scholarly journals The Role of Rigid Residues in Modulating TEM-1 β-Lactamase Function and Thermostability

2021 ◽  
Vol 22 (6) ◽  
pp. 2895
Author(s):  
Bethany Kolbaba-Kartchner ◽  
I. Can Kazan ◽  
Jeremy H. Mills ◽  
S. Banu Ozkan
Keyword(s):  
Protein Dynamics ◽  
Protein Design ◽  
Active Site ◽  
Design Methods ◽  
Computational Protein Design ◽  
Protein Motions ◽  
Enzymatic Function ◽  
Function Relationship ◽  
And Function ◽  
The Relationship

The relationship between protein motions (i.e., dynamics) and enzymatic function has begun to be explored in β-lactamases as a way to advance our understanding of these proteins. In a recent study, we analyzed the dynamic profiles of TEM-1 (a ubiquitous class A β-lactamase) and several ancestrally reconstructed homologues. A chief finding of this work was that rigid residues that were allosterically coupled to the active site appeared to have profound effects on enzyme function, even when separated from the active site by many angstroms. In the present work, our aim was to further explore the implications of protein dynamics on β-lactamase function by altering the dynamic profile of TEM-1 using computational protein design methods. The Rosetta software suite was used to mutate amino acids surrounding either rigid residues that are highly coupled to the active site or to flexible residues with no apparent communication with the active site. Experimental characterization of ten designed proteins indicated that alteration of residues surrounding rigid, highly coupled residues, substantially affected both enzymatic activity and stability; in contrast, native-like activities and stabilities were maintained when flexible, uncoupled residues, were targeted. Our results provide additional insight into the structure-function relationship present in the TEM family of β-lactamases. Furthermore, the integration of computational protein design methods with analyses of protein dynamics represents a general approach that could be used to extend our understanding of the relationship between dynamics and function in other enzyme classes.

scholarly journals Network-based approaches to quantify multicellular development

2017 ◽  
Vol 14 (135) ◽  
pp. 20170484 ◽  
Author(s):  
Matthew D. B. Jackson ◽  
Salva Duran-Nebreda ◽  
George W. Bassel
Keyword(s):  
Structure Function ◽  
Spatial Relations ◽  
Higher Order ◽  
Cellular Interaction ◽  
Cellular Organization ◽  
Multicellular Development ◽  
Cell Organization ◽  
Function Relationship ◽  
And Function ◽  
The Relationship

Multicellularity and cellular cooperation confer novel functions on organs following a structure–function relationship. How regulated cell migration, division and differentiation events generate cellular arrangements has been investigated, providing insight into the regulation of genetically encoded patterning processes. Much less is known about the higher-order properties of cellular organization within organs, and how their functional coordination through global spatial relations shape and constrain organ function. Key questions to be addressed include: why are cells organized in the way they are? What is the significance of the patterns of cellular organization selected for by evolution? What other configurations are possible? These may be addressed through a combination of global cellular interaction mapping and network science to uncover the relationship between organ structure and function. Using this approach, global cellular organization can be discretized and analysed, providing a quantitative framework to explore developmental processes. Each of the local and global properties of integrated multicellular systems can be analysed and compared across different tissues and models in discrete terms. Advances in high-resolution microscopy and image analysis continue to make cellular interaction mapping possible in an increasing variety of biological systems and tissues, broadening the further potential application of this approach. Understanding the higher-order properties of complex cellular assemblies provides the opportunity to explore the evolution and constraints of cell organization, establishing structure–function relationships that can guide future organ design.

scholarly journals A Single Point Mutation Controls the Rate of Interconversion Between the g+ and g− Rotamers of the Histidine 189 χ2 Angle That Activates Bacterial Enzyme I for Catalysis

2021 ◽  
Vol 8 ◽  
Author(s):  
Jeffrey A. Purslow ◽  
Jolene N. Thimmesch ◽  
Valeria Sivo ◽  
Trang T. Nguyen ◽  
Balabhadra Khatiwada ◽  
...  
Keyword(s):  
Protein Design ◽  
Active Site ◽  
Single Point ◽  
Conformational Dynamics ◽  
Phosphorylation Site ◽  
Phosphoryl Group ◽  
Single Point Mutation ◽  
Phosphotransferase System ◽  
Function Relationship ◽  
Enzyme I

Enzyme I (EI) of the bacterial phosphotransferase system (PTS) is a master regulator of bacterial metabolism and a promising target for development of a new class of broad-spectrum antibiotics. The catalytic activity of EI is mediated by several intradomain, interdomain, and intersubunit conformational equilibria. Therefore, in addition to its relevance as a drug target, EI is also a good model for investigating the dynamics/function relationship in multidomain, oligomeric proteins. Here, we use solution NMR and protein design to investigate how the conformational dynamics occurring within the N-terminal domain (EIN) affect the activity of EI. We show that the rotameric g+-to-g− transition of the active site residue His189 χ2 angle is decoupled from the state A-to-state B transition that describes a ∼90° rigid-body rearrangement of the EIN subdomains upon transition of the full-length enzyme to its catalytically competent closed form. In addition, we engineered EIN constructs with modulated conformational dynamics by hybridizing EIN from mesophilic and thermophilic species, and used these chimeras to assess the effect of increased or decreased active site flexibility on the enzymatic activity of EI. Our results indicate that the rate of the autophosphorylation reaction catalyzed by EI is independent from the kinetics of the g+-to-g− rotameric transition that exposes the phosphorylation site on EIN to the incoming phosphoryl group. In addition, our work provides an example of how engineering of hybrid mesophilic/thermophilic chimeras can assist investigations of the dynamics/function relationship in proteins, therefore opening new possibilities in biophysics.

scholarly journals Design to Data for mutants of β-glucosidase B from Paenibacillus polymyxa: L171M, H178M, M221L, E406W, N160E, F415M

2020 ◽  
Author(s):  
Xiaoqing Huang ◽  
Daniel Kim ◽  
Peishan Huang ◽  
Ashley Vater ◽  
Justin B. Siegel
Keyword(s):  
Thermal Stability ◽  
Protein Design ◽  
Single Point ◽  
Point Mutations ◽  
Paenibacillus Polymyxa ◽  
Biophysical Parameters ◽  
Limited Degree ◽  
Function Relationship ◽  
The Stability ◽  
And Function

ABSTRACTComputational protein design is growing in popularity as a means to engineer enzymes. Currently, protein design algorithms can predict the stability and function of the enzymes to only a limited degree. Thus, further experimental data is required for training software to more accurately characterize the structure-function relationship of enzymes. To date, the Design2Data (D2D) database holds 129 single point mutations of β-glucosidase B (BglB) characterized by kinetic and thermal stability biophysical parameters. In this study, we introduced six mutants into the BglB database and examined their catalytic activity and thermal stability: L171M, H178M, M221L, E406W, N160E, and F415M.

Enzyme redesign and interactions of substrate analogues with sterol methyltransferase to understand phytosterol diversity, reaction mechanism and the nature of the active site

2005 ◽  
Vol 33 (5) ◽  
pp. 1189-1196 ◽  
Author(s):  
W.D. Nes
Keyword(s):  
Active Site ◽  
Functional Divergence ◽  
Product Distribution ◽  
Site Directed Mutagenesis ◽  
Site Model ◽  
Bifunctional Enzymes ◽  
And Function ◽  
The Relationship ◽  
Sterol Methyltransferase

Several STM (sterol methyltransferase) genes have been cloned, sequenced and expressed in bacteria recently, making it possible to address questions of the relationship between sterol structure and function. The active site and mechanism of action of a set of phylogenetically diverse SMTs have been probed by site-directed mutagenesis as well as by using substrate and related analogues of the SMT-catalysed reaction. An active-site model has been developed that is in accord with the results presented, which is consistent with the hypothesis that SMTs are bifunctional enzymes kinetically responsible to bind Δ24-acceptor sterols of specific steric and electronic character and rigid orientation imposed by multiple hydrophobic active site contacts exacted from a common waxy core. Functional divergence influenced by the architectural role of sterols in membranes is considered to govern the evolution of product distribution and specificity of individual SMTs as discussed.

scholarly journals Evolutionary Features in the Structure and Function of Bacterial Toxins

Toxins ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 15 ◽  
Author(s):  
Raj Kumar ◽  
Thomas M. Feltrup ◽  
Roshan V. Kukreja ◽  
Kruti B. Patel ◽  
Shuowei Cai ◽  
...  
Keyword(s):  
Structure Function ◽  
Protein Dynamics ◽  
Evolutionary Model ◽  
Structure And Function ◽  
Bacterial Toxins ◽  
Dimensional Structure ◽  
Careful Study ◽  
Enzymatic Function ◽  
Evolutionary Features ◽  
And Function

Toxins can function both as a harmful and therapeutic molecule, depending on their concentrations. The diversity in their function allows us to ask some very pertinent questions related to their origin and roles: (a) What makes them such effective molecules? (b) Are there evolutionary features encoded within the structures of the toxins for their function? (c) Is structural hierarchy in the toxins important for maintaining their structure and function? (d) Do protein dynamics play a role in the function of toxins? and (e) Do the evolutionary connections to these unique features and functions provide the fundamental points in driving evolution? In light of the growing evidence in structural biology, it would be appropriate to suggest that protein dynamics and flexibility play a much bigger role in the function of the toxin than the structure itself. Discovery of IDPs (intrinsically disorder proteins), multifunctionality, and the concept of native aggregation are shaking the paradigm of the requirement of a fixed three-dimensional structure for the protein’s function. Growing evidence supporting the above concepts allow us to redesign the structure-function aspects of the protein molecules. An evolutionary model is necessary and needs to be developed to study these important aspects. The criteria for a well-defined model would be: (a) diversity in structure and function, (b) unique functionality, and (c) must belong to a family to define the evolutionary relationships. All these characteristics are largely fulfilled by bacterial toxins. Bacterial toxins are diverse and widely distributed in all three forms of life (Bacteria, Archaea and Eukaryotes). Some of the unique characteristics include structural folding, sequence and functional combination of domains, targeting a cellular process to execute their function, and most importantly their flexibility and dynamics. In this work, we summarize certain unique aspects of bacterial toxins, including role of structure in defining toxin function, uniqueness in their enzymatic function, and interaction with their substrates and other proteins. Finally, we have discussed the evolutionary aspects of toxins in detail, which will help us rethink the current evolutionary theories. A careful study, and appropriate interpretations, will provide answers to several questions related to the structure-function relationship of proteins, in general. Additionally, this will also allow us to refine the current evolution theories.

Structure and function of carbonic anhydrases

2016 ◽  
Vol 473 (14) ◽  
pp. 2023-2032 ◽  
Author(s):  
Claudiu T. Supuran
Keyword(s):  
Active Site ◽  
Metal Ion ◽  
Deep Understanding ◽  
Carbonic Anhydrases ◽  
Structure Based Drug Design ◽  
Antitumour Agents ◽  
Active Site Cavity ◽  
Function Relationship ◽  
And Function ◽  
New Generation

Carbonic anhydrases (CAs, EC 4.2.1.1) catalyse the interconversion between CO2 and bicarbonate as well as other hydrolytic reactions. Among the six genetic families known to date, the α-, β-, γ-, δ-, ζ- and η-CAs, detailed kinetic and X-ray crystallographic studies have allowed a deep understanding of the structure–function relationship in this superfamily of proteins. A metal hydroxide nucleophilic species of the enzyme, and a unique active site architecture, with half of it hydrophilic and the opposing part hydrophobic, allow these enzymes to act as some of the most effective catalysts known in Nature. The CA activation and inhibition mechanisms are also known in detail, with a large number of new inhibitor classes being described in the last years. Apart from the zinc binders, some classes of inhibitors anchor to the metal ion coordinated nucleophile, others occlude the entrance of the active site cavity and more recently, compounds binding outside the active site were described. CA inhibition has therapeutic applications for drugs acting as diuretics, antiepileptics, antiglaucoma, antiobesity and antitumour agents. Targeting such enzymes from pathogens may lead to novel anti-infectives. Successful structure-based drug design campaigns allowed the discovery of highly isoform selective CA inhibitors (CAIs), which may lead to a new generation of drugs targeting these widespread enzymes. The use of CAs in CO2 capture processes for mitigating the global temperature rise has also been investigated more recently.

scholarly journals Comparison of the Humphrey Field Analyzer and Photopic Negative Response of Focal Macular Electroretinograms in the Evaluation of the Relationship Between Macula Structure and Function

2021 ◽  
Vol 8 ◽  
Author(s):  
Kazuyuki Hirooka ◽  
Kenji Yokoyama ◽  
Kana Tokumo ◽  
Yoshiaki Kiuchi
Keyword(s):  
Structure Function ◽  
Ganglion Cell ◽  
Layer Thickness ◽  
Mean Deviation ◽  
Retinal Layer ◽  
Negative Wave ◽  
Humphrey Field Analyzer ◽  
Function Relationship ◽  
And Function ◽  
The Relationship

Purpose: To investigate the association between macular inner retinal layer thickness and macula visual field (VF) mean deviation as measured by the Humphrey Field Analyzer (HFA) or macular function as measured by focal macular electroretinograms (ERGs) in patients with glaucoma.Methods: The participants in this cross-sectional study were 71 patients with glaucoma and 10 healthy controls. Macular inner retinal layer thickness and function were measured in all participants using optical coherence tomography (OCT) and HFA or focal macular ERGs, respectively. Macular OCT images were segmented into the macular retinal nerve fiber layer (mRNFL), macular ganglion cell layer/inner plexiform layer (GCL/IPL), and ganglion cell complex (GCC). Spearman correlation analysis was used to assess the relationship between macular inner retinal layer thickness and function.Results: Focal macular ERGs were composed of a negative wave (N1), a positive wave (P1), and a slow negative wave (N2). The N2 response density was significantly reduced in eyes with glaucoma, and was significantly associated with the thickness of the mRNFL (R = 0.317), GCL/IPL (R = 0.372), or GCC (R = 0.367). The observed structure–function relationship was also significantly correlated with the HFA VF mean deviation for each thickness [mRNFL (R = 0.728), GCL/IPL (R = 0.603), or GCC (R = 0.754)].Conclusions: Although a significant correlation was found between the N2 response density and the thickness of the macular inner layer, the observed structure–function relationship with the mean deviation of the HFA VF was higher than that of the N2 response density.

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