Modeling membrane geometries implicitly in Rosetta
AbstractInteractions between membrane proteins (MPs) and lipid bilayers are critical for many cellular functions. In the Rosetta molecular modeling suite, the implicit membrane energy function is based on a “slab” model, which represent the membrane as a flat bilayer. However, in nature membranes often have a curvature that is important for function and/or stability. Even more prevalent, in structural biology research MPs are reconstituted in model membrane systems such as micelles, bicelles, nanod iscs, or liposomes. Thus, we have modified the existing membrane energy potentials within the RosettaMP framework to allow...
Source: Protein Science - February 15, 2024 Category: Biochemistry Authors: Hope Woods,
Julia Koehler Leman,
Jens Meiler Tags: METHODS AND APPLICATIONS Source Type: research
The effects of biological crowders on fibrillization, structure, diffusion, and conformational dynamics of α‐synuclein
In this study, α-synuc lein was studied in the presence of both a synthetic crowder, Ficoll70, and a biological crowder composed of lysed cells that better mimics the biocomplexity of the cellular environment.15N-1H HSQC NMR results show similar α-synuclein chemical shifts in non-crowded and all crowded conditions implying that it remains similarly unstructured in all conditions. Nevertheless, both HSQC NMR and fluorescence measurements indicate that, only in the cell lysate, α-synuclein forms aggregates over a timescale of 48 h.15N-edited diffusion measurements indicate that all crowders slow down the α-synuclein's ...
Source: Protein Science - February 15, 2024 Category: Biochemistry Authors: Sina Heravi,
Jude Vincent Dobbin Power,
Anand Yethiraj,
Valerie Booth Tags: RESEARCH ARTICLE Source Type: research
Discovery of broadly ‐neutralizing antibodies against brown recluse spider and Gadim scorpion sphingomyelinases using consensus toxins as antigens
AbstractBroadly-neutralizing monoclonal antibodies are becoming increasingly important tools for treating infectious diseases and animal envenomings. However, designing and developing broadly-neutralizing antibodies can be cumbersome using traditional low-throughput iterative protein engineering methods. Here, we present a new high-throughput approach for the standardized discovery of broadly-neutralizing monoclonal antibodies relying on phage display technology and consensus antigens representing average sequences of related proteins. We showcase the utility of this approach by applying it to toxic sphingomyelinases from ...
Source: Protein Science - February 15, 2024 Category: Biochemistry Authors: Esperanza Rivera ‐de‐Torre,
Stefanos Lampadariou,
Mark Møiniche,
Markus F. Bohn,
Seyed Mahdi Kazemi,
Andreas H. Laustsen Tags: RESEARCH ARTICLE Source Type: research
Systematic enhancement of protein crystallization efficiency by bulk lysine ‐to‐arginine (KR) substitution
AbstractStructural genomics consortia established that protein crystallization is the primary obstacle to structure determination using x-ray crystallography. We previously demonstrated that crystallization propensity is systematically related to primary sequence, and we subsequently performed computational analyses showing that arginine is the most overrepresented amino acid in crystal-packing interfaces in the Protein Data Bank. Given the similar physicochemical characteristics of arginine and lysine, we hypothesized that multiple lysine-to-arginine (KR) substitutions should improve crystallization. To test this hypothes...
Source: Protein Science - February 15, 2024 Category: Biochemistry Authors: Nooriel E. Banayan,
Blaine J. Loughlin,
Shikha Singh,
Farhad Forouhar,
Guanqi Lu,
Kam ‐Ho Wong,
Matthew Neky,
Henry S. Hunt,
Larry B. Bateman Jr,
Angel Tamez,
Samuel K. Handelman,
W. Nicholson Price,
John F. Hunt Tags: RESEARCH ARTICLE Source Type: research
Toward physics ‐based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants
AbstractThe goal of precision medicine is to utilize our knowledge of the molecular causes of disease to better diagnose and treat patients. However, there is a substantial mismatch between the small number of food and drug administration (FDA)-approved drugs and annotated coding variants compared to the needs of precision medicine. This review introduces the concept of physics-based precision medicine, a scalable framework that promises to improve our understanding of sequence –function relationships and accelerate drug discovery. We show that accounting for the ensemble of structures a protein adopts in solution with c...
Source: Protein Science - February 15, 2024 Category: Biochemistry Authors: Artur Meller,
Devin Kelly,
Louis G. Smith,
Gregory R. Bowman Tags: REVIEW ARTICLE Source Type: research
Issue information
(Source: Protein Science)
Source: Protein Science - February 15, 2024 Category: Biochemistry Tags: Issue Information Source Type: research
Cover Image
Conformational landscape of the 4-helix bundle HAMP signaling domain family represented by AlphaFold2 models. Each point represents a single model of a HAMP domain, with their relative positions reflecting structural similarity. The conformational landscape shows four basic motions that the HAMP domains can undergo and is colored according to each of these motions. For details, see: Aleksander Winski et al., Protein Science, 2023.https://doi.org/10.1002/pro.4846 (Source: Protein Science)
Source: Protein Science - February 15, 2024 Category: Biochemistry Tags: Cover Image Source Type: research
Emerging role of carbonyl –carbonyl interactions in the classification of beta turns
AbstractCarbonyl –carbonyl interactions in peptides and proteins attracted considerable interest in recent years. Here, we report a survey of carbonyl–carbonyl interactions in cyclic peptides, depsipeptides, peptoids and discuss the relationship between backbone torsion angles and CO∙∙∙CO distances. In gen eral, φ values in the range between −40° and −90° and between 40° and 90° correspond to CO∙∙∙CO distances below 3.22 Å. By extending the analysis of carbonyl–carbonyl interactions in different types of beta turns in proteins, we also highlight the role of direct or reciprocal car bonyl–car...
Source: Protein Science - January 24, 2024 Category: Biochemistry Authors: Nancy D'Arminio,
Valentina Ruggiero,
Giovanni Pierri,
Anna Marabotti,
Consiglia Tedesco Tags: RESEARCH ARTICLE Source Type: research
A significance score for protein –protein interaction models through random docking
AbstractComparing accuracies of structural protein –protein interaction (PPI) models for different complexes on an absolute scale is a challenge, requiring normalization of scores across structures of different sizes and shapes. To help address this challenge, we have developed a statistical significance metric for docking models, called random-do cking (RD)p-value. This score evaluates a PPI model based on how likely a random docking process is to produce a model of better or equal accuracy. The binding partners are randomly docked against each other a large number of times, and the probability of sampling a model of eq...
Source: Protein Science - January 24, 2024 Category: Biochemistry Authors: Katherine Maia McCoy,
Margaret E. Ackerman,
Gevorg Grigoryan Tags: RESEARCH ARTICLE Source Type: research
Energy, water, and protein folding: A molecular dynamics ‐based quantitative inventory of molecular interactions and forces that make proteins stable
AbstractProtein folding energetics can be determined experimentally on a case-by-case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics si...
Source: Protein Science - January 24, 2024 Category: Biochemistry Authors: Juan Jos é Galano‐Frutos,
Javier Sancho Tags: RESEARCH ARTICLE Source Type: research
Improving enzyme functional annotation by integrating in vitro and in silico approaches: The example of histidinol phosphate phosphatases
AbstractAdvances in sequencing technologies have led to a rapid growth of public protein sequence databases, whereby the fraction of proteins with experimentally verified function continuously decreases. This problem is currently addressed by automated functional annotations with computational tools, which however lack the accuracy of experimental approaches and are susceptible to error propagation. Here, we present an approach that combines the efficiency of functional annotation by in silico methods with the rigor of enzyme characterization in vitro. First, a thorough experimental analysis of a representative enzyme of a...
Source: Protein Science - January 23, 2024 Category: Biochemistry Authors: Thomas Kinateder,
Carina Mayer,
Julian Nazet,
Reinhard Sterner Tags: RESEARCH ARTICLE Source Type: research
ATP ‐independent assembly machinery of bacterial outer membranes: BAM complex structure and function set the stage for next‐generation therapeutics
AbstractDiderm bacteria employ β-barrel outer membrane proteins (OMPs) as their first line of communication with their environment. These OMPs are assembled efficiently in the asymmetric outer membrane by the β-Barrel Assembly Machinery (BAM). The multi-subunit BAM complex comprises the transmembrane OMP BamA as its functional subunit, with associated lipoproteins (e.g., BamB/C/D/E/F, RmpM) varying across phyla and performing different regulatory roles. The ability of BAM complex to recognize and fold OM β-barrels of diverse sizes, and reproducibly execute their membrane insertion, is independent of electrochemical ener...
Source: Protein Science - January 23, 2024 Category: Biochemistry Authors: Anjana George,
Akanksha Gajanan Patil,
Radhakrishnan Mahalakshmi Tags: REVIEW ARTICLE Source Type: research
Tandem repeats of highly bioluminescent NanoLuc are refolded noncanonically by the Hsp70 machinery
In this study, we further investigate these properties through in vitro bulk experiments. Similar to monomeric Nluc, engineered Nluc dyads and triads proved to be highly biolumines cent. Using the bioluminescence signal as the proxy for their structural integrity, we determined that heat-denatured Nluc dyads and triads can be efficiently refolded by theE. coli Hsp70 chaperone system, which comprises DnaK, DnaJ, and GrpE. In contrast to previous studies with other substrates, we observed that Nluc repeats can be efficiently refolded by DnaK and DnaJ, even in the absence of GrpE co-chaperone. Taken together, our study offers...
Source: Protein Science - January 23, 2024 Category: Biochemistry Authors: Dimitra Apostolidou,
Pan Zhang,
Devanshi Pandya,
Kaden Bock,
Qinglian Liu,
Weitao Yang,
Piotr E. Marszalek Tags: RESEARCH ARTICLE Source Type: research
Identification of the pyridoxal 5 ′‐phosphate allosteric site in human pyridox(am)ine 5′‐phosphate oxidase
AbstractAdequate levels of pyridoxal 5 ′-phosphate (PLP), the catalytically active form of vitamin B6, and its proper distribution in the body are essential for human health. The PLP recycling pathway plays a crucial role in these processes and its defects cause severe neurological diseases. The enzyme pyridox(am)ine 5 ′-phosphate oxidase (PNPO), whose catalytic action yields PLP, is one of the key players in this pathway. Mutations in the gene encoding PNPO are responsible for a severe form of neonatal epilepsy. Recently, PNPO has also been described as a potential target for chemotherapeutic agents. Our labora tory h...
Source: Protein Science - January 23, 2024 Category: Biochemistry Authors: Anna Barile,
Claudio Graziani,
Lorenzo Antonelli,
Alessia Parroni,
Annarita Fiorillo,
Martino Luigi di Salvo,
Andrea Ilari,
Alessandra Giorgi,
Serena Rosignoli,
Alessandro Paiardini,
Roberto Contestabile,
Angela Tramonti Tags: RESEARCH ARTICLE Source Type: research
Distinct specificities of the HEMK2 protein methyltransferase in methylation of glutamine and lysine residues
AbstractThe HEMK2 protein methyltransferase has been described as glutamine methyltransferase catalyzing ERF1-Q185me1 and lysine methyltransferase catalyzing H4K12me1. Methylation of two distinct target residues is unique for this class of enzymes. To understand the specific catalytic adaptations of HEMK2 allowing it to master this chemically challenging task, we conducted a detailed investigation of the substrate sequence specificities of HEMK2 for Q- and K-methylation. Our data show that HEMK2 prefers methylation of Q over K at peptide and protein level. Moreover, the ERF1 sequence is strongly preferred as substrate over...
Source: Protein Science - January 23, 2024 Category: Biochemistry Authors: Sara Weirich,
Gizem T. Ulu,
Thyagarajan T. Chandrasekaran,
Jana Kehl,
Jasmin Schmid,
Franziska Dorscht,
Margarita Kublanovsky,
Dan Levy,
Albert Jeltsch Tags: RESEARCH ARTICLE Source Type: research
