Topaz-Denoise: general deep denoising models for cryoEM and cryoET by Bepler, Tristan, Kelley, Kotaro, Noble, Alex J, Berger, Bonnie

“…<jats:title>Abstract</jats:title> <jats:p>Cryo-electron microscopy (cryoEM) is becoming the preferred method for resolving protein structures. Low signal-to-noise ratio (SNR) in cryoEM images reduces the confidence and throughput of structure determination during several steps of data processing, resulting in impediments such as missing particle orientations. …”
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Comparing Native Crystal Structures and AlphaFold2 Predicted Water-Soluble G Protein-Coupled Receptor QTY Variants by Skuhersky, Michael A., Tao, Fei, Qing, Rui, Smorodina, Eva, Jin, David, Zhang, Shuguang

“…Accurate predictions of 3-dimensional protein structures by AlphaFold2 is a game-changer for biology, especially for structural biology. …”
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Examination of two remarkable AAA+ proteases: unraveling substrate-enzyme interactions of the double-ringed ClpAP and direct thermal activation of HslUV proteolysis by Shih, Tsai-Ting (Irene)

“…Furthermore, I establish an initial map of sequence determinants located within the substrate that provides the ClpAP protease with contacts to enhance its grip, thereby improving the probability of successful unfolding of stable protein structures, and thus the efficiency of substrate degradation.…”
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Computational modeling of protein-biomolecule interactions with application to mechanotransduction and antibody maturation by Zyto, Aurore

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Computational analysis of protein tertiary structures by Theresia.

“…The objective of this research is to identify catalytic residues in protein sequences using protein structural information, as previous studies has shown that a more accurate prediction can be yielded with the usage of structural information rather than pure sequence information alone. …”
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Modeling solution X-ray scattering of biomacromolecules using an explicit solvent model and the fast Fourier transform by Tong, Dudu, Yang, Jianbin, Lu, Lanyuan

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Recent advances in understanding mammalian prion structure: a mini review by Terry, Cassandra, Wadsworth, Jonathan D. F.

“…Prions are clearly distinguishable from non-infectious recombinant PrP fibrils generated and from all other propagating protein structures so far described in other neurodegenerative diseases. …”
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Proceedings of the 6th Neurological Disorders Summit (NDS-2021). Recent advances in understanding mammalian prion structure by Terry, Cassandra, Wadsworth, Jonathan D. F.

“…Prions are clearly distinguishable from non-infectious recombinant PrP fibrils generated in vitro and from all other propagating protein structures so far described in other neurodegenerative diseases. …”
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Structural studies on the reaction of isopenicillin N synthase with the truncated substrate analogues delta-(L-alpha-aminoadipoyl)-L-cysteinyl-glycine and delta-(L-alpha-aminoadipo... by Long, A, Clifton, I, Roach, P, Baldwin, J, Rutledge, P, Schofield, C

“…We report X-ray crystal structures for the anaerobic IPNS/Fe(II)/ACG and IPNS/Fe(II)/ACA complexes, both in the absence and presence of the dioxygen analogue nitric oxide. The overall protein structures are very similar to those of the corresponding IPNS/Fe(II)/ACV complexes; however, significant differences are apparent in the vicinity of the active site iron. …”

An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid by Shmool, TA, Martin, LK, Bui-Le, L, Moya-Ramirez, I, Kotidis, P, Matthews, RP, Venter, GA, Kontoravdi, C, Polizzi, KM, Hallett, JP

“…Understanding protein folding in different environmental conditions is fundamentally important for predicting protein structures and developing innovative antibody formulations. …”

Lipid binding attenuates channel closure of the outer membrane protein OmpF by Liko, I, Degiacomi, M, Lee, S, Newport, T, Gault, J, Reading, E, Hopper, J, Housden, N, White, P, Colledge, M, Sula, A, Wallace, B, Kleanthous, C, Stansfeld, P, Bayley, H, Benesch, J, Allison, T, Robinson, C

“…To understand these different sensitivities, we performed an extensive bioinformatics analysis of membrane protein structures and found that OmpF, and to a lesser extent FpvA and VDAC, have atypically high local densities of basic and acidic residues in their lipid headgroup-binding regions. …”

Structural comparison of two strains of foot-and-mouth disease virus subtype O1 and a laboratory antigenic variant, G67. by Lea, S, Abu-Ghazaleh, R, Blakemore, W, Curry, S, Fry, E, Jackson, T, King, A, Logan, D, Newman, J, Stuart, D

“…CONCLUSIONS: The conservation of conformation of the GH loop of VP1 adds to the evidence implicating an integrin as the cellular receptor for FMDV, since this loop contains a conserved RGD (Arg-Gly-Asp) sequence structurally similar to the same tripeptide in some other integrin-binding proteins. Structural changes required for the virus to escape neutralization by monoclonal antibodies are generally small. …”

Biological investigation of glycosylated macromolecular structures by De Munari, S

“…</p> <p>The controlled glycosylation of proteins still represents a challenge, hence we decided to exploit the ability to diversify carbohydrates from a common precursor, and developed three glycosylating reagents which allowed the use of different glycosylation strategies on different protein structures.</p> <p>In order to follow the <em>in vivo</em> distribution of the selected carbohydrates, we activated them into the 2-imino-2-methoxyethyl derivatives and used them to decorate amino-functionalised magnetic nanoparticles. …”

Regulation of the expression and positioning of chemotaxis and motor proteins in Rhodobacter sphaeroides by Wilkinson, D, David Wilkinson

“…Central to this process are the macromolecular protein structures of the flagellar motor and the chemoreceptor arrays, which are responsible for motility and chemical sensing, respectively. …”

Diversity in coding tandem repeats in related Neisseria spp. by Jordan, P, Snyder, L, Saunders, N

“…This is the first study to address coding tandem repeats that may affect protein structures using comparative genomics, combined with a population survey to investigate which show interstrain variability. …”

Genome-wide analysis of selection in insects, mammals and fungi by Ridout, KE

“…</p> <p>The investigation of this question is the central aim of this thesis, which is addressed via the analysis of selective pressures in secondary protein structures in insects, mammals and fungi. The analyses for the first two groups were conducted using publically available datasets. …”

Detection of alpha-rod protein repeats using a neural network and application to huntingtin by Palidwor, G, Shcherbinin, S, Huska, MR, Rasko, T, Stelzl, U, Arumughan, A, Foulle, R, Porras, P, Sanchez-Pulido, L, Wanker, E, Andrade-Navarro, M

“…A growing number of solved protein structures display an elongated structural domain, denoted here as alpha-rod, composed of stacked pairs of anti-parallel alpha-helices. …”

Precipitation pattern as a proxy for protein crystallization by Ng, J

“…<p>X-ray crystallography has been the workhorse behind most 3D protein structures, which are crucial in the understanding of their biological function and interaction with other molecules. …”

Functional and structural analysis of double and triple mutants reveals the contribution of protein instability to clinical manifestations of G6PD variants by Praoparotai, A, Junkree, T, Imwong, M, Boonyuen, U

“…G6PD Guadalajara, G6PD Mount Sinai and G6PD No name are inactive variants and, correlating with the observed clinical manifestations, exhibit complete loss of enzyme activity. Protein structural instability, causing a reduction in catalytic efficiency, contributes to the clinical phenotypes of all variants. …”

The role and predicted propensity of conserved proline residues in the 5-HT3 receptor. by Deane, C, Lummis, S

“…To explore the conformational preference (propensity) of these residues we examined the proportion of cis-prolines and the influence of adjacent residues in known protein structures. 4.7% of prolines in the protein data base were in the cis conformation, and the distribution of amino acids adjacent to cis-prolines was not randomly distributed. …”