scholarly journals Thermodynamics of semi-specific ligand recognition: the binding of dipeptides to the E.coli dipeptide binding protein DppA

2021 ◽  
Author(s):  
Mohamad K. M. Zainol ◽  
Robert J. C. Linforth ◽  
Donald J. Winzor ◽  
David J. Scott
Keyword(s):  
Hydrophobic Interactions ◽  
Chemical Reactivity ◽  
Water Structure ◽  
Binding Pocket ◽  
Titration Calorimetry ◽  
Water Molecules ◽  
Aqueous Environment ◽  
Arginine Residues ◽  
Structure Flexibility

AbstractThis investigation of the temperature dependence of DppA interactions with a subset of three dipeptides (AA. AF and FA) by isothermal titration calorimetry has revealed the negative heat capacity ($$\Delta {C}_{p}^{o}$$ Δ C p o ) that is a characteristic of hydrophobic interactions. The observation of enthalpy–entropy compensation is interpreted in terms of the increased structuring of water molecules trapped in a hydrophobic environment, the enthalpic energy gain from which is automatically countered by the entropy decrease associated with consequent loss of water structure flexibility. Specificity for dipeptides stems from appropriate spacing of designated DppA aspartate and arginine residues for electrostatic interaction with the terminal amino and carboxyl groups of a dipeptide, after which the binding pocket closes to become completely isolated from the aqueous environment. Any differences in chemical reactivity of the dipeptide sidechains are thereby modulated by their occurrence in a hydrophobic environment where changes in the structural state of entrapped water molecules give rise to the phenomenon of enthalpy–entropy compensation. The consequent minimization of differences in the value of ΔG0 for all DppA–dipeptide interactions thus provides thermodynamic insight into the biological role of DppA as a transporter of all dipeptides across the periplasmic membrane.

scholarly journals Ablation of the Complementarity-Determining Region H3 Apex of the Anti-HIV-1 Broadly Neutralizing Antibody 2F5 Abrogates Neutralizing Capacity without Affecting Core Epitope Binding

2010 ◽  
Vol 84 (9) ◽  
pp. 4136-4147 ◽  
Author(s):  
Jean-Philippe Julien ◽  
Nerea Huarte ◽  
Rubén Maeso ◽  
Stefka G. Taneva ◽  
Annie Cunningham ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Hydrophobic Interactions ◽  
Neutralizing Antibody ◽  
Titration Calorimetry ◽  
Peptide Epitope ◽  
Neutralizing Capacity ◽  
Epitope Binding ◽  
Hiv 1 ◽  
Complementarity Determining Region

ABSTRACT The identification and characterization of broadly neutralizing antibodies (bnAbs) against HIV-1 has formed a major research focus, with the ultimate goal to help in the design of an effective AIDS vaccine. One of these bnAbs, 2F5, has been extensively characterized, and residues at the apex of its unusually long complementarity-determining region (CDR) H3 loop have been shown to be crucial for neutralization. Structural studies, however, have revealed that the 100TLFGVPI100F apex residues of the CDR H3 loop do not interact directly with residues of its core gp41 epitope. In an attempt to gain better insight into the functional role of this element, we have recombinantly expressed native 2F5 Fab and two mutants in which either the apical Phe100B(H) residue was changed to an alanine or the CDR H3 residues 100TLFGVPI100F were replaced by a Ser-Gly dipeptide linker. Isothermal titration calorimetry (ITC) and competitive-binding enzyme-linked immunosorbent assays (ELISAs) rendered strikingly similar affinity constants (Kd [dissociation constant] of ∼20 nM) for linear peptide epitope binding by 2F5 Fabs, independent of the presence or absence of the apex residues. Ablation of the CDR H3 apex residues, however, abolished the cell-cell fusion inhibition and pseudovirus neutralization capacities of 2F5 Fab. We report competitive ELISA data that suggest a role of 2F5 CDR H3 apex residues in mediating weak hydrophobic interactions with residues located at the C terminus of the gp41 membrane proximal external region and/or membrane components in the context of core epitope binding. The present data therefore imply an extended 2F5 paratope that includes weak secondary interactions that are crucial for neutralization of Env-mediated fusion.

scholarly journals Role of water in sweet taste chemoreception

2002 ◽  
Vol 74 (7) ◽  
pp. 1103-1108 ◽  
Author(s):  
Gordon G. Birch
Keyword(s):  
Water Structure ◽  
Sweet Taste ◽  
Taste Quality ◽  
Water Molecules ◽  
Ionic Charge ◽  
Hydration Shells ◽  
Specific Volumes ◽  
The Ideal

The mechanistic understanding of sweet taste chemoreception has been advanced by the microscopic and macroscopic studies of sweetener­water interactions. This approach has led to the concept of water mobility as a key to interpreting sweetness. The apparent specific volume of a solution is a determinant of its taste quality, as sweetness is known to be confined to the range 0.51­0.71 cm3 g-1. Thus, the "ideal" quality of the sugars is presumed to be due to their occupancy of the center of this range (i.e., 0.618 cm3 g-1). Most sweeteners elicit off-tastes and flavors and exhibit different apparent specific volumes. This leads to the conclusion that taste quality is broadly determined by the packing characteristics of sweet molecules among water molecules and the compactness of their hydration shells, expressed as their apparent specific isentropic compressibilities. The role of water can, therefore, be applied in modern attempts to optimize sweet taste quality, and different food salts can be explored as useful taste modifiers. Salts interact more strongly with water structure than do any other taste solutes, and it emerges that the ionic charge density is an important criterion. Such studies show how sweetener formulations are likely to improve within the next decade.

scholarly journals Elucidation of Molecular Mechanism of a Selective PPARα Modulator, Pemafibrate, through Combinational Approaches of X-ray Crystallography, Thermodynamic Analysis, and First-Principle Calculations

2020 ◽  
Vol 21 (1) ◽  
pp. 361 ◽  
Author(s):  
Mayu Kawasaki ◽  
Akira Kambe ◽  
Yuta Yamamoto ◽  
Sundaram Arulmozhiraja ◽  
Sohei Ito ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Molecular Mechanism ◽  
Structural Changes ◽  
Molecular Level ◽  
Hydrophobic Interactions ◽  
Binding Pocket ◽  
Titration Calorimetry ◽  
X Ray ◽  
X Ray Crystallography ◽  
Steroid Receptor Coactivator

The selective PPARα modulator (SPPARMα) is expected to medicate dyslipidemia with minimizing adverse effects. Recently, pemafibrate was screened from the ligand library as an SPPARMα bearing strong potency. Several clinical pieces of evidence have proved the usefulness of pemafibrate as a medication; however, how pemafibrate works as a SPPARMα at the molecular level is not fully known. In this study, we investigate the molecular mechanism behind its novel SPPARMα character through a combination of approaches of X-ray crystallography, isothermal titration calorimetry (ITC), and fragment molecular orbital (FMO) analysis. ITC measurements have indicated that pemafibrate binds more strongly to PPARα than to PPARγ. The crystal structure of PPARα-ligand binding domain (LBD)/pemafibrate/steroid receptor coactivator-1 peptide (SRC1) determined at 3.2 Å resolution indicates that pemafibrate binds to the ligand binding pocket (LBP) of PPARα in a Y-shaped form. The structure also reveals that the conformation of the phenoxyalkyl group in pemafibrate is flexible in the absence of SRC1 coactivator peptide bound to PPARα; this gives a freedom for the phenoxyalkyl group to adopt structural changes induced by the binding of coactivators. FMO calculations have indicated that the accumulation of hydrophobic interactions provided by the residues at the LBP improve the interaction between pemafibrate and PPARα compared with the interaction between fenofibrate and PPARα.

scholarly journals High integrin αVβ6 affinity reached by hybrid domain deletion slows ligand-binding on-rate

2018 ◽  
Vol 115 (7) ◽  
pp. E1429-E1436 ◽  
Author(s):  
Xianchi Dong ◽  
Bo Zhao ◽  
Fu-Yang Lin ◽  
Chafen Lu ◽  
Bruce N. Rogers ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Pocket ◽  
Titration Calorimetry ◽  
Closed Conformation ◽  
Hybrid Domain ◽  
Open Conformation ◽  
Integrin Αvβ6 ◽  
Domain Truncation ◽  
Kinetics Of

The role of the hybrid domain in integrin affinity regulation is unknown, as is whether the kinetics of ligand binding is modulated by integrin affinity state. Here, we compare cell surface and soluble integrin αVβ6 truncation mutants for ligand-binding affinity, kinetics, and thermodynamics. Removal of the integrin transmembrane/cytoplasmic domains or lower legs has little effect on αVβ6 affinity, in contrast to β1 integrins. In integrin opening, rearrangement at the interface between the βI and hybrid domains is linked to remodeling at the ligand-binding site at the opposite end of the βI domain, which greatly increases in affinity in the open conformation. The larger size of the βI-hybrid interface in the closed state suggests that the hybrid domain stabilizes closing. In agreement, deletion of the hybrid domain raised affinity by 50-fold. Surface plasmon resonance and isothermal titration calorimetry gave similar results and the latter revealed tradeoffs between enthalpy and entropy not apparent from affinity. At extremely high affinity reached in Mn2+ with hybrid domain truncation, αVβ6 on-rate for both pro-TGF-β1 and fibronectin declined. The results suggest that the open conformation of αVβ6 has lower on-rate than the closed conformation, correlate with constriction of the ligand-binding pocket in open αVβ6 structures, and suggest that the extended-closed conformation is kinetically selected for ligand binding. Subsequent transition to the extended-open conformation is stabilized by its much higher affinity for ligand and would also be stabilized by force exerted across ligand-bound integrins by the actin cytoskeleton.

scholarly journals Recognition of N6-methyladenosine by the YTHDC1 YTH domain studied by molecular dynamics and NMR spectroscopy: The role of hydration

2021 ◽  
Author(s):  
Miroslav Krepl ◽  
Fred Franz Damberger ◽  
Christine von Schroetter ◽  
Dominik Theler ◽  
Pavlína Pokorná ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Binding Pocket ◽  
Bulk Water ◽  
Titration Calorimetry ◽  
Water Molecules ◽  
Water Network ◽  
Solvent Interactions ◽  
Yth Domain ◽  
The Cost

AbstractBackgroundThe YTH domain of YTHDC1 belongs to a class of protein “readers”, recognizing the N6-methyladenosine (m6A) chemical modification in mRNA. Static ensemble-averaged structures revealed details of N6-methyl recognition via a conserved aromatic cage.MethodsWe performed molecular dynamics (MD) simulations along with nuclear magnetic resonance (NMR) and isothermal titration calorimetry (ITC) measurements to examine how dynamics and solvent interactions contribute to the m6A recognition and negative selectivity towards unmethylated substrate.ResultsAn intricate network of water-mediated interactions surrounds bound m6A. The unmethylated adenosine allows disruptive intrusions of bulk water deep into the binding pocket, increasing selectivity for m6A. We furthermore show that the YTHDC1’s preference for the 5′-Gm6A-3′ motif is partially facilitated by a network of water-mediated interactions between the 2-amino group of the preceding guanosine and residues deep in the m6A binding pocket. The 5′-Im6A-3′ (where I is inosine) motif can be recognized as well at the cost of disrupting the water network and a small decrease in affinity. The YTHDC1 D479A mutant, which interrupts the water network, also destabilizes m6A binding. Lastly, we formulate and test an easy-to-implement approach for increasing the agreement between simulations and NMR experiments by using the HBfix potential function for stabilization of key NOE distances. We call the new approach NOEfix.ConclusionsThe structured water molecules surrounding the bound RNA and the methylated substrate’s ability to exclude bulk water molecules are important elements of the YTH domain’s preference for m6A. Network of water molecules also fine tunes the specificity towards 5′-Gm6A-3′ motifs.General SignificanceOur interdisciplinary study of YTHDC1 protein/RNA complex reveals an unusual mechanism by which solvent dynamics can contribute towards recognition of methylation by proteins.

Isolation of Natural Compounds from Syzygium densiflorum Fruits and Exploring its Chemical Property, Therapeutic Role in Diabetic Management

2020 ◽  
Vol 10 (2) ◽  
pp. 168-176
Author(s):  
Krishnasamy Gopinath ◽  
Nagarajan Subbiah ◽  
Muthusamy Karthikeyan
Keyword(s):  
Density Functional ◽  
Chemical Reactivity ◽  
Natural Compounds ◽  
Structure Activity Relationship ◽  
Activity Relationship ◽  
Computational Studies ◽  
Therapeutic Role ◽  
Relationship Analysis ◽  
Structure Activity

Background: Syzygium densiflorum Wall. ex Wight & Arn (Myrtaceae) has been traditionally used by the local tribes of the Nilgiris, Tamil Nadu, India, for the treatment of diabetes. Objective: This study aimed to isolate the major phytoconstituents from the S. densiflorum fruits and to perform computational studies for chemical reactivity and biological activity of the isolated compound. Materials and Methods: Two different compounds were isolated from ethanolic extract of S. densiflorum fruits and purified using HPLC. The structures of the compounds were elucidated on the basis of their 1H NMR, 13C NMR, 1H-1H COSY, HMBC, HRESIMS, and FT-IR data. Further, the chemical reactivity of the compounds was analyzed by density functional theory calculations and its therapeutic role in diabetic management was examined by comparing the structure of isolated compounds with previously reported bioactive compounds. Results: Of the two compounds ((6,6 & 1-kestopentaose (1) and 6-(hydroxymethyl)-3-[3,4,5- trihydroxy- 6-[(3,4,5-trihydroxyoxan-2-yl)oxymethyl]oxan-2-yl]oxyoxane-2,4,5-triol)(2)). β-glucosidase, β-galactosidase, α-glucosidase and β-amylase inhibition activity of the compounds were predicted by structure activity relationship. Conclusion: Structure-activity relationship analysis was performed to predict the therapeutic role of isolated compounds. These computational studies may be performed to minimize the efforts to determine the therapeutic role of natural compounds.

Effect of aqueous environment in chemical reactivity of monolignols. A New Fukui Function Study

2009 ◽  
Vol 28 (2) ◽  
pp. 196-201 ◽  
Author(s):  
Carmen Martínez ◽  
Miriam Sedano ◽  
Jorge Mendoza ◽  
Rafael Herrera ◽  
Jose G. Rutiaga ◽  
...  
Keyword(s):  
Chemical Reactivity ◽  
Fukui Function ◽  
Aqueous Environment ◽  
Function Study

scholarly journals Mr 46,000 mannose 6-phosphate receptor. The role of histidine and arginine residues for binding of ligand.

1991 ◽  
Vol 266 (5) ◽  
pp. 2917-2923 ◽  
Author(s):  
M Wendland ◽  
A Waheed ◽  
K von Figura ◽  
R Pohlmann
Keyword(s):  
Arginine Residues ◽  
Mannose 6 Phosphate

scholarly journals Substrate wettability guided oriented self assembly of Janus particles

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Meneka Banik ◽  
Shaili Sett ◽  
Chirodeep Bakli ◽  
Arup Kumar Raychaudhuri ◽  
Suman Chakraborty ◽  
...  
Keyword(s):  
Self Assembly ◽  
Janus Particles ◽  
Water Molecules ◽  
Functional Coatings ◽  
Hexagonal Close Packed ◽  
Local Densities ◽  
Inhomogeneous Properties ◽  
Metal Polymer ◽  
Specific Orientation

AbstractSelf-assembly of Janus particles with spatial inhomogeneous properties is of fundamental importance in diverse areas of sciences and has been extensively observed as a favorably functionalized fluidic interface or in a dilute solution. Interestingly, the unique and non-trivial role of surface wettability on oriented self-assembly of Janus particles has remained largely unexplored. Here, the exclusive role of substrate wettability in directing the orientation of amphiphilic metal-polymer Bifacial spherical Janus particles, obtained by topo-selective metal deposition on colloidal Polymestyere (PS) particles, is explored by drop casting a dilute dispersion of the Janus colloids. While all particles orient with their polymeric (hydrophobic) and metallic (hydrophilic) sides facing upwards on hydrophilic and hydrophobic substrates respectively, they exhibit random orientation on a neutral substrate. The substrate wettability guided orientation of the Janus particles is captured using molecular dynamic simulation, which highlights that the arrangement of water molecules and their local densities near the substrate guide the specific orientation. Finally, it is shown that by spin coating it becomes possible to create a hexagonal close-packed array of the Janus colloids with specific orientation on differential wettability substrates. The results reported here open up new possibilities of substrate-wettability driven functional coatings of Janus particles, which has hitherto remained unexplored.

Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4

Glycobiology ◽  
2021 ◽  
Author(s):  
Margrethe Gaardløs ◽  
Sergey A Samsonov ◽  
Marit Sletmoen ◽  
Maya Hjørnevik ◽  
Gerd Inger Sætrom ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Conformational Changes ◽  
Molecular Mechanisms ◽  
Hydrophobic Interactions ◽  
Substrate Binding ◽  
Interdisciplinary Approach ◽  
Product Formation ◽  
Titration Calorimetry ◽  
Binding Groove ◽  
Dynamics Simulations

Abstract Mannuronan C-5 epimerases catalyse the epimerization of monomer residues in the polysaccharide alginate, changing the physical properties of the biopolymer. The enzymes are utilized to tailor alginate to numerous biological functions by alginate-producing organisms. The underlying molecular mechanisms that control the processive movement of the epimerase along the substrate chain is still elusive. To study this, we have used an interdisciplinary approach combining molecular dynamics simulations with experimental methods from mutant studies of AlgE4, where initial epimerase activity and product formation were addressed with NMR spectroscopy, and characteristics of enzyme-substrate interactions were obtained with isothermal titration calorimetry and optical tweezers. Positive charges lining the substrate-binding groove of AlgE4 appear to control the initial binding of poly-mannuronate, and binding also seems to be mediated by both electrostatic and hydrophobic interactions. After the catalytic reaction, negatively charged enzyme residues might facilitate dissociation of alginate from the positive residues, working like electrostatic switches, allowing the substrate to translocate in the binding groove. Molecular simulations show translocation increments of two monosaccharide units before the next productive binding event resulting in MG-block formation, with the epimerase moving with its N-terminus towards the reducing end of the alginate chain. Our results indicate that the charge pair R343-D345 might be directly involved in conformational changes of a loop that can be important for binding and dissociation. The computational and experimental approaches used in this study complement each other, allowing for a better understanding of individual residues’ roles in binding and movement along the alginate chains.

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