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Article ; Conference proceedings ; Online: A ComputationalTool for Structural Biology

Brünger, Axel T.

Crystallographic Refinement by Simulated Annealing

2023

Abstract: Conventional refinementof biological macromolecules involvesa series of steps, each of which consists ofa few cyclesofrestrained least-squares refinement with stereochemical and internal packingconstraints orrestraints that are followed by rebuilding the ...

Abstract	Conventional refinementof biological macromolecules involvesa series of steps, each of which consists ofa few cyclesofrestrained least-squares refinement with stereochemical and internal packingconstraints orrestraints that are followed by rebuilding the modelstructure with interactive computer graphics. Duringthefinal stages of refinement solvent molecules are usually included and alternative conformations for some atomsor residues in the protein may be introduced.
Language	English
Publishing date	2023-11-03
Publisher	GBF Gesellschaft für Biotechnologische Forschung mbH, Braunschweig
Publishing country	de
Document type	Article ; Conference proceedings ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Core Complex of the Ca

Brunger, Axel T / Leitz, Jeremy

Journal of molecular biology

2022 Volume 435, Issue 1, Page(s) 167853

Abstract: Synaptic neurotransmitter release is mediated by an orchestra of presynaptic proteins that precisely control and trigger fusion between synaptic vesicles and the neuron terminal at the active zone upon the arrival of an action potential. Critical to this ...

Abstract	Synaptic neurotransmitter release is mediated by an orchestra of presynaptic proteins that precisely control and trigger fusion between synaptic vesicles and the neuron terminal at the active zone upon the arrival of an action potential. Critical to this process are the neuronal SNAREs (Soluble N-ethylmaleimide sensitive factor Attachment protein REceptor), the Ca
MeSH term(s)	Calcium/metabolism ; Membrane Fusion ; Neurons/metabolism ; SNARE Proteins/metabolism ; Synaptic Transmission/physiology ; Synaptic Vesicles/metabolism ; Synaptotagmins/metabolism
Chemical Substances	Calcium (SY7Q814VUP) ; SNARE Proteins ; Synaptotagmins (134193-27-4)
Language	English
Publishing date	2022-10-13
Publishing country	Netherlands
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167853
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Zs.A 867: Show issues

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Article ; Online: A new method for isolation and purification of fusion-competent inhibitory synaptic vesicles.

Gopal, Nisha / Leitz, Jeremy / Wang, Chuchu / Esquivies, Luis / Pfuetzner, Richard A / Brunger, Axel T

Current research in physiology

2024 Volume 7, Page(s) 100121

Abstract: Synaptic vesicles specific to inhibitory GABA-releasing neurons are critical for regulating neuronal excitability. To study the specific molecular composition, architecture, and function of inhibitory synaptic vesicles, we have developed a new method to ... ...

Abstract	Synaptic vesicles specific to inhibitory GABA-releasing neurons are critical for regulating neuronal excitability. To study the specific molecular composition, architecture, and function of inhibitory synaptic vesicles, we have developed a new method to isolate and purify GABA synaptic vesicles from mouse brains. GABA synaptic vesicles were immunoisolated from mouse brain tissue using an engineered fragment antigen-binding region (Fab) against the vesicular GABA transporter (vGAT) and purified. Western blot analysis confirmed that the GABA synaptic vesicles were specifically enriched for vGAT and largely depleted of contaminants from other synaptic vesicle types, such as vesicular glutamate transporter (vGLUT1), and other cellular organelles. This degree of purity was achieved despite the relatively low abundance of vGAT vesicles compared to the total synaptic vesicle pool in mammalian brains. Cryo-electron microscopy images of these isolated GABA synaptic vesicles revealed intact morphology with circular shape and protruding proteinaceous densities. The GABA synaptic vesicles are functional, as assessed by a hybrid (
Language	English
Publishing date	2024-02-23
Publishing country	Netherlands
Document type	Journal Article
ISSN	2665-9441
ISSN (online)	2665-9441
DOI	10.1016/j.crphys.2024.100121
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Article ; Online: The protein-folding problem: Not yet solved.

Moore, Peter B / Hendrickson, Wayne A / Henderson, Richard / Brunger, Axel T

Science (New York, N.Y.)

2022 Volume 375, Issue 6580, Page(s) 507

MeSH term(s)	Protein Conformation ; Protein Folding
Language	English
Publishing date	2022-02-03
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abn9422
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Zs.A 27: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 77: Show issues

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Article ; Online: Association of the neonatal Fc receptor promoter variable number of tandem repeat polymorphism with immunoglobulin response in patients with chronic inflammatory demyelinating polyneuropathy.

Fisse, Anna Lena / Schäfer, Emelie / Hieke, Alina / Schröder, Maximilian / Klimas, Rafael / Brünger, Jil / Huckemann, Sophie / Grüter, Thomas / Sgodzai, Melissa / Schneider-Gold, Christiane / Gold, Ralf / Nguyen, Huu Phuc / Pitarokoili, Kalliopi / Motte, Jeremias / Arning, Larissa

European journal of neurology

2024 Volume 31, Issue 4, Page(s) e16205

Abstract: Background and purpose: Chronic inflammatory demyelinating polyneuropathy (CIDP) is an autoimmune disease with humoral and cellular autoimmunity causing demyelination of peripheral nerves, commonly treated with intravenous immunoglobulins (IVIg). The ... ...

Abstract	Background and purpose: Chronic inflammatory demyelinating polyneuropathy (CIDP) is an autoimmune disease with humoral and cellular autoimmunity causing demyelination of peripheral nerves, commonly treated with intravenous immunoglobulins (IVIg). The neonatal Fc receptor (FcRn), encoded by the FCGRT gene, prevents the degradation of immunoglobulin G (IgG) by recycling circulating IgG. A variable number of tandem repeat (VNTR) polymorphism in the promoter region of the FCGRT gene is associated with different expression levels of mRNA and protein. Thus, patients with genotypes associated with relatively low FcRn expression may show a poorer treatment response to IVIg due to increased IVIg degradation. Methods: VNTR genotypes were analyzed in 144 patients with CIDP. Patients' clinical data, including neurological scores and treatment data, were collected as part of the Immune-Mediated Neuropathies Biobank registry. Results: Most patients (n = 124, 86%) were VNTR 3/3 homozygotes, and 20 patients (14%) were VNTR 2/3 heterozygotes. Both VNTR 3/3 and VNTR 2/3 genotype groups showed no difference in clinical disability and immunoglobulin dosage. However, patients with a VNTR 2 allele were more likely to receive subcutaneous immunoglobulins (SCIg) than patients homozygous for the VNTR 3 allele (25% vs. 9.7%, p = 0.02) and were more likely to receive second-line therapy (75% vs. 54%, p = 0.05). Conclusions: The VNTR 2/3 genotype is associated with the administration of SCIg, possibly reflecting a greater benefit from SCIg due to more constant immunoglobulin levels without lower IVIg levels between the treatment circles. Also, the greater need for second-line treatment in VNTR 2/3 patients could be an indirect sign of a lower response to immunoglobulins.
MeSH term(s)	Infant, Newborn ; Humans ; Polyradiculoneuropathy, Chronic Inflammatory Demyelinating/drug therapy ; Immunoglobulins, Intravenous/therapeutic use ; Minisatellite Repeats ; Immunoglobulin G ; Promoter Regions, Genetic ; Receptors, Fc ; Histocompatibility Antigens Class I
Chemical Substances	Immunoglobulins, Intravenous ; Fc receptor, neonatal (TW3XAW0RCY) ; Immunoglobulin G ; Receptors, Fc ; Histocompatibility Antigens Class I
Language	English
Publishing date	2024-01-11
Publishing country	England
Document type	Journal Article
ZDB-ID	1280785-0
ISSN	1468-1331 ; 1351-5101 ; 1471-0552
ISSN (online)	1468-1331
ISSN	1351-5101 ; 1471-0552
DOI	10.1111/ene.16205
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Zs.A 4738: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 592: Show issues

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Article ; Online: The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines.

Khan, Yousuf A / White, K Ian / Brunger, Axel T

Critical reviews in biochemistry and molecular biology

2021 Volume 57, Issue 2, Page(s) 156–187

Abstract: ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. ... ...

Abstract	ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. Typically, AAA+ proteins transduce chemical energy from the hydrolysis of ATP into mechanical energy through conformational change, which can drive a variety of biological processes. AAA+ proteins operate in a variety of cellular contexts with diverse functions including disassembly of SNARE proteins, protein quality control, DNA replication, ribosome assembly, and viral replication. This breadth of function illustrates both the importance of AAA+ proteins in health and disease and emphasizes the importance of understanding conserved mechanisms of chemo-mechanical energy transduction. This review is divided into three major portions. First, the core AAA+ fold is presented. Next, the seven different clades of AAA+ proteins and structural details and reclassification pertaining to proteins in each clade are described. Finally, two well-known AAA+ proteins, NSF and its close relative p97, are reviewed in detail.
MeSH term(s)	AAA Proteins/metabolism ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/chemistry ; N-Ethylmaleimide-Sensitive Proteins/chemistry ; N-Ethylmaleimide-Sensitive Proteins/genetics ; N-Ethylmaleimide-Sensitive Proteins/metabolism ; SNARE Proteins/chemistry ; SNARE Proteins/metabolism
Chemical Substances	SNARE Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; Adenosine Triphosphatases (EC 3.6.1.-) ; AAA Proteins (EC 3.6.4.-) ; N-Ethylmaleimide-Sensitive Proteins (EC 3.6.4.6)
Language	English
Publishing date	2021-10-11
Publishing country	England
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1000977-2
ISSN	1549-7798 ; 1381-3455 ; 1040-9238
ISSN (online)	1549-7798
ISSN	1381-3455 ; 1040-9238
DOI	10.1080/10409238.2021.1979460
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Zs.A 1024: Show issues

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Article: ATP1A3-Related Disorders: An Ever-Expanding Clinical Spectrum.

Salles, Philippe A / Mata, Ignacio F / Brünger, Tobias / Lal, Dennis / Fernandez, Hubert H

Frontiers in neurology

2021 Volume 12, Page(s) 637890

Abstract: The Na+/K+ ATPases are Sodium-Potassium exchanging pumps, with a heteromeric α-β-γ protein complex. The α3 isoform is required as a rescue pump, after repeated action potentials, with a distribution predominantly in neurons of the central nervous system. ...

Abstract	The Na+/K+ ATPases are Sodium-Potassium exchanging pumps, with a heteromeric α-β-γ protein complex. The α3 isoform is required as a rescue pump, after repeated action potentials, with a distribution predominantly in neurons of the central nervous system. This isoform is encoded by the ATP1A3 gene. Pathogenic variants in this gene have been implicated in several phenotypes in the last decades. Carriers of pathogenic variants in this gene manifest neurological and non-neurological features in many combinations, usually with an acute onset and paroxysmal episodes triggered by fever or other factors. The first three syndromes described were: (1) rapid-onset dystonia parkinsonism; (2) alternating hemiplegia of childhood; and, (3) cerebellar ataxia, pes cavus, optic atrophy, and sensorineural hearing loss (CAPOS syndrome). Since their original description, an expanding number of cases presenting with atypical and overlapping features have been reported. Because of this, ATP1A3-disorders are now beginning to be viewed as a phenotypic continuum representing discrete expressions along a broadly heterogeneous clinical spectrum.
Language	English
Publishing date	2021-04-01
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2564214-5
ISSN	1664-2295
ISSN	1664-2295
DOI	10.3389/fneur.2021.637890
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Article: Free R value: cross-validation in crystallography.

Brünger, A T

Methods in enzymology

2008 Volume 277, Page(s) 366–396

Language	English
Publishing date	2008-01-18
Publishing country	United States
Document type	Journal Article
ISSN	0076-6879
ISSN	0076-6879
DOI	10.1016/s0076-6879(97)77021-6
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Article ; Online: Morphological Differentiation of Corneal Inflammatory Cells: Proposal of Pragmatic Protocol.

Cornea

2024

Abstract: Purpose: Corneal confocal microscopy is a noninvasive imaging technique to analyze corneal nerve fibers and corneal inflammatory cells (CICs). The amount of CICs is a potential biomarker of disease activity in chronic autoinflammatory diseases. To date, ...

Abstract	Purpose: Corneal confocal microscopy is a noninvasive imaging technique to analyze corneal nerve fibers and corneal inflammatory cells (CICs). The amount of CICs is a potential biomarker of disease activity in chronic autoinflammatory diseases. To date, there are no standardized criteria for the morphological characterization of CICs. The aim was to establish a protocol for a standardized morphological classification of CICs based on a literature search and to test this protocol for applicability and reliability. Methods: A systematic review of the literature about definitions of CICs was conducted. Existing morphological descriptions were translated into a structured algorithm and applied by raters. Subsequently, the protocol was optimized by reducing and defining the criteria of the cell types. The optimized algorithm was applied by 4 raters. The interrater reliability was calculated using Fleiss kappa (K). Results: A systematic review of the literature revealed no uniform morphological criteria for the differentiation of the individual cell types in CICs. Our first protocol achieved only a low level of agreement between 3 raters (K = 0.09; 1062 rated cells). Our revised protocol was able to achieve a higher interrater reliability with 3 (K = 0.64; 471 rated cells) and 4 (K = 0.61; 628 rated cells) raters. Conclusions: The indirect use of criteria from the literature leads to a high error rate. By clearly defining the individual cell types and standardizing the protocol, reproducible results were obtained, allowing the introduction of this protocol for the future evaluation of CICs in the corneal confocal microscopy.
Language	English
Publishing date	2024-04-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	604826-2
ISSN	1536-4798 ; 0277-3740
ISSN (online)	1536-4798
ISSN	0277-3740
DOI	10.1097/ICO.0000000000003543
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Zs.A 1790: Show issues

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Article: Nerve Echogenicity in Polyneuropathies of Various Etiologies-Results of a Retrospective Semi-Automatic Analysis of High-Resolution Ultrasound Images.

Erdmann, Anke / Motte, Jeremias / Brünger, Jil / Grüter, Thomas / Gold, Ralf / Pitarokoili, Kalliopi / Fisse, Anna Lena

Diagnostics (Basel, Switzerland)

2022 Volume 12, Issue 6

Abstract: Echogenicity of peripheral nerves in high-resolution ultrasound (HRUS) provides insight into the structural damage of peripheral nerves in various polyneuropathies. The aim of this study was to compare nerve echogenicity in different primarily axonal or ... ...

Abstract	Echogenicity of peripheral nerves in high-resolution ultrasound (HRUS) provides insight into the structural damage of peripheral nerves in various polyneuropathies. The aim of this study was to compare nerve echogenicity in different primarily axonal or demyelinating polyneuropathies to examine the significance of this parameter. Performing semi-automated echogenicity analysis and applying Image J, we retrospectively used HRUS images of 19 patients with critical illness polyneuropathy (CIP), and 27 patients with chemotherapy-induced polyneuropathy (CIN) and compared them to 20 patients with chronic inflammatory demyelinating polyneuropathy (CIDP). The fraction of black representing echogenicity was measured after converting the images into black and white. The nerves of patients with progressive CIDP significantly differed from the hyperechogenic nerves of patients with other polyneuropathies at the following sites: the median nerve at the forearm (p < 0.001), the median nerve at the upper arm (p < 0.004), and the ulnar nerve at the upper arm (p < 0.001). The other polyneuropathies showed no notable differences. Altogether, the comparison of echogenicity between different polyneuropathies supports the assumption that there are differences depending on the genesis of the structural nerve damage. However, these differences are slight, and cannot be used to show clear differences between each polyneuropathy form.
Language	English
Publishing date	2022-05-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics12061341
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