimeric proteins", the authors introduce a refinement method that accepts complexes consisting of any number of monomeric units. In "Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method," the authors present a robotics-inspired tree-based method to sample energetically-credible conformational pathways connecting diverse functional states in multimodal proteins. The paper "An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility" applies protein structure prediction algorithms to enhance the classification of homologous proteins according to their binding preferences. In "DINC: A new AutoDock-based protocol for docking large ligands", an enhanced method was demonstrated for docking large ligands. The paper "Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods" presents an efficient approach involving robotics concepts.

Overexpression of myristoylated methionine sulfoxide reductase A in the mouse protects the heart against ischemia‐reperfusion injury

Methionine sulfoxide reductase A (MsrA) has been reported to function as an antioxidant protein, either by scavenging reactive oxygen species via cyclic interconversion of the reduced and oxidized forms of methionine residues or by protecting critical protein residues from oxidation. However, the mechanisms and requirements for providing an effective oxidative defense in vivo are not known. In mammalian cells, ~75% of MsrA is located in the cytosol and is myristoylated while ~25% is in the mitochondria and not myristoylated. We created several strains of transgenic mice overexpressing MsrA directed to the cytosol or mitochondria or both. Quantitative Western blotting and activity measurements demonstrated a high level of functional MsrA in most tissues tested, with the highest in the heart. We tested whether the increased MsrA in heart protected against ischemia‐reperfusion injury in a Langendorff model. We found that MsrA overexpression in the cytosol but not in the mitochondria protected. We then examined whether myristoylation affected this protection. We created another transgenic mouse overexpressing MsrA only in the cytosol, but in this strain glycine at position 2 was mutated to alanine to prevent myristoylation. Analysis of heart tissue confirmed that the overexpressed MsrA was active but not myristoylated. However, this non‐myristoylated MsrA heart experienced no protection. These experimental results indicate that myristoylation of cytosolic MsrA is key to its ability to provide cardioprotection.This research was supported by the Intramural Research Program of the NIH, NHLBI.

All-codon scanning identifies p53 cancer rescue mutations

In vitro scanning mutagenesis strategies are valuable tools to identify critical residues in proteins and to generate proteins with modified properties. We describe the fast and simple All-Codon Scanning (ACS) strategy that creates a defined gene library wherein each individual codon within a specific target region is changed into all possible codons with only a single codon change per mutagenesis product. ACS is based on a multiplexed overlapping mutagenesis primer design that saturates only the targeted gene region with single codon changes. We have used ACS to produce single amino-acid changes in small and large regions of the human tumor suppressor protein p53 to identify single amino-acid substitutions that can restore activity to inactive p53 found in human cancers. Single-tube reactions were used to saturate defined 30-nt regions with all possible codon changes. The same technique was used in 20 parallel reactions to scan the 600-bp fragment encoding the entire p53 core domain. Identification of several novel p53 cancer rescue mutations demonstrated the utility of the ACS approach. ACS is a fast, simple and versatile method, which is useful for protein structure–function analyses and protein design or evolution problems.

Exhaled NO and iNOS expression in sputum cells of healthy, obese and OSA subjects

Obstructive sleep apnoea (OSA) is associated with airways inflammation; a key role in this regard seems to be played by nitric oxide (NO). The aim of this study was to measure exhaled NO and expression of its enzyme, the inducible nitric oxide synthase (iNOS) in cells of induced sputum in OSA patients and in obese subjects without sleep apnoea and to correlate these inflammatory markers with severity of OSA. We enrolled 18 obese patients with OSA (10 men, age 48.2 +/- 8.4 years), 15 obese patients without OSA (eight men, age 52.8 +/- 11 years) and 10 healthy subjects (five men, age 42 +/- 4 years). Exhaled NO was measured using a chemiluminescence analyser; iNOS expression was measured in the sputum cells by immunocytochemistry. Exhaled NO resulted significantly increased in OSA and in obese patients (23.1 +/- 2.1 and 17.9 +/- 2.1 p.p.b.) than in healthy subjects (7.2 +/- 0.6 p.p.b.; P < 0.001). OSA and obese patients showed a higher percentage of neutrophils and a lower percentage of macrophages in the induced sputum compared to healthy subjects. In addition, OSA and obese patients showed higher iNOS expression in neutrophils and in macrophages with respect to healthy subjects. A positive correlation between exhaled NO, iNOS expression and AHI was observed. These data confirm the presence of airway inflammation in OSA and in obese patients, and suggest the possible role for NO and iNOS expression in neutrophils of the induced sputum as noninvasive markers to identify and monitor the airway inflammation in these subjects.

Plasticity in cell defence: access to and reactivity of critical protein residues and DNA response elements

Cellular and whole organ defence against pathogenic or chemical challenge is manifest as an adaptive response. Where appropriate, this may lead to induction of a cellular defence programme, thereby enhancing cell survival. When the challenge is overwhelming, the defence is breached and a switch is made to yield cell death, either by apoptosis or necrosis. Thus, a cell will defend itself where possible, but in extremis, it may recognise the futility of its resistance and allow itself to die. Transcription factor activation and access to the DNA regulatory elements that control a particular pattern of expression of defence genes is a major issue that may ultimately decide the fate of a cell in a changed environment. It is possible to visualise the access to the nucleus and to the genome, of paradigm gene loci or transcription factors, using a number of molecular techniques such as chromatin immunoprecipitation, in vivo footprinting and live/whole cell imaging. These methods are informative as to the array of transcription factors that may regulate a given gene, as well as the transitory nature of the transcriptional activation. The initial triggering of active transcription factor complexes typically occurs within the cytoplasm of the cell. Protein-protein interactions and signal transduction pathways, elucidated using a classical molecular genetics approach, have long been recognised as pivotal to the initial control of the levels and activity of transcription factors. We can now visualise modifications in critical residues of transcription factors and regulators during cellular response to chemical stress. These modifications may yield enhanced or repressed activity of transcription factors, they may be non-covalent or covalent, and they may occur in response to a variety of classes of chemicals. Such promiscuous signalling can provide plasticity in the cellular response to a wide array of chemical agents.

Nitric oxide and nitrotyrosine in the lungs of patients with acute respiratory distress syndrome.

Nitric oxide (NO) end-products (nitrate and nitrite) are present in bronchoalveolar lavage (BAL) fluid of patients with inflammatory lung diseases. Reactive oxygen-nitrogen intermediates damage macromolecules by oxidation or nitration of critical residues in proteins. The goal of this study was to measure NO end-products (nitrate+ nitrite), in BAL fluid before and after the onset of acute respiratory distress syndrome (ARDS) and to determine if these products are associated with expression of inducible nitric oxide synthase enzyme (iNOS) in BAL cells and nitration of BAL proteins. We performed bronchoalveolar lavage (BAL) in patients at risk for ARDS (n = 19), or with ARDS (n = 41) on Days 1, 3, 7, 14, and 21 after onset, and measured total nitrite (after reducing nitrate to nitrite) and protein-associated nitrotyrosine concentration in each BAL fluid sample. Cytospin preparations of BAL cells were analyzed by immunocytochemistry for iNOS and nitrotyrosine. Nitrate+nitrite were detected in BAL fluid from patients at risk for ARDS, and for as long as 21 d after the onset of ARDS. Nitrotyrosine was detectable in all BAL fluid samples for as long as 14 d after the onset of ARDS (range, 38.8 to 278.5 pmol/mg of protein), but not in BAL of normal volunteers. Alveolar macrophages of patients with ARDS were positive for iNOS and nitrotyrosine, and remained positive for as long as 14 d after onset of ARDS. The BAL nitrate+nitrite did not predict the onset of ARDS, but the concentration was significantly higher on Days 3 and 7 of ARDS in patients who died. Thus, NO end products accumulate in the lungs before and after onset of ARDS; iNOS is expressed at high levels in AM during ARDS; and nitration of intracellular and extracellular proteins occurs in the lungs in ARDS. The data support the concept that NO-dependent pathways are important in the lungs of patients before and after the onset of ARDS.

Investigation of ionizable residues critical for sequence-specific enzymatic DNA modification: protein modification and steady-state and pre-steady-state kinetic pH analyses of EcoRI DNA methyltransferase.

Steady-and pre-steady-state pH kinetic analyses are widely used methods to investigate important ionizable groups in enzyme-catalyzed reactions. The first such analysis to identify ionizable residues critical for sequence-specific modification of DNA is presented. EcoRI DNA methyltransferase uses S-adenosyl-L-methionine (AdoMet) to catalyze the N6 methylation of the second adenine in the double-stranded DNA sequence GAATTC. The kinetic mechanism was previously shown to be steady-state-ordered bi bi in which AdoMet binds first followed by DNA addition [Reich, N. O., & Mashhoon, N. (1991) Biochemistry 30, 2933-2939]. Steady-state parameters are strongly dependent on pH and implicate at least four residues with pKa values between 8.2 and 8.9 in the free enzyme and AdoMet-Bound enzyme and one residue with an apparent pKa of 6.0. The data obtained are consistent with the enzyme binding the form of AdoMet in which the alpha amino group is protonated. Two protein residues with an apparent pKa between 8.9 and 9.2 were implicated within the central complex (enzyme-DNA-AdoMet). The general insensitivity of all steady-state parameters to pH changes between pH 6.0 and 8.0 suggests that no critical protein residues undergo ionization-state changes in this range. The lack of significant pH-dependent changes in protein fluorescence and DNA thermal stability suggests minimal structural changes in either macromolecule. In support of the steady-state results single-turnover experiments reveal minimal pH dependence of the methylation rate constant between pH 5.53 and 8.6. Thus, no amino acids critical for catalysis undergo ionization-state changes in this range.(ABSTRACT TRUNCATED AT 250 WORDS)

Engineering an enzyme by site-directed mutagenesis to be resistant to chemical oxidation.

Site-directed mutagenesis can be employed to alter activity critical residues in proteins which are susceptible to chemical oxidation. Previous studies have implicated methionine 222 as a primary site for oxidative inactivation of subtilisin (Stauffer, C. E., and Etson, D. (1969) J. Biol. Chem. 244, 5333-5338). Because of uncertainties in predicting which amino acid would be the optimal substitute for methionine 222, we prepared all 19 amino acid substitutions at this site in the cloned subtilisin gene using a cassette mutagenesis method (Wells, J. A., Vasser, M., and Powers, D. P. (1985) Gene (Amst.), in press). Mutant enzymes were expressed in Bacillus subtilis and were found to vary widely in specific activity. Mutants containing nonoxidizable amino acids (i.e. Ser, Ala, and Leu) were resistant to inactivation by 1 M H2O2, whereas methionine and cysteine enzymes were rapidly inactivated. These studies demonstrate the feasibility of improving oxidative stability in proteins by site-directed mutagenesis.

Enzymatic activation of chemicals to toxic metabolites.

A variety of enzymes function in the oxygenation, oxidation-reduction, conjugation, and hydrolysis of drugs and other foreign chemicals. Often these enzymes detoxicate chemicals to prevent detrimental effects. In this review we will, however, concentrate on cases in which metabolism activates chemicals to reactive species which cause cellular damage. Particular attention will be given to mixed-function oxidases, which carry out a variety of oxygenations, as well as other reactions. (We will focus on cellular toxicity as opposed to initiation of tumorigenesis in this review.) In many cases, considerable circumstantial evidence exists linking these enzymes to enhanced toxicity of chemicals, although causal relationships have seldom been demonstrated. Further, in very few cases is the explicit cause of toxicity known. Modification of critical protein residues is suspected, although oxidative stress may also be involved in some cases. We discuss general aspects of mechanisms of toxic action, briefly list all cases in which metabolism is suspected to play a role in enhancing toxicity, and review a few examples in detail where substantial chemical and enzymatic information is available. The latter instances would involve knowledge of the enzymes involved, chemical evidence on the structures of the reactive metabolites, identification of adducts, and some inference into the biological processes which are effected to elicit toxicity. We consider, in this regard, vinyl halides (which have been a focus in our own laboratory), acetaminophen, pyrrolizidine alkaloids, and fluoroxene.