Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes

JO Cifuente, C Colleoni, R Kalscheuer… - Chemical …, 2024 - ACS Publications
Bacteria have acquired sophisticated mechanisms for assembling and disassembling
polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α …

[PDF][PDF] Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0

JM Krieger, COS Sorzano, JM Carazo… - … Section D: Structural …, 2022 - journals.iucr.org
Cryo-electron microscopy (cryoEM) has become a well established technique with the
potential to produce structures of large and dynamic supramolecular complexes that are not …

Identification of novel protein lysine acetyltransferases in Escherichia coli

DG Christensen, JG Meyer, JT Baumgartner… - MBio, 2018 - Am Soc Microbiol
Posttranslational modifications, such as N ε-lysine acetylation, regulate protein function. N ε-
lysine acetylation can occur either nonenzymatically or enzymatically. The nonenzymatic …

Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity

S Zhang, H Li, JM Krieger, I Bahar - Molecular biology and …, 2019 - academic.oup.com
Recent studies have drawn attention to the evolution of protein dynamics, in addition to
sequence and structure, based on the premise structure-encodes-dynamics-encodes …

Characterization of differential dynamics, specificity, and allostery of lipoxygenase family members

K Mikulska-Ruminska, I Shrivastava… - Journal of chemical …, 2019 - ACS Publications
Accurate modeling of structural dynamics of proteins and their differentiation across different
species can help us understand generic mechanisms of function shared by family members …

Hydrogen–deuterium exchange within adenosine deaminase, a TIM barrel hydrolase, identifies networks for thermal activation of catalysis

S Gao, EJ Thompson, SL Barrow… - Journal of the …, 2020 - ACS Publications
Proteins are intrinsically flexible macromolecules that undergo internal motions with time
scales spanning femtoseconds to milliseconds. These fluctuations are implicated in the …

Enhancing functional expression of codon‐optimized heterologous enzymes in Escherichia coli BL21(DE3) by selective introduction of synonymous rare codons

C Zhong, P Wei, YHP Zhang - Biotechnology and …, 2017 - Wiley Online Library
Rare codon in a heterologous gene may cause premature termination of protein synthesis,
misincorporation of amino acids, and/or slow translation of mRNA, decreasing the …

Identification of thermal conduits that link the protein–water interface to the active site loop and catalytic base in enolase

EJ Thompson, A Paul, AT Iavarone… - Journal of the American …, 2021 - ACS Publications
We report here on the salient role of protein mobility in accessing conformational
landscapes that enable efficient enzyme catalysis. We are focused on yeast enolase, a …

Conservation of intrinsic dynamics in proteins—what have computational models taught us?

SP Tiwari, N Reuter - Current Opinion in Structural Biology, 2018 - Elsevier
Highlights•Intrinsic flexibility of proteins is more conserved than structure and
sequence.•Protein flexibility can be derived from coarse-grained elastic network …

Search and subvert: minimalist bacterial phosphatidylinositol-specific phospholipase C enzymes

MF Roberts, HM Khan, R Goldstein, N Reuter… - Chemical …, 2018 - ACS Publications
Phosphatidylinositol-specific phospholipase C (PI-PLC) enzymes from Gram-positive
bacteria are secreted virulence factors that aid in downregulating host immunity. These PI …