Formation and Function of Formate in the Side-Chain Alkylation of Toluene with Methanol

AbstractC407 is a compound that corrects the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein carrying the p.Phe508del (F508del) mutation. We investigated the corrector effect of c407 and its derivatives on F508del-CFTR protein. Molecular docking and dynamics simulations combined with site-directed mutagenesis suggested that c407 stabilizes the F508del-Nucleotide Binding Domain 1 (NBD1) during the co-translational folding process by occupying the position of the p.Phe1068 side chain located at the fourth intracellular loop (ICL4). After CFTR domains assembly, c407 occupies the position of the missing p.Phe508 side chain. C407 alone or in combination with the F508del-CFTR corrector VX-809, increased CFTR activity in cell lines but not in primary respiratory cells carrying the F508del mutation. A structure-based approach resulted in the synthesis of an extended c407 analog G1, designed to improve the interaction with ICL4. G1 significantly increased CFTR activity and response to VX-809 in primary nasal cells of F508del homozygous patients. Our data demonstrate that in-silico optimized c407 derivative G1 acts by a mechanism different from the reference VX-809 corrector and provide insights into its possible molecular mode of action. These results pave the way for novel strategies aiming to optimize the flawed ICL4–NBD1 interface.

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Acetylcholine Receptor Gating at Extracellular Transmembrane Domain Interface: the “Pre-M1” Linker

The Journal of General Physiology ◽

10.1085/jgp.200709857 ◽

2007 ◽

Vol 130 (6) ◽

pp. 559-568 ◽

Cited By ~ 43

Author(s):

Prasad Purohit ◽

Anthony Auerbach

Keyword(s):

Acetylcholine Receptors ◽

State Energy ◽

Transmembrane Domain ◽

Salt Bridge ◽

Side Chain ◽

Coupling Energy ◽

And Function ◽

Loop 2 ◽

Α Subunits ◽

Α1 Subunit

Charged residues in the β10–M1 linker region (“pre-M1”) are important in the expression and function of neuromuscular acetylcholine receptors (AChRs). The perturbation of a salt bridge between pre-M1 residue R209 and loop 2 residue E45 has been proposed as being a principle event in the AChR gating conformational “wave.” We examined the effects of mutations to all five residues in pre-M1 (positions M207–P211) plus E45 in loop 2 in the mouse α1-subunit. M207, Q208, and P211 mutants caused small (approximately threefold) changes in the gating equilibrium constant (Keq), but the changes for R209, L210, and E45 were larger. Of 19 different side chain substitutions at R209 on the wild-type background, only Q, K, and H generated functional channels, with the largest change in Keq (67-fold) from R209Q. Various R209 mutants were functional on different E45 backgrounds: H, Q, and K (E45A), H, A, N, and Q (E45R), and K, A, and N (E45L). Φ values for R209 (on the E45A background), L210, and E45 were 0.74, 0.35, and 0.80, respectively. Φ values for R209 on the wt and three other backgrounds could not be estimated because of scatter. The average coupling energy between 209/45 side chains (six different pairs) was only −0.33 kcal/mol (for both α subunits, combined). Pre-M1 residues are important for expression of functional channels and participate in gating, but the relatively modest changes in closed- vs. open-state energy caused mutations, the weak coupling energy between these residues and the functional activity of several unmatched-charge pairs are not consistent with the perturbation of a salt bridge between R209 and E45 playing the principle role in gating.

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Dynamics and mechanism of ultrafast water–protein interactions

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1602916113 ◽

2016 ◽

Vol 113 (30) ◽

pp. 8424-8429 ◽

Cited By ~ 77

Author(s):

Yangzhong Qin ◽

Lijuan Wang ◽

Dongping Zhong

Keyword(s):

Protein Interactions ◽

Hydration Shell ◽

Water Dynamics ◽

Side Chain ◽

Water Molecules ◽

Ultrafast Dynamics ◽

Hydration Water ◽

Water Side ◽

Dynamics And Function ◽

And Function

Protein hydration is essential to its structure, dynamics, and function, but water–protein interactions have not been directly observed in real time at physiological temperature to our awareness. By using a tryptophan scan with femtosecond spectroscopy, we simultaneously measured the hydration water dynamics and protein side-chain motions with temperature dependence. We observed the heterogeneous hydration dynamics around the global protein surface with two types of coupled motions, collective water/side-chain reorientation in a few picoseconds and cooperative water/side-chain restructuring in tens of picoseconds. The ultrafast dynamics in hundreds of femtoseconds is from the outer-layer, bulk-type mobile water molecules in the hydration shell. We also found that the hydration water dynamics are always faster than protein side-chain relaxations but with the same energy barriers, indicating hydration shell fluctuations driving protein side-chain motions on the picosecond time scales and thus elucidating their ultimate relationship.

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Conformational stability, dynamics and function of human frataxin: Tryptophan side chain interplay

Archives of Biochemistry and Biophysics ◽

10.1016/j.abb.2021.109086 ◽

2021 ◽

pp. 109086

Author(s):

Lucía D. Espeche ◽

Karl Ellioth Sewell ◽

Ignacio H. Castro ◽

Luciana Capece ◽

María Florencia Pignataro ◽

...

Keyword(s):

Conformational Stability ◽

Side Chain ◽

Dynamics And Function ◽

Stability Dynamics ◽

And Function

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Contribution of leucine 85 to the structure and function of Saccharomyces cerevisiae iso-1 cytochrome c

Biochemistry and Cell Biology ◽

10.1139/o01-077 ◽

2001 ◽

Vol 79 (4) ◽

pp. 517-524 ◽

Cited By ~ 2

Author(s):

Jonathan C Parrish ◽

J Guy Guillemette ◽

Carmichael JA Wallace

Keyword(s):

Saccharomyces Cerevisiae ◽

Electron Transfer ◽

Electron Transport ◽

Cytochrome C ◽

Transport Processes ◽

Complex Iii ◽

Side Chain ◽

Inner Mitochondrial Membrane ◽

And Function ◽

First Time

Cytochrome c is a small electron-transport protein whose major role is to transfer electrons between complex III (cytochrome reductase) and complex IV (cytochrome c oxidase) in the inner mitochondrial membrane of eukaryotes. Cytochrome c is used as a model for the examination of protein folding and structure and for the study of biological electron-transport processes. Amongst 96 cytochrome c sequences, residue 85 is generally conserved as either isoleucine or leucine. Spatially, the side chain is associated closely with that of the invariant residue Phe82, and this interaction may be important for optimal cytochrome c activity. The functional role of residue 85 has been examined using six site-directed mutants of Saccharomyces cerevisiae iso-1 cytochrome c, including, for the first time, kinetic data for electron transfer with the principle physiological partners. Results indicate two likely roles for the residue: first, heme crevice resistance to ligand exchange, sensitive to both the hydrophobicity and volume of the side chain; second, modulation of electron-transport activity through maintenance of the hydrophobic character of the protein in the vicinity of Phe82 and the exposed heme edge, and possibly of the ability of this region to facilitate redox-linked conformational change.Key words: protein engineering, cytochrome c, structure-function relations, electron transfer, hydrophobic packing.

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The structure and function of HPr

Biochemistry and Cell Biology ◽

10.1139/o98-043 ◽

1998 ◽

Vol 76 (2-3) ◽

pp. 359-367 ◽

Cited By ~ 12

Author(s):

E Bruce Waygood

Keyword(s):

Structure And Function ◽

Side Chain ◽

Phosphoryl Group ◽

Phosphotransferase System ◽

Tertiary Structures ◽

E Coli ◽

H Nmr ◽

Early Protein ◽

Alpha Beta ◽

And Function

Histidine-containing phosphocarrier protein, HPr, was one of the early protein tertiary structures determined by two-dimensional 1H-NMR. Tertiary structures for HPrs from Escherichia coli, Bacillus subtilis, and Staphylococcus aureus have been obtained by 1H NMR and the overall folding pattern of HPr is highly conserved, a beta alpha beta beta alpha beta alpha arrangement of three alpha-helices overlaying a four-stranded beta-sheet. High-resolution structures for HPrs from E. coli and B. subtilis have been obtained using 15N- and 13C-labeled proteins. The first application of NMR to the understanding of the structure and function of HPr was to describe the phosphohistidine isomer, Ndelta1-P-histidine in S. aureus phospho-HPr, and the unusual pKas of the His-15 side chain. The pKa values for the His-15 imidazole from more recent studies are 5.4 for HPr and 7.8 for phospho-HPr from E. coli, for example. A consensus description of the active site is proposed for HPr and phospho-HPr. In HPr, His-15 has a defined conformation and N-caps helix A, and is thus affected by the helix dipole. His-15 undergoes a small conformational change upon phosphorylation, a movement to allow the phosphoryl group to be positioned such that it forms hydrogen bonds with the main chain amide nitrogens of residue 16 (not conserved) and Arg-17. Interactions between residue 12 side chain (not conserved: asparagine, serine, and threonine) and His-15, and between the Arg-17 guanidinium group and the phosphoryl group, are either weak or transitory.Key words: HPr, NMR, phosphoenolpyruvate:sugar phosphotransferase system, phosphohistidine, phosphoserine.

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3-Nitrotyrosine and related derivatives in proteins: precursors, radical intermediates and impact in function

Essays in Biochemistry ◽

10.1042/ebc20190052 ◽

2020 ◽

Vol 64 (1) ◽

pp. 111-133 ◽

Cited By ~ 6

Author(s):

Nicolás Campolo ◽

Federico M. Issoglio ◽

Darío A. Estrin ◽

Silvina Bartesaghi ◽

Rafael Radi

Keyword(s):

Reactive Species ◽

Side Chain ◽

Tyrosyl Radical ◽

Post Translational Modification ◽

Tyrosine Residues ◽

Oxidative Products ◽

Usual Process ◽

And Function

Abstract Oxidative post-translational modification of proteins by molecular oxygen (O2)- and nitric oxide (•NO)-derived reactive species is a usual process that occurs in mammalian tissues under both physiological and pathological conditions and can exert either regulatory or cytotoxic effects. Although the side chain of several amino acids is prone to experience oxidative modifications, tyrosine residues are one of the preferred targets of one-electron oxidants, given the ability of their phenolic side chain to undergo reversible one-electron oxidation to the relatively stable tyrosyl radical. Naturally occurring as reversible catalytic intermediates at the active site of a variety of enzymes, tyrosyl radicals can also lead to the formation of several stable oxidative products through radical–radical reactions, as is the case of 3-nitrotyrosine (NO2Tyr). The formation of NO2Tyr mainly occurs through the fast reaction between the tyrosyl radical and nitrogen dioxide (•NO2). One of the key endogenous nitrating agents is peroxynitrite (ONOO−), the product of the reaction of superoxide radical (O2•−) with •NO, but ONOO−-independent mechanisms of nitration have been also disclosed. This chemical modification notably affects the physicochemical properties of tyrosine residues and because of this, it can have a remarkable impact on protein structure and function, both in vitro and in vivo. Although low amounts of NO2Tyr are detected under basal conditions, significantly increased levels are found at pathological states related with an overproduction of reactive species, such as cardiovascular and neurodegenerative diseases, inflammation and aging. While NO2Tyr is a well-established stable oxidative stress biomarker and a good predictor of disease progression, its role as a pathogenic mediator has been laboriously defined for just a small number of nitrated proteins and awaits further studies.

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New Insights into the Mechanism of NO3- Selectivity in the Human Kidney Chloride Channel ClC-Ka and the CLC Protein Family

Journal of the American Society of Nephrology ◽

10.1681/asn.2018060593 ◽

2019 ◽

Vol 30 (2) ◽

pp. 293-302

Author(s):

Laura Lagostena ◽

Giovanni Zifarelli ◽

Alessandra Picollo

Keyword(s):

Chloride Channel ◽

Chloride Channels ◽

Human Kidney ◽

Protein Family ◽

Side Chain ◽

Anion Selectivity ◽

And Function ◽

The Relationship ◽

Insight Into

BackgroundThe mechanism of anion selectivity in the human kidney chloride channels ClC-Ka and ClC-Kb is unknown. However, it has been thought to be very similar to that of other channels and antiporters of the CLC protein family, and to rely on anions interacting with a conserved Ser residue (Sercen) at the center of three anion binding sites in the permeation pathway Scen. In both CLC channels and antiporters, mutations of Sercen alter the anion selectivity. Structurally, the side chain of Sercen of CLC channels and antiporters typically projects into the pore and coordinates the anion bound at Scen.MethodsTo investigate the role of several residues in anion selectivity of ClC-Ka, we created mutations that resulted in amino acid substitutions in these residues. We also used electrophysiologic techniques to assess the properties of the mutants.ResultsMutations in ClC-Ka that change Sercen to Gly, Pro, or Thr have only minor effects on anion selectivity, whereas the mutations in residues Y425A, F519A, and Y520A increase the NO3−/Cl− permeability ratio, with Y425A having a particularly strong effect.Conclusions ClC-Ka’s mechanism of anion selectivity is largely independent of Sercen, and it is therefore unique in the CLC protein family. We identified the residue Y425 in ClC-Ka—and the corresponding residue (A417) in the chloride channel ClC-0—as residues that contribute to NO3− discrimination in these channels. This work provides important and timely insight into the relationship between structure and function for the kidney chloride channels ClC-Ka and ClC-Kb, and for CLC proteins in general.

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FASPR: an open-source tool for fast and accurate protein side-chain packing

Bioinformatics ◽

10.1093/bioinformatics/btaa234 ◽

2020 ◽

Vol 36 (12) ◽

pp. 3758-3765 ◽

Cited By ~ 6

Author(s):

Xiaoqiang Huang ◽

Robin Pearce ◽

Yang Zhang

Keyword(s):

Protein Structure ◽

Protein Design ◽

Structure Prediction ◽

Protein Structures ◽

Scoring Function ◽

Supplementary Information ◽

Side Chain ◽

Chain Packing ◽

And Function ◽

Side Chain Packing

Abstract Motivation Protein structure and function are essentially determined by how the side-chain atoms interact with each other. Thus, accurate protein side-chain packing (PSCP) is a critical step toward protein structure prediction and protein design. Despite the importance of the problem, however, the accuracy and speed of current PSCP programs are still not satisfactory. Results We present FASPR for fast and accurate PSCP by using an optimized scoring function in combination with a deterministic searching algorithm. The performance of FASPR was compared with four state-of-the-art PSCP methods (CISRR, RASP, SCATD and SCWRL4) on both native and non-native protein backbones. For the assessment on native backbones, FASPR achieved a good performance by correctly predicting 69.1% of all the side-chain dihedral angles using a stringent tolerance criterion of 20°, compared favorably with SCWRL4, CISRR, RASP and SCATD which successfully predicted 68.8%, 68.6%, 67.8% and 61.7%, respectively. Additionally, FASPR achieved the highest speed for packing the 379 test protein structures in only 34.3 s, which was significantly faster than the control methods. For the assessment on non-native backbones, FASPR showed an equivalent or better performance on I-TASSER predicted backbones and the backbones perturbed from experimental structures. Detailed analyses showed that the major advantage of FASPR lies in the optimal combination of the dead-end elimination and tree decomposition with a well optimized scoring function, which makes FASPR of practical use for both protein structure modeling and protein design studies. Availability and implementation The web server, source code and datasets are freely available at https://zhanglab.ccmb.med.umich.edu/FASPR and https://github.com/tommyhuangthu/FASPR. Supplementary information Supplementary data are available at Bioinformatics online.

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Posttranslational modifications in proteins: resources, tools and prediction methods

Database ◽

10.1093/database/baab012 ◽

2021 ◽

Author(s):

Shahin Ramazi ◽

Javad Zahiri

Keyword(s):

Computational Methods ◽

Posttranslational Modifications ◽

Side Chain ◽

Amino Acid Side Chain ◽

Cellular Processes ◽

Online Databases ◽

Different Types ◽

Protein Functions ◽

And Function ◽

Molecular Regulatory Mechanisms

Abstract Posttranslational modifications (PTMs) refer to amino acid side chain modification in some proteins after their biosynthesis. There are more than 400 different types of PTMs affecting many aspects of protein functions. Such modifications happen as crucial molecular regulatory mechanisms to regulate diverse cellular processes. These processes have a significant impact on the structure and function of proteins. Disruption in PTMs can lead to the dysfunction of vital biological processes and hence to various diseases. High-throughput experimental methods for discovery of PTMs are very laborious and time-consuming. Therefore, there is an urgent need for computational methods and powerful tools to predict PTMs. There are vast amounts of PTMs data, which are publicly accessible through many online databases. In this survey, we comprehensively reviewed the major online databases and related tools. The current challenges of computational methods were reviewed in detail as well.

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