Nathan Mih
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View article: Establishing comprehensive quaternary structural proteomes from genome sequence
Establishing comprehensive quaternary structural proteomes from genome sequence Open
A critical body of knowledge has developed through advances in protein microscopy, protein-fold modeling, structural biology software, availability of sequenced bacterial genomes, large-scale mutation databases, and genome-scale models. Ba…
View article: Establishing comprehensive quaternary structural proteomes from genome sequence
Establishing comprehensive quaternary structural proteomes from genome sequence Open
A critical body of knowledge has developed through advances in protein microscopy, protein-fold modeling, structural biology software, availability of sequenced bacterial genomes, large-scale mutation databases, and genome-scale models. Ba…
View article: Protein structure, a genetic encoding for glycosylation
Protein structure, a genetic encoding for glycosylation Open
DNA, RNA, and proteins are synthesized using template molecules, but glycosylation is not believed to be constrained by a template. However, if cellular environment is the only determinant of glycosylation, all sites should receive the sam…
View article: Establishing comprehensive quaternary structural proteomes from genome sequence
Establishing comprehensive quaternary structural proteomes from genome sequence Open
A critical body of knowledge has developed through advances in protein microscopy, protein-fold modeling, structural biology software, availability of sequenced bacterial genomes, large-scale mutation databases, and genome-scale models. Ba…
View article: Establishing comprehensive quaternary structural proteomes from genome sequence
Establishing comprehensive quaternary structural proteomes from genome sequence Open
A critical body of knowledge has developed through advances in protein microscopy, protein-fold modeling, structural biology software, availability of sequenced bacterial genomes, large-scale mutation databases, and genome-scale models. Ba…
View article: Genome‐scale metabolic modeling reveals key features of a minimal gene set
Genome‐scale metabolic modeling reveals key features of a minimal gene set Open
View article: Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types Open
The fitness landscape is a concept commonly used to describe evolution towards optimal phenotypes. It can be reduced to mechanistic detail using genome-scale models (GEMs) from systems biology. We use recently developed GEMs of Metabolism …
View article: Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes Open
Background The reconstruction of metabolic networks and the three-dimensional coverage of protein structures have reached the genome-scale in the widely studied Escherichia coli K-12 MG1655 strain. The combination of the two leads to the f…
View article: Additional file 1 of Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes
Additional file 1 of Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes Open
Additional file 1.
View article: Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment
Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment Open
Galactarate dehydratase (GarD) is the first enzyme in the galactarate/glucarate pathway and catalyzes the dehydration of galactarate to 3‐keto‐5‐dehydroxygalactarate. This protein is known to increase colonization fitness of intestinal pat…
View article: Expanding the uses of genome‐scale models with protein structures
Expanding the uses of genome‐scale models with protein structures Open
Biology is reaching a convergence point of its historic reductionist and modern holistic approaches to understanding the living system. Structural biology has historically taken the reductionist approach to deeply probe the inner workings …
View article: Cellular responses to reactive oxygen species are predicted from molecular mechanisms
Cellular responses to reactive oxygen species are predicted from molecular mechanisms Open
Catalysis using iron–sulfur clusters and transition metals can be traced back to the last universal common ancestor. The damage to metalloproteins caused by reactive oxygen species (ROS) can prevent cell growth and survival when unmanaged,…
View article: A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types Open
S. aureus is classified as a serious threat pathogen and is a priority that guides the discovery and development of new antibiotics. Despite growing knowledge of S. aureus metabolic capabilities, our understanding of its systems-level resp…
View article: Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant
Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant Open
View article: Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models Open
Knowing the catalytic turnover numbers of enzymes is essential for understanding the growth rate, proteome composition, and physiology of organisms, but experimental data on enzyme turnover numbers is sparse and noisy. Here, we demonstrate…
View article: Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance
Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance Open
Mycobacterium tuberculosis is a serious human pathogen threat exhibiting complex evolution of antimicrobial resistance (AMR). Accordingly, the many publicly available datasets describing its AMR characteristics demand disparate data-type a…
View article: Systematic discovery of uncharacterized transcription factors in <i>Escherichia coli</i> K-12 MG1655
Systematic discovery of uncharacterized transcription factors in <i>Escherichia coli</i> K-12 MG1655 Open
Transcriptional regulation enables cells to respond to environmental changes. Of the estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 have been experimentally identified, but ChIP methods have been u…
View article: Systematic discovery of uncharacterized transcription factors in<i>Escherichia coli</i>K-12 MG1655
Systematic discovery of uncharacterized transcription factors in<i>Escherichia coli</i>K-12 MG1655 Open
Transcriptional regulation enables cells to respond to environmental changes. Yet, among the estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 have been experimentally identified and only a few tens o…
View article: Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa Open
Taken together, these results suggest that the metabolic capabilities of B2 strains vary significantly from those of other strains, enabling B2 strains to colonize intestinal mucosa.The results from this study motivate a broad experimental…
View article: The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures
The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures Open
Two-component systems (TCSs) consist of a histidine kinase and a response regulator. Here, we evaluated the conservation of the AgrAC TCS among 149 completely sequenced Staphylococcus aureus strains. It is composed of four genes:
View article: The <i>Staphylococcus aureus</i> Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures
The <i>Staphylococcus aureus</i> Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures Open
Two-component systems (TCSs) consist of a histidine kinase and a response regulator. Here, we evaluated the conservation of the AgrAC TCS among 149 completely sequenced S. aureus strains. It is composed of four genes: agrBDCA . We found th…
View article: Recon3D enables a three-dimensional view of gene variation in human metabolism
Recon3D enables a three-dimensional view of gene variation in human metabolism Open
View article: ssbio: a Python framework for structural systems biology
ssbio: a Python framework for structural systems biology Open
Summary Working with protein structures at the genome-scale has been challenging in a variety of ways. Here, we present ssbio, a Python package that provides a framework to easily work with structural information in the context of genome-s…
View article: Additional file 1 of Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa
Additional file 1 of Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa Open
Table S1: Metadata of 110 strains. Table S2: Genes associated with mucus degradation. Table S3: Metabolic reactions added to previous reconstruction. (XLSX 32 kb)
View article: Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit
Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit Open
The computational representation of metabolic networks has traditionally abstracted the representation of enzymatic components that catalyze their associated reactions. However, the long history of reductionism in studying biological compo…
View article: Cellular responses to reactive oxygen species can be predicted on multiple biological scales from molecular mechanisms
Cellular responses to reactive oxygen species can be predicted on multiple biological scales from molecular mechanisms Open
Summary Catalysis using iron-sulfur clusters and transition metals can be traced back to the last universal common ancestor. The damage to metalloproteins caused by reactive oxygen species (ROS) can completely inhibit cell growth when unma…
View article: Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation
Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation Open
Significance How do bacteria adapt to the diverse thermal niches on earth? Evidence accumulates in the protein sequence and structural determinants of thermosensitivity and mechanisms by which molecular chaperones aid protein folding. Howe…
View article: iML1515, a knowledgebase that computes Escherichia coli traits
iML1515, a knowledgebase that computes Escherichia coli traits Open
View article: Global transcriptional regulatory network for <i>Escherichia coli</i> robustly connects gene expression to transcription factor activities
Global transcriptional regulatory network for <i>Escherichia coli</i> robustly connects gene expression to transcription factor activities Open
Significance While the transcriptional regulatory network (TRN) of Escherichia coli has expanded considerably in recent years through new chromatin immunoprecipitation (ChIP) data, an open question remains: Does the global TRN, reconstruct…
View article: ssbio: A Python Framework for Structural Systems Biology
ssbio: A Python Framework for Structural Systems Biology Open
Summary Working with protein structures at the genome-scale has been challenging in a variety of ways. Here, we present ssbio , a Python package that provides a framework to easily work with structural information in the context of genome-…