Binding of Amino Acids with a Bifunctional Metalloporphyrin via Concurrent Metal-Coordination and Electrostatic Interactions

1989 ◽  
Vol 18 (10) ◽  
pp. 1877-1880 ◽  
Author(s):  
Yasuhiro Aoyama ◽  
Shin-ichi Nonaka ◽  
Tadahiro Motomura ◽  
Hisanobu Ogoshi
Keyword(s):  
Amino Acids ◽  
Electrostatic Interactions ◽  
Metal Coordination

A biomimetic strategy for the selective recognition of organophosphates in 100% water: synergies of electrostatic interactions, cavity embedment and metal coordination

2019 ◽  
Vol 6 (10) ◽  
pp. 1627-1636 ◽  
Author(s):  
Solène Collin ◽  
Nicolas Giraud ◽  
Elise Dumont ◽  
Olivia Reinaud
Keyword(s):  
Electrostatic Interactions ◽  
Metal Coordination ◽  
Selective Recognition

A biomimetic receptor allows selective recognition of organophosphates in water thanks to multipoint recognition associating coordination, electrostatics and cavity hosting.

scholarly journals Role of a tryptophan anchor in human topoisomerase I structure, function and inhibition

2008 ◽  
Vol 411 (3) ◽  
pp. 523-530 ◽  
Author(s):  
Gary S. Laco ◽  
Yves Pommier
Keyword(s):  
Amino Acids ◽  
Topoisomerase I ◽  
Electrostatic Interactions ◽  
Functional Domain ◽  
Site Mutation ◽  
Supercoiled Dna ◽  
Terminal Domain ◽  
Tryptophan Residues ◽  
N Terminus

Human Top1 (topoisomerase I) relaxes supercoiled DNA during cell division and transcription. Top1 is composed of 765 amino acids and contains an unstructured N-terminal domain of 200 amino acids, and a structured functional domain of 565 amino acids that binds and relaxes supercoiled DNA. In the present study we examined the region spanning the junction of the N-terminal domain and functional domain (junction region). Analysis of several published Top1 structures revealed that three tryptophan residues formed a network of aromatic stacking interactions and electrostatic interactions that anchored the N-terminus of the functional domain to sub-domains containing the nose cone and active site. Mutation of the three tryptophan residues (Trp203/Trp205/Trp206) to an alanine residue, either individually or together, in silico revealed that the individual tryptophan residue's contribution to the tryptophan ‘anchor’ was additive. When the three tryptophan residues were mutated to alanine in vitro, the resulting mutant Top1 differed from wild-type Top1 in that it lacked processivity, exhibited resistance to camptothecin and was inactivated by urea. The results indicated that the tryptophan anchor stabilized the N-terminus of the functional domain and prevented the loss of Top1 structure and function.

scholarly journals Homochirality Is Originated from Handedness of Helices

2020 ◽  
Author(s):  
Shubin Liu
Keyword(s):  
Amino Acids ◽  
Asymmetric Synthesis ◽  
Electrostatic Interactions ◽  
Alpha Helix ◽  
Root Cause ◽  
Macromolecular Assembly ◽  
Nucleotide Sugars ◽  
Cooperativity Effects ◽  
Natural Amino Acids ◽  
Origin Of Homochirality

Homochirality is a common feature of amino acids and carbohydrates, whose origin is still unknown. For example, 19 of 20 natural amino acids are L-chiral but deoxyribose sugars in DNA are always D-chiral. Meanwhile, right-handed helices are ubiquitous in nature. Are these two phenomena intrinsically correlated? Here, we propose that homochirality of amino acids and nucleotide sugars is originated from the handedness of helices. We show that right-handed 3<sub>10-</sub>helix and alpha-helix favor the L-chiral form for amino acids, but for deoxyribose sugars right-handed helices prefer the D-chiral form instead. Our analyses unveil that there exist strong cooperativity effects dominated by electrostatic interactions. This work not only resolves the mystery of homochirality by providing a unified explanation for the origin of homochirality in proteins and DNA using helical secondary structures as the root cause, but also ratifies the Principle of Chirality Hierarchy, where chirality of a higher hierarchy dictates that of lower ones. Possible applications of the present work to asymmetric synthesis and macromolecular assembly are discussed.

scholarly journals SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure

2019 ◽  
Vol 24 (9) ◽  
pp. 928-938 ◽  
Author(s):  
Luca Palazzolo ◽  
Chiara Paravicini ◽  
Tommaso Laurenzi ◽  
Sara Adobati ◽  
Simona Saporiti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Amino Acid ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Amino Acid Residues ◽  
Dibasic Amino Acid ◽  
Novel Target ◽  
Function Relationship ◽  
Dynamics Simulations

SLC6A14 (ATB0,+) is a sodium- and chloride-dependent neutral and dibasic amino acid transporter that regulates the distribution of amino acids across cell membranes. The transporter is overexpressed in many human cancers characterized by an increased demand for amino acids; as such, it was recently acknowledged as a novel target for cancer therapy. The knowledge on the molecular mechanism of SLC6A14 transport is still limited, but some elegant studies on related transporters report the involvement of the 12 transmembrane α-helices in the transport mechanism, and describe structural rearrangements mediated by electrostatic interactions with some pivotal gating residues. In the present work, we constructed a SLC6A14 model in outward-facing conformation via homology modeling and used molecular dynamics simulations to predict amino acid residues critical for substrate recognition and translocation. We docked the proteinogenic amino acids and other known substrates in the SLC6A14 binding site to study both gating regions and the exposed residues involved in transport. Interestingly, some of these residues correspond to those previously identified in other LeuT-fold transporters; however, we could also identify a novel relevant residue with such function. For the first time, by combined approaches of molecular docking and molecular dynamics simulations, we highlight the potential role of these residues in neutral amino acid transport. This novel information unravels new aspects of the human SLC6A14 structure–function relationship and may have important outcomes for cancer treatment through the design of novel inhibitors of SLC6A14-mediated transport.

scholarly journals Diverse protein assembly driven by metal and chelating amino acids with selectivity and tunability

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Minwoo Yang ◽  
Woon Ju Song
Keyword(s):  
Amino Acids ◽  
Self Assembly ◽  
Protein Structures ◽  
Functional Materials ◽  
Building Blocks ◽  
Unnatural Amino Acid ◽  
Metal Coordination ◽  
Specific Chemical ◽  
Natural Building ◽  
Kinetics Of

AbstractProteins are versatile natural building blocks with highly complex and multifunctional architectures, and self-assembled protein structures have been created by the introduction of covalent, noncovalent, or metal-coordination bonding. Here, we report the robust, selective, and reversible metal coordination properties of unnatural chelating amino acids as the sufficient and dominant driving force for diverse protein self-assembly. Bipyridine-alanine is genetically incorporated into a D3 homohexamer. Depending on the position of the unnatural amino acid, 1-directional, crystalline and noncrystalline 2-directional, combinatory, and hierarchical architectures are effectively created upon the addition of metal ions. The length and shape of the structures is tunable by altering conditions related to thermodynamics and kinetics of metal-coordination and subsequent reactions. The crystalline 1-directional and 2-directional biomaterials retain their native enzymatic activities with increased thermal stability, suggesting that introducing chelating ligands provides a specific chemical basis to synthesize diverse protein-based functional materials while retaining their native structures and functions.

Peculiarities of electrostatic interactions between amino acids and salicylic acid in aqueous solution

BIOPHYSICS ◽  
2009 ◽  
Vol 54 (2) ◽  
pp. 139-142
Author(s):  
V. P. Barannikov ◽  
V. G. Badelin ◽  
M. B. Berezin
Keyword(s):  
Aqueous Solution ◽  
Amino Acids ◽  
Salicylic Acid ◽  
Electrostatic Interactions

Electrostatic and potential cation-π forces may guide the interaction of extracellular loop III with Na+ and bile acids for human apical Na+-dependent bile acid transporter

2008 ◽  
Vol 410 (2) ◽  
pp. 391-400 ◽  
Author(s):  
Antara Banerjee ◽  
Naissan Hussainzada ◽  
Akash Khandelwal ◽  
Peter W. Swaan
Keyword(s):  
Amino Acids ◽  
Bile Acid ◽  
Bile Acids ◽  
Conformational Changes ◽  
Electrostatic Interactions ◽  
Extracellular Loop ◽  
Membrane Expression ◽  
Ligand Interaction ◽  
Bile Acid Transporter ◽  
Acid Transporter

The hASBT (human apical Na+-dependent bile acid transporter) constitutes a key target of anti-hypercholesterolaemic therapies and pro-drug approaches; physiologically, hASBT actively reclaims bile acids along the terminal ileum via Na+ co-transport. Previously, TM (transmembrane segment) 7 was identified as part of the putative substrate permeation pathway using SCAM (substitute cysteine accessibility mutagenesis). In the present study, SCAM was extended through EL3 (extracellular loop 3; residues Arg254–Val286) that leads into TM7 from the exofacial matrix. Activity of most EL3 mutants was significantly hampered upon cysteine substitution, whereas ten (out of 31) were functionally inactive (<10% activity). Since only E282C lacked plasma membrane expression, EL3 amino acids predominantly fulfill critical functional roles during transport. Oppositely charged membrane-impermeant MTS (methanethiosulfonate) reagents {MTSET [(2-trimethylammonium) ethyl MTS] and MTSES [(2-sulfonatoethyl) MTS]} produced mostly similar inhibition profiles wherein only middle and descending loop segments (residues Thr267–Val286) displayed significant MTS sensitivity. The presence of bile acid substrate significantly reduced the rates of MTS modification for all MTS-sensitive mutants, suggesting a functional association between EL3 residues and bile acids. Activity assessments at equilibrative [Na+] revealed numerous Na+-sensitive residues, possibly performing auxiliary functions during transport such as transduction of protein conformational changes during translocation. Integration of these data suggests ligand interaction points along EL3 via electrostatic interactions with Arg256, Glu261 and probably Glu282 and a potential cation-π interaction with Phe278. We conclude that EL3 amino acids are essential for hASBT activity, probably as primary substrate interaction points using long-range electrostatic attractive forces.

scholarly journals Intra-helical salt bridge contribution to membrane protein insertion

2021 ◽  
Author(s):  
Gerard Duart ◽  
John Lamb ◽  
Arne Elofsson ◽  
Ismael Mingarro
Keyword(s):  
Amino Acids ◽  
Membrane Protein ◽  
Electrostatic Interactions ◽  
Salt Bridge ◽  
Protein Stabilization ◽  
Membrane Insertion ◽  
Salt Bridges ◽  
Protein Insertion

ABSTRACTSalt bridges between negatively (D, E) and positively charged (K, R, H) amino acids play an important role in protein stabilization. This has a more prevalent effect in membrane proteins where polar amino acids are exposed to a very hydrophobic environment. In transmembrane (TM) helices the presence of charged residues can hinder the insertion of the helices into the membrane. This can sometimes be avoided by TM region rearrangements after insertion, but it is also possible that the formation of salt bridges could decrease the cost of membrane integration. However, the presence of intra-helical salt bridges in TM domains and their effect on insertion has not been properly studied yet. In this work, we use an analytical pipeline to study the prevalence of charged pairs of amino acid residues in TM α-helices, which shows that potentially salt-bridge forming pairs are statistically over-represented. We then selected some candidates to experimentally determine the contribution of these electrostatic interactions to the translocon-assisted membrane insertion process. Using both in vitro and in vivo systems, we confirm the presence of intra-helical salt bridges in TM segments during biogenesis and determined that they contribute between 0.5-0.7 kcal/mol to the apparent free energy of membrane insertion (ΔGapp). Our observations suggest that salt bridge interactions can be stabilized during translocon-mediated insertion and thus could be relevant to consider for the future development of membrane protein prediction software.

scholarly journals Mechanism and site of action of big dynorphin on ASIC1a

2019 ◽  
Author(s):  
C.B. Borg ◽  
N. Braun ◽  
S.A. Heusser ◽  
Y. Bay ◽  
D. Weis ◽  
...  
Keyword(s):  
Amino Acids ◽  
Ischemic Stroke ◽  
Amino Acid ◽  
Binding Site ◽  
Neuronal Death ◽  
Electrostatic Interactions ◽  
Rational Design ◽  
Site Of Action ◽  
Canonical Amino Acid

AbstractAcid-sensing ion channels (ASICs) are proton-gated cation channels that contribute to neurotransmission, as well as initiation of pain and neuronal death following ischemic stroke. As such, there is a great interest in understanding the in vivo regulation of ASICs, especially by endogenous neuropeptides that potently modulate ASICs. The most potent endogenous ASIC modulator known to date is the opioid neuropeptide big dynorphin (BigDyn). BigDyn is upregulated in chronic pain and increases ASIC-mediated neuronal death during acidosis. Understanding the mechanism and site of action of BigDyn on ASICs could thus enable the rational design of compounds potentially useful in the treatment of pain and ischemic stroke. To this end, we employ a combination of electrophysiology, voltage-clamp fluorometry, synthetic BigDyn analogs and non-canonical amino acid-mediated photocrosslinking. We demonstrate that BigDyn binding results in an ASIC1a closed resting conformation that is distinct from open and desensitized states induced by protons. Using alanine-substituted BigDyn analogs, we find that the BigDyn modulation of ASIC1a is mediated through electrostatic interactions of basic amino acids in the BigDyn N-terminus. Furthermore, neutralizing acidic amino acids in the ASIC1a extracellular domain reduces BigDyn effects, suggesting a binding site at the acidic pocket. This is confirmed by photocrosslinking using the non-canonical amino acid azido-phenylalanine. Overall, our data define the mechanism of how BigDyn modulates ASIC1a, identify the acidic pocket as the binding site for BigDyn and thus highlight this cavity as an important site for the development of ASIC-targeting therapeutics.Significance StatementNeuropeptides such as big dynorphin (BigDyn) play important roles in the slow modulation of fast neurotransmission, which is mediated by membrane-embedded receptors. In fact, BigDyn is the most potent known endogenous modulator of one such receptor, the acid-sensing ion channel (ASIC), but the mode of action remains unknown. In this work, we employ a broad array of technologies to unravel the details of where big dynorphin binds to ASIC and how it modulates its activity. As both BigDyn and ASIC are implicated in pain pathways, this work might pave the way towards future analgesics.

scholarly journals PtdIns4P-mediated electrostatic forces influence S-acylation of peripheral proteins at the Golgi complex

2020 ◽  
Vol 40 (1) ◽  
Author(s):  
Sabrina Chumpen Ramirez ◽  
Micaela R. Astrada ◽  
Jose L. Daniotti
Keyword(s):  
Amino Acids ◽  
Golgi Complex ◽  
Electrostatic Interactions ◽  
Transmembrane Protein ◽  
Basic Amino Acid ◽  
Soluble Proteins ◽  
Post Translational Modification ◽  
Hydrophobic Region ◽  
Membrane Interaction ◽  
Basic Amino Acids

Abstract Protein S-acylation is a reversible post-translational modification involving the addition of fatty acids to cysteines and is catalyzed by transmembrane protein acyltransferases (PATs) mainly expressed at the Golgi complex. In case of soluble proteins, S-acylation confers stable membrane attachment. Myristoylation or farnesylation of many soluble proteins constitutes the initial transient membrane adsorption step prior to S-acylation. However, some S-acylated soluble proteins, such as the neuronal growth-associated protein Growth-associated protein-43 (GAP-43), lack the hydrophobic modifications required for this initial membrane interaction. The signals for GAP-43 S-acylation are confined to the first 13 amino acids, including the S-acylatable cysteines 3 and 4 embedded in a hydrophobic region, followed by a cluster of basic amino acids. We found that mutation of critical basic amino acids drastically reduced membrane interaction and hence S-acylation of GAP-43. Interestingly, acute depletion of phosphatidylinositol 4-phosphate (PtdIns4P) at the Golgi complex reduced GAP-43 membrane binding, highlighting a new, pivotal role for this anionic lipid and supporting the idea that basic amino acid residues are involved in the electrostatic interactions between GAP-43 and membranes of the Golgi complex where they are S-acylated.

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