The recognition of carbohydrates by proteins is a fundamental aspect communication within and between living cells. Understanding the molecular basis carbohydrate–protein interactions prerequisite for rational design synthetic ligands. Here we report high- to ultra-high-resolution crystal structures carbohydrate domain galectin-3 (Gal3C) in ligand-free state (1.08 Å at 100 K, 1.25 298 K) complex with lactose (0.86 Å) or glycerol (0.9 Å). These reveal striking similarities positions water...

Reaction network starting from monomer mixtures of Aβ40 and Aβ42. Interaction at the level primary nucleation only accelerates fibril formation. Separate fibrils form as secondary elongation are highly specific.

The deposition of α-synuclein fibrils is one hallmark Parkinson's disease. Here, we investigate how ganglioside lipids, present in high amounts neurons and exosomes, influence the aggregation kinetics α-synuclein. Gangliosides, as well as, other anionic lipid species with small or large headgroups were found to induce conformational changes monomers catalyse their at mildly acidic conditions. Although extent this catalytic effect was slightly higher for gangliosides, results imply that...

Structure-based protein design offers a possibility of optimizing the overall shape engineered binding scaffolds to match their targets better. We developed computational approach for structure-based repeat proteins that allows adjustment geometrical features like length, curvature, and helical twist. By combining sequence optimization existing repeats de novo capping structures, we designed leucine-rich (LRRs) from ribonuclease inhibitor (RI) family assemble into structures with predefined...

Intramolecular motions of proteins are critical for biological function. Transient structural fluctuations underlie a wide range processes, including enzyme catalysis, ligand binding to buried sites, and generic protein motions, such as 180° rotation aromatic side chains in the interior, but remain poorly understood. Understanding dynamics molecular nature concerted requires characterization their rates energy barriers. Here we use recently developed 13C transverse relaxation dispersion...

The human molecular chaperone DNAJB6, an oligomeric protein with a conserved S/T-rich region, is efficient suppressor of amyloid fibril formation by highly aggregation-prone peptides such as the Aβ and polyQ associated Alzheimer's Huntington's disease, respectively. We previously showed that DNAJB6 can inhibit processes through which fibrils are formed via strong interactions aggregated forms Aβ42 become sequestered. Here we report concentration-dependent capability to suppress in thioflavin...

The nucleation of Alzheimer-associated Aβ peptide monomers can be catalyzed by preexisting fibrils. This leads to autocatalytic amplification aggregate mass and underlies self-replication generation toxic oligomers associated with several neurodegenerative diseases. However, the nature interactions between monomeric species fibrils during this key process, indeed ultrastructural localization interaction sites have remained elusive. Here we used NMR optical spectroscopy identify conditions...

Allosteric communication pathways in the glucocorticoid receptor ligand-binding domain respond to ligand structure.

Histidine is a key amino-acid residue in proteins with unique properties engendered by its imidazole side chain that can exist three different states: two neutral tautomeric forms and protonated, positively charged one p

Abstract The B domain of protein A is a biotechnologically important three‐helix bundle protein. It binds the Fc fragment antibodies with helix 1/2 and Fab region 2/3. Here we designed shuffled variant by changing connectivity helices, in order to redesign bundle, yielding altered helix–loop–helix properties. new loops that generate were created several libraries, binding variants selected for detailed biochemical characterization. We able create affinity at same level as wild type but...

Prolyl cis/trans isomerization is a rate-limiting step in protein folding, often coupling directly to the acquisition of native structure. Here, we investigated interplay between folding and prolyl N2 domain gene-3-protein from filamentous phage fd, which adopts native-state equilibrium at Pro161. Using mutational Φ-value analysis, identified discrete nucleus encompassing β-strands surrounding These native-like interactions form early pathway provide energy shift toward cis form. Variations...

Protein dynamics on the millisecond time scale commonly reflect conformational transitions between distinct functional states. NMR relaxation dispersion experiments have provided important insights into biologically relevant with site-specific resolution, primarily targeting protein backbone and methyl-bearing side chains. Aromatic chains represent attractive probes of because they are over-represented in binding interfaces, play critical roles enzyme catalysis, form an part core. Here we...

Proton-transfer dynamics plays a critical role in many biochemical processes, such as proton pumping across membranes and enzyme catalysis. The large majority of enzymes utilize acid–base catalysis proton-transfer mechanisms, where the rates transfer can be rate limiting for overall reaction. However, measurement proton-exchange kinetics individual side-chain carboxyl groups proteins has been achieved only handful cases, which typically have involved comparative analysis mutant context...

Cold shock proteins (CSP) belong to the family of single-stranded nucleic acid binding with OB-fold. CSP are believed function as 'RNA chaperones' and during anti-termination. We determined solution structure Bs-CspB bound DNA (ssDNA) fragment heptathymidine (dT7) by NMR spectroscopy. reveals an almost invariant conformation when dT7 only minor reorientations in loop β1–β2 β3–β4 few aromatic side chains involved base stacking. Binding studies protein variants mutated ssDNA demonstrated that...

The Drosophila Spätzle protein, involved in the embryonic development of dorsal-ventral axis and adult immune response, is expressed as a proprotein activated by serine proteinases Easter or Spätzle-processing enzyme. Proteolytic cleavage generates 106-amino acid COOH-terminal fragment, C106, homologous to mature form nerve growth factor NGF, cystine knot protein. Through alternative splicing, gene encodes for several isoforms that (with one exception, "propeptide isoform") share C106 but...

Protein dynamics on the micro- to millisecond time scale is increasingly found be critical for biological function, as demonstrated by numerous NMR relaxation dispersion studies. Methyl groups are excellent probes of protein interactions and because their favorable properties, which lead sharp signals in (1)H (13)C spectra. Out six different methyl-bearing amino acid residue types proteins, methionine plays a special role its extensive side-chain flexibility high polarizability sulfur atom....

Peptidyl-prolyl isomerases (PPIases) catalyze cis/trans isomerization of peptidyl-prolyl bonds, which is often rate-limiting for protein folding. SlyD a two-domain enzyme containing both PPIase FK506-binding (FKBP) domain and an insert-in-flap (IF) chaperone domain. To date, the interactions these domains with unfolded proteins have remained rather obscure, structural information on binding to FKBP being limited complexes involving various inhibitor compounds or chemically modified...

Repeat proteins are widespread in nature, with many of them functioning as binding molecules protein–protein recognition. Their simple structural architecture is used biotechnology for generating high affinities to target proteins. Recent folding studies ankyrin repeat (AR) revealed a new mechanism protein folding. The formation an intermediate state rate limiting the reaction, suggesting scaffold function this transient intrinsically less stable ARs. To investigate possible common AR...

Abstract PpiD is a periplasmic folding helper protein of Escherichia coli . It consists an N‐terminal helix that anchors in the inner membrane near SecYEG translocon, followed by three domains. The second domain (residues 264–357) shows homology to parvulin‐like prolyl isomerases. This well folded, stable and follows simple two‐state mechanism. In its solution structure, as determined NMR spectroscopy, it resembles most closely first parvulin SurA protein, which resides periplasm E. well. A...

Aromatic ring flips of Phe and Tyr residues are a hallmark protein dynamics with long history in molecular biophysics. Ring lead to symmetric exchange nuclei between sites distinct magnetic environments, which can be probed by NMR spectroscopy. Current knowledge ring-flip rates originates from rare cases the chemical shift difference two is sufficiently large rate slow, typically kflip < 10(3) s(-1), so that separate peaks observed spectrum for nuclei, enabling direct measurement flip rate....