1
|
Pinillos P, Camiruaga A, Torres-Hernández F, Basterrechea FJ, Usabiaga I, Fernández JA. Exploring the interaction sites in glucose and galactose using phenol as a probe. Phys Chem Chem Phys 2023; 25:7205-7212. [PMID: 36846922 DOI: 10.1039/d2cp06036a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Sugars, together with amino acids and nucleobases, are the fundamental building blocks of a cell. They are involved in many fundamental processes and they especially play relevant roles as part of the immune system. The latter is connected to their ability to establish a collection of intermolecular interactions, depending on the position of their hydroxyl groups. Here we explore how the position of the OH in C4, the anomeric conformation and the nature substituent affect the interaction with phenol, which serves as a probe of the preferred site for the interaction. Using mass-resolved excitation spectroscopy and density functional calculations, we unravel the structure of the dimers and compare their conformation with those found for similar systems. The main conclusion is that the hydroxymethyl group has a very strong influence, guiding the whole aggregation process and that the position of the substituent in C4 has a stronger influence on the final structure of the dimer than the anomeric conformation.
Collapse
Affiliation(s)
- Paúl Pinillos
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Ander Camiruaga
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Fernando Torres-Hernández
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Francisco J Basterrechea
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Imanol Usabiaga
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - José A Fernández
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| |
Collapse
|
2
|
Khavani M, Mehranfar A, Mofrad MRK. On the potentials of sialic acid derivatives as inhibitors for the mumps virus: A molecular dynamics and quantum chemistry investigation. Virus Res 2023; 326:199050. [PMID: 36682462 DOI: 10.1016/j.virusres.2023.199050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/21/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Mumps virus is an infectious pathogen causing major health problems for humans such as encephalitis, orchitis, and parotitis. Therefore, designing an inhibitor for this virus is of great medical and public health importance. With this goal in mind, we investigate the affinity of different sialic acid-based compounds (ligands) against the hemagglutinin-neuraminidase (HN) protein of the mumps virus, using a combination of molecular dynamics (MD) simulations and quantum chemistry calculations. Our MD simulation results indicate that the ligands form stable complexes with the HN protein through a combination of electrostatic, van der Waals (vdW), and hydrogen bond (H-bond) interactions, which the electrostatic interactions play a more important role in the complexation process. Based on the obtained results from the structural analysis Arg381, Arg291, and Arg49 play a key role in the binding site interactions with the different ligands, in comparison with other residues. There are some candidates such as Neu5Acα2-6Galβ1-4GlcNAcβ, Neu5Acα2-3Galβ1-3GlcNacβ1-3Galβ1-4Glc, and Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4Glc that form more stable complexes with the HN than the α2-3-Sialyllactose confirmed by the calculated Gibbs binding energies (-39.65, -46.93, and -36.49 kcal.mol-1, respectively). To investigate the relationship between the molecular properties of the selected compounds and their affinity to the HN receptor, density functional theory dispersion corrected (DFT-D3) calculations were employed. According to our DFT-D3 results, neutral sialic acid-based compounds have lower reactivity to the mumps virus than the negativity charge structures. Moreover, by increasing the electronic chemical potential (μ) the vdW and H-bond interactions between drugs and the HN protein increase. In other words, by elevating the electron tendency of the selected ligands their affinity to the mumps virus increases. Our quantum chemistry calculations reveal that in addition to the structural features the molecular properties of the drugs can play important roles in their affinity and reactivity against the virus. The results of this study can provide useful details to design new compounds or improve their properties against the mumps virus.
Collapse
Affiliation(s)
- Mohammad Khavani
- Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Aliyeh Mehranfar
- Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Mohammad R K Mofrad
- Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California Berkeley, Berkeley, CA 94720, USA.
| |
Collapse
|
3
|
Carbohydrate-aromatic interface and molecular architecture of lignocellulose. Nat Commun 2022; 13:538. [PMID: 35087039 PMCID: PMC8795156 DOI: 10.1038/s41467-022-28165-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
Plant cell walls constitute the majority of lignocellulosic biomass and serve as a renewable resource of biomaterials and biofuel. Extensive interactions between polysaccharides and the aromatic polymer lignin make lignocellulose recalcitrant to enzymatic hydrolysis, but this polymer network remains poorly understood. Here we interrogate the nanoscale assembly of lignocellulosic components in plant stems using solid-state nuclear magnetic resonance and dynamic nuclear polarization approaches. We show that the extent of glycan-aromatic association increases sequentially across grasses, hardwoods, and softwoods. Lignin principally packs with the xylan in a non-flat conformation via non-covalent interactions and partially binds the junction of flat-ribbon xylan and cellulose surface as a secondary site. All molecules are homogeneously mixed in softwoods; this unique feature enables water retention even around the hydrophobic aromatics. These findings unveil the principles of polymer interactions underlying the heterogeneous architecture of lignocellulose, which may guide the rational design of more digestible plants and more efficient biomass-conversion pathways. The plant biomass is a composite formed by a variety of polysaccharides and an aromatic polymer named lignin. Here, the authors use solid-state NMR spectroscopy to unveil the carbohydrate-aromatic interface that leads to the variable architecture of lignocellulose biomaterials.
Collapse
|
4
|
Kóňa J. How inverting β-1,4-galactosyltransferase-1 can quench a high charge of the by-product UDP3−in catalysis: a QM/MM study of enzymatic reaction with native and UDP-5′ thio galactose substrates. Org Biomol Chem 2020; 18:7585-7596. [DOI: 10.1039/d0ob01490g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The function of Asp252 in the catalysis of β-1,4-galactosyltransferase-1 may be the stabilization of a high charge of the by-product UDP3−by a substrate-assisted proton transfer reaction.
Collapse
Affiliation(s)
- J. Kóňa
- Institute of Chemistry
- Center for Glycomics
- Slovak Academy of Sciences
- 84538 Bratislava
- Slovak Republic
| |
Collapse
|
5
|
Yang H, Watts HD, Gibilterra V, Weiss TB, Petridis L, Cosgrove DJ, Kubicki JD. Quantum Calculations on Plant Cell Wall Component Interactions. Interdiscip Sci 2018; 11:485-495. [DOI: 10.1007/s12539-018-0293-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/13/2018] [Accepted: 03/21/2018] [Indexed: 10/17/2022]
|
6
|
Abstract
Many carbohydrate-binding proteins contain aromatic amino acid residues in their binding sites. These residues interact with carbohydrates in a stacking geometry via CH/π interactions. These interactions can be found in carbohydrate-binding proteins, including lectins, enzymes and carbohydrate transporters. Besides this, many non-protein aromatic molecules (natural as well as artificial) can bind saccharides using these interactions. Recent computational and experimental studies have shown that carbohydrate–aromatic CH/π interactions are dispersion interactions, tuned by electrostatics and partially stabilized by a hydrophobic effect in solvated systems.
Collapse
|
7
|
Host-guest complex of nabumetone: β-cyclodextrin: quantum chemical study and QTAIM analysis. J INCL PHENOM MACRO 2017. [DOI: 10.1007/s10847-016-0690-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
8
|
Jaiyong P, Bryce RA. Approximate quantum chemical methods for modelling carbohydrate conformation and aromatic interactions: β-cyclodextrin and its adsorption on a single-layer graphene sheet. Phys Chem Chem Phys 2017; 19:15346-15355. [DOI: 10.1039/c7cp02160g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adsorption of carbohydrates on graphene has the potential to improve graphene dispersibility in water. Here we assess the ability of DFTB-based and NDDO-based quantum chemical methods to model β-cyclodextrin conformations and interactions with graphene.
Collapse
Affiliation(s)
- Panichakorn Jaiyong
- Division of Pharmacy and Optometry
- School of Health Sciences
- Faculty of Biology
- Medicine and Health
- University of Manchester
| | - Richard A. Bryce
- Division of Pharmacy and Optometry
- School of Health Sciences
- Faculty of Biology
- Medicine and Health
- University of Manchester
| |
Collapse
|
9
|
Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
10
|
Verma K, Dave K, Viswanathan KS. Hydrogen-Bonded Complexes of Phenylacetylene-Acetylene: Who is the Proton Donor? J Phys Chem A 2015; 119:12656-64. [PMID: 26643730 DOI: 10.1021/acs.jpca.5b08559] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen-bonded complexes of C2H2 and phenylacetylene (PhAc) were studied using matrix isolation infrared spectroscopy and quantum chemical computations. Both C2H2 and PhAc, being potential proton donors, the question arises as to which of the two species would be the proton donor in the PhAc-C2H2 complex; a question that this work primarily addresses. The molecular structures, vibrational frequencies, and interaction energies of the PhAc-C2H2 complexes were calculated at the M06-2X and MP2 levels of theory, employing both 6-311++G(d,p) and aug-cc-pVDZ basis sets. At the M06-2X/aug-cc-pVDZ level, two nearly isoenergetic complexes (BSSE corrected) were indicated to be the global minima; one a C-H···π complex, where C2H2 served as a proton donor to the phenyl π-system in PhAc, and the other a C-H···π complex, where C2H2 served as a proton donor to the acetylene π-system in PhAc. Of the two, only the second complex was identified in the matrix, evidenced by a characteristic large shift in the ≡C-H stretch of C2H2. Experiments were also performed using PhAc deuterated at the acetylene hydrogen (PhAcD) to study the isotopic effects on the vibrational spectra of complexes. The isotopic studies further confirmed the structure of the complex trapped in the matrix, thereby presenting unambiguous evidence that C2H2 served as the proton donor to the acetylene π-system of PhAc. The theory of atoms-in-molecules (AIM), energy decomposition (EDA), and natural bond orbital (NBO) analysis were performed to understand the nature of the interactions involved in the complexes.
Collapse
Affiliation(s)
- Kanupriya Verma
- Department of Chemistry, Indian Institute of Science Education and Research , Sector 81, Mohali 140306, Punjab, India
| | - Kapil Dave
- Department of Chemistry, Indian Institute of Science Education and Research , Sector 81, Mohali 140306, Punjab, India
| | - K S Viswanathan
- Department of Chemistry, Indian Institute of Science Education and Research , Sector 81, Mohali 140306, Punjab, India
| |
Collapse
|
11
|
Pandey KK. Structure and bonding analysis of germanones [(Eind) 2 Ge O], [((Tbt))(Tip)Ge O] and [R 2 Ge O] (R = Me, Ph): Significance of the dispersion interactions. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
12
|
Wilson KA, Wells RA, Abendong MN, Anderson CB, Kung RW, Wetmore SD. Landscape of π-π and sugar-π contacts in DNA-protein interactions. J Biomol Struct Dyn 2015; 34:184-200. [PMID: 25723403 DOI: 10.1080/07391102.2015.1013157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There were 1765 contacts identified between DNA nucleobases or deoxyribose and cyclic (W, H, F, Y) or acyclic (R, E, D) amino acids in 672 X-ray structures of DNA-protein complexes. In this first study to compare π-interactions between the cyclic and acyclic amino acids, visual inspection was used to categorize amino acid interactions as nucleobase π-π (according to biological edge) or deoxyribose sugar-π (according to sugar edge). Overall, 54% of contacts are nucleobase π-π interactions, which involve all amino acids, but are more common for Y, F, and R, and involve all DNA nucleobases with similar frequencies. Among binding arrangements, cyclic amino acids prefer more planar (stacked) π-systems than the acyclic counterparts. Although sugar-π interactions were only previously identified with the cyclic amino acids and were found to be less common (38%) than nucleobase-cyclic amino acid contacts, sugar-π interactions are more common than nucleobase π-π contacts for the acyclic series (61% of contacts). Similar to DNA-protein π-π interactions, sugar-π contacts most frequently involve Y and R, although all amino acids adopt many binding orientations relative to deoxyribose. These DNA-protein π-interactions stabilize biological systems, by up to approximately -40 kJ mol(-1) for neutral nucleobase or sugar-amino acid interactions, but up to approximately -95 kJ mol(-1) for positively or negatively charged contacts. The high frequency and strength, despite variation in structure and composition, of these π-interactions point to an important function in biological systems.
Collapse
Affiliation(s)
- Katie A Wilson
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Rachael A Wells
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Minette N Abendong
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Colin B Anderson
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Ryan W Kung
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Stacey D Wetmore
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| |
Collapse
|
13
|
Wilson KA, Wetmore SD. A Survey of DNA–Protein π–Interactions: A Comparison of Natural Occurrences and Structures, and Computationally Predicted Structures and Strengths. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
14
|
Hussain HB, Wilson KA, Wetmore SD. Serine and Cysteine π-Interactions in Nature: A Comparison of the Frequency, Structure, and Stability of Contacts Involving Oxygen and Sulfur. Aust J Chem 2015. [DOI: 10.1071/ch14598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Despite many DNA–protein π-interactions in high-resolution crystal structures, only four X–H···π or X···π interactions were found between serine (Ser) or cysteine (Cys) and DNA nucleobase π-systems in over 100 DNA–protein complexes (where X = O for Ser and X = S for Cys). Nevertheless, 126 non-covalent contacts occur between Ser or Cys and the aromatic amino acids in many binding arrangements within proteins. Furthermore, Ser and Cys protein–protein π-interactions occur with similar frequencies and strengths. Most importantly, due to the great stability that can be provided to biological macromolecules (up to –20 kJ mol–1 for neutral π-systems or –40 kJ mol–1 for cationic π-systems), Ser and Cys π-interactions should be considered when analyzing protein stability and function.
Collapse
|
15
|
Govender KK, Naidoo KJ. Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations. J Chem Theory Comput 2014; 10:4708-17. [DOI: 10.1021/ct500373p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Krishna K. Govender
- Scientific Computing
Research Unit and Department
of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kevin J. Naidoo
- Scientific Computing
Research Unit and Department
of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| |
Collapse
|
16
|
Vincent MA, Hillier IH. Accurate Prediction of Adsorption Energies on Graphene, Using a Dispersion-Corrected Semiempirical Method Including Solvation. J Chem Inf Model 2014; 54:2255-60. [DOI: 10.1021/ci5003729] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Mark A. Vincent
- School of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Ian H. Hillier
- School of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| |
Collapse
|
17
|
Nieto CT, Díez D, Garrido NM. To be or not to be butterfly: New mechanistic insights in the Aza-Michael asymmetric addition of lithium (R)-N-benzyl-N-(α-methylbenzyl)amide. J Comput Chem 2014; 35:1846-53. [PMID: 25052741 DOI: 10.1002/jcc.23694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/07/2014] [Accepted: 07/09/2014] [Indexed: 11/08/2022]
Abstract
The asymmetric Aza-Michael addition of homochiral lithium benzylamides to α,β-unsaturated esters represents an extended protocol to obtain enantioenriched β-amino esters. An exhaustive mechanistic revision of the originally proposed mechanism is reported, developing a quantum mechanics/molecular mechanics protocol for the asymmetric Aza-Michael reaction of homochiral lithium benzylamides. Explicit and implicit solvent schemes were considered, together with a proper account of long-range dispersion forces, evaluated through a density functional theory benchmark of different functionals. Theoretical results showed that the diastereoselectivity is mainly controlled by the N-α-methylbenzyl moiety placing, deriving a Si/Re 99:1 diastereoselective ratio, in good agreement with reported experimental results. The main transition state geometries are two transition state conformers in a "V-stacked" orientation of the amide's phenyl rings, differing in the tetrahydrofuran molecule arrangement coordinated to the metal center. Extensive conformational sampling and quantum-level refinement give reasonable good speed/accuracy results, allowing this protocol to be extended to other similar Aza-Michael reaction systems.
Collapse
Affiliation(s)
- Carlos T Nieto
- Departamento de Química Orgánica, Universidad de Salamanca, Pza de la Merced 1-5, 37007, Salamanca, Spain
| | | | | |
Collapse
|
18
|
Wheeler SE, Bloom JWG. Toward a more complete understanding of noncovalent interactions involving aromatic rings. J Phys Chem A 2014; 118:6133-47. [PMID: 24937084 DOI: 10.1021/jp504415p] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Noncovalent interactions involving aromatic rings, which include π-stacking interactions, anion-π interactions, and XH-π interactions, among others, are ubiquitous in chemical and biochemical systems. Despite dramatic advances in our understanding of these interactions over the past decade, many aspects of these noncovalent interactions have only recently been uncovered, with many questions remaining. We summarize our computational studies aimed at understanding the impact of substituents and heteroatoms on these noncovalent interactions. In particular, we discuss our local, direct interaction model of substituent effects in π-stacking interactions. In this model, substituent effects are dominated by electrostatic interactions of the local dipoles associated with the substituents and the electric field of the other ring. The implications of the local nature of substituent effects on π-stacking interactions in larger systems are discussed, with examples given for complexes with carbon nanotubes and a small graphene model, as well as model stacked discotic systems. We also discuss related issues involving the interpretation of electrostatic potential (ESP) maps. Although ESP maps are widely used in discussions of noncovalent interactions, they are often misinterpreted. Next, we provide an alternative explanation for the origin of anion-π interactions involving substituted benzenes and N-heterocycles, and show that these interactions are well-described by simple models based solely on charge-dipole interactions. Finally, we summarize our recent work on the physical nature of substituent effects in XH-π interactions. Together, these results paint a more complete picture of noncovalent interactions involving aromatic rings and provide a firm conceptual foundation for the rational exploitation of these interactions in a myriad of chemical contexts.
Collapse
Affiliation(s)
- Steven E Wheeler
- Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
| | | |
Collapse
|
19
|
Wilson KA, Kellie JL, Wetmore SD. DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar. Nucleic Acids Res 2014; 42:6726-41. [PMID: 24744240 PMCID: PMC4041443 DOI: 10.1093/nar/gku269] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π-π stacking, π-π T-shaped or sugar-π contacts. Three hundred forty-four nucleobase-amino acid π-π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA-protein sugar-π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C-H···π and/or lone-pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π-π and sugar-π interactions display a range of relative monomer orientations and therefore interaction energies (up to -50 (-70) kJ mol(-1) for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA-protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered.
Collapse
Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| | - Jennifer L Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| |
Collapse
|
20
|
Bobovská A, Tvaroška I, Kóňa J. A theoretical study on the catalytic mechanism of the retaining α-1,2-mannosyltransferase Kre2p/Mnt1p: the impact of different metal ions on catalysis. Org Biomol Chem 2014; 12:4201-10. [DOI: 10.1039/c4ob00286e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
21
|
|
22
|
|
23
|
Stanca-Kaposta EC, Carçabal P, Cocinero EJ, Hurtado P, Simons JP. Carbohydrate-aromatic interactions: vibrational spectroscopy and structural assignment of isolated monosaccharide complexes with p-hydroxy toluene and N-acetyl l-tyrosine methylamide. J Phys Chem B 2013; 117:8135-42. [PMID: 23773008 DOI: 10.1021/jp404527s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The nature of carbohydrate binding first to p-hydroxy toluene and then the capped amino acid, N-acetyl l-tyrosine methyl amide (AcTyrNHMe), has been investigated in a solvent-free environment under molecular beam conditions. A combination of double resonance IR-UV spectroscopy and quantum chemical calculations has established the structures of complexes with the α and β anomers of methyl d-gluco- and d-galacto- and l-fucopyranosides (α/βMeGlc, MeGal, MeFuc). The new results, when combined with dispersion-corrected DFT calculations, reveal gas phase structures which are dominated by hydrogen bonding but also with evidence of CH-π bonded interactions in complexes with α/βMeGal. These adopt stacked intermolecular structures in marked contrast to those with α/βMeGlc; p-OH → O bonds linking AcTyrNHMe, or p-hydroxy toluene, to the carbohydrate provide an anchor that facilitates further binding, both through OH → O and NH → O hydrogen bonds to the peptide backbone and through CH-π dispersion interactions with the aromatic side group. "Stacked" structures associated with dispersion interactions with the aromatic ring are not detected in the corresponding complexes of capped phenylalanine, despite their common occurrence in bound carbohydrate-protein structures.
Collapse
Affiliation(s)
- E Cristina Stanca-Kaposta
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | | | | | | | | |
Collapse
|
24
|
Kumari M, Sunoj RB, Balaji PV. Exploration of CH⋯π mediated stacking interactions in saccharide: aromatic residue complexes through conformational sampling. Carbohydr Res 2012; 361:133-40. [DOI: 10.1016/j.carres.2012.08.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/20/2012] [Accepted: 08/28/2012] [Indexed: 11/26/2022]
|
25
|
In search of OH–π interactions between 1-methylimidazole and water using a combined computational quantum chemistry and ATR-FTIR spectroscopy approach. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
26
|
Bloom JWG, Raju RK, Wheeler SE. Physical Nature of Substituent Effects in XH/π Interactions. J Chem Theory Comput 2012; 8:3167-74. [DOI: 10.1021/ct300520n] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jacob W. G. Bloom
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Rajesh K. Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
27
|
Hunter RS, van Mourik T. DNA base stacking: The stacked uracil/uracil and thymine/thymine minima. J Comput Chem 2012; 33:2161-72. [DOI: 10.1002/jcc.23052] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 06/01/2012] [Accepted: 06/04/2012] [Indexed: 01/24/2023]
|
28
|
Tsuzuki S, Uchimaru T, Mikami M. Magnitude of CH/O interactions between carbohydrate and water. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1192-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
29
|
|
30
|
Kyne SH, Miles JAL, Percy JM, Singh K. Executing and Rationalizing the Synthesis of a Difluorinated Analogue of a Ring-Expanded Calystegine B2. J Org Chem 2011; 77:991-8. [DOI: 10.1021/jo2022845] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sara H. Kyne
- WestCHEM, Department of Pure
and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U. K
| | - Jonathan A. L. Miles
- Department of Chemistry, University of Leicester, University Road, Leicester
LE1 7RH, U. K
| | - Jonathan M. Percy
- WestCHEM, Department of Pure
and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U. K
| | - Kuldip Singh
- Department of Chemistry, University of Leicester, University Road, Leicester
LE1 7RH, U. K
| |
Collapse
|
31
|
Cao J, Bjornsson R, Bühl M, Thiel W, van Mourik T. Modelling zwitterions in solution: 3-fluoro-γ-aminobutyric acid (3F-GABA). Chemistry 2011; 18:184-95. [PMID: 22161781 DOI: 10.1002/chem.201101674] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Indexed: 12/18/2022]
Abstract
The conformations and relative stabilities of folded and extended 3-fluoro-γ-aminobutyric acid (3F-GABA) conformers were studied using explicit solvation models. Geometry optimisations in the gas phase with one or two explicit water molecules favour folded and neutral structures containing intramolecular NH···O-C hydrogen bonds. With three or five explicit water molecules zwitterionic minima are obtained, with folded structures being preferred over extended conformers. The stability of folded versus extended zwitterionic conformers increases on going from a PCM continuum solvation model to the microsolvated complexes, though extended structures become less disfavoured with the inclusion of more water molecules. Full explicit solvation was studied with a hybrid quantum-mechanical/molecular-mechanical (QM/MM) scheme and molecular dynamics simulations, including more than 6000 TIP3P water molecules. According to free energies obtained from thermodynamic integration at the PM3/MM level and corrected for B3LYP/MM total energies, the fully extended conformer is more stable than folded ones by about -4.5 kJ mol(-1). B3LYP-computed (3)J(F,H) NMR spin-spin coupling constants, averaged over PM3/MM-MD trajectories, agree best with experiment for this fully extended form, in accordance with the original NMR analysis. The seeming discrepancy between static PCM calculations and experiment noted previously is now resolved. That the inexpensive semiempirical PM3 method performs so well for this archetypical zwitterion is encouraging for further QM/MM studies of biomolecular systems.
Collapse
Affiliation(s)
- Jie Cao
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, UK
| | | | | | | | | |
Collapse
|
32
|
Marom N, Tkatchenko A, Rossi M, Gobre VV, Hod O, Scheffler M, Kronik L. Dispersion Interactions with Density-Functional Theory: Benchmarking Semiempirical and Interatomic Pairwise Corrected Density Functionals. J Chem Theory Comput 2011; 7:3944-51. [PMID: 26598340 DOI: 10.1021/ct2005616] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a comparative assessment of the accuracy of two different approaches for evaluating dispersion interactions: interatomic pairwise corrections and semiempirical meta-generalized-gradient-approximation (meta-GGA)-based functionals. This is achieved by employing conventional (semi)local and (screened-)hybrid functionals, as well as semiempirical hybrid and nonhybrid meta-GGA functionals of the M06 family, with and without interatomic pairwise Tkatchenko-Scheffler corrections. All of those are tested against the benchmark S22 set of weakly bound systems, a representative larger molecular complex (dimer of NiPc molecules), and a representative dispersively bound solid (hexagonal boron nitride). For the S22 database, we also compare our results with those obtained from the pairwise correction of Grimme (DFT-D3) and nonlocal Langreth-Lundqvist functionals (vdW-DF1 and vdW-DF2). We find that the semiempirical kinetic-energy-density dependence introduced in the M06 functionals mimics some of the nonlocal correlation needed to describe dispersion. However, long-range contributions are still missing. Pair-wise interatomic corrections, applied to conventional semilocal or hybrid functionals, or to M06 functionals, provide for a satisfactory level of accuracy irrespectively of the underlying functional. Specifically, screened-hybrid functionals such as the Heyd-Scuseria-Ernzerhof (HSE) approach reduce self-interaction errors in systems possessing both localized and delocalized orbitals and can be applied to both finite and extended systems. Therefore, they serve as a useful underlying functional for dispersion corrections.
Collapse
Affiliation(s)
- Noa Marom
- Department of Materials and Interfaces, Weizmann Institute of Science , Rehovoth 76100, Israel.,Center for Computational Materials, Institute for Computational Engineering and Sciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Vivekanand V Gobre
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Oded Hod
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 69978, Israel
| | - Matthias Scheffler
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science , Rehovoth 76100, Israel
| |
Collapse
|
33
|
Raju RK, Bloom JWG, An Y, Wheeler SE. Substituent effects on non-covalent interactions with aromatic rings: insights from computational chemistry. Chemphyschem 2011; 12:3116-30. [PMID: 21928437 DOI: 10.1002/cphc.201100542] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Indexed: 02/01/2023]
Abstract
Non-covalent interactions with aromatic rings pervade modern chemical research. The strength and orientation of these interactions can be tuned and controlled through substituent effects. Computational studies of model complexes have provided a detailed understanding of the origin and nature of these substituent effects, and pinpointed flaws in entrenched models of these interactions in the literature. Here, we provide a brief review of efforts over the last decade to unravel the origin of substituent effects in π-stacking, XH/π, and ion/π interactions through detailed computational studies. We highlight recent progress that has been made, while also uncovering areas where future studies are warranted.
Collapse
Affiliation(s)
- Rajesh K Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, USA
| | | | | | | |
Collapse
|
34
|
Tsuzuki S, Uchimaru T, Mikami M. Magnitude and nature of carbohydrate-aromatic interactions in fucose-phenol and fucose-indole complexes: CCSD(T) level interaction energy calculations. J Phys Chem A 2011; 115:11256-62. [PMID: 21812469 DOI: 10.1021/jp2045756] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The CH/π contact structures of the fucose-phenol and fucose-indole complexes and the stabilization energies by formation of the complexes (E(form)) were studied by ab initio molecular orbital calculations. The three types of interactions (CH/π and OH/π interactions and OH/O hydrogen bonds) were compared and evaluated in a single molecular system and at the same level of theory. The E(form) calculated for the most stable CH/π contact structure of the fucose-phenol complex at the CCSD(T) level (-4.9 kcal/mol) is close to that for the most stable CH/π contact structure of the fucose-benzene complex (-4.5 kcal/mol). On the other hand the most stable CH/π contact structure of the fucose-indole complex has substantially larger E(form) (-6.5 kcal/mol). The dispersion interaction is the major source of the attraction in the CH/π contact structures of the fucose-phenol and fucose-indole complexes as in the case of the fucose-benzene complex. The electrostatic interactions in the CH/π contact structures are small (less than 1.5 kcal/mol). The nature of the interactions between the nonpolar surface of the carbohydrate and aromatic rings is completely different from that of the conventional hydrogen bonds where the electrostatic interaction is the major source of the attraction. The distributed multipole analysis and DFT-SATP analysis show that the dispersion interactions in the CH/π contact structure of fucose-indole complex are substantially larger than those in the CH/π contact structures of fucose-benzene and fucose-phenol complexes. The large dispersion interactions are responsible for the large E(form) for the fucose-indole complex.
Collapse
Affiliation(s)
- Seiji Tsuzuki
- CREST, JST, and Research Initiative of Computational Sciences (RICS), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
| | | | | |
Collapse
|
35
|
Kozmon S, Matuška R, Spiwok V, Koča J. Dispersion interactions of carbohydrates with condensate aromatic moieties: theoretical study on the CH-π interaction additive properties. Phys Chem Chem Phys 2011; 13:14215-22. [PMID: 21755090 DOI: 10.1039/c1cp21071h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this article we present the first systematic study of the additive properties (i.e. degree of additivity) of the carbohydrate-aromatic moiety CH-π dispersion interaction. The additive properties were studied on the β-D-glucopyranose, β-D-mannopyranose and α-L-fucopyranose complexes with the naphthalene molecule by comparing the monodentate (single CH-π) and bidentate (two CH-π) complexes. All model complexes were optimized using the DFT-D approach, at the BP/def2-TZVPP level of theory. The interaction energies were refined using single point calculations at highly correlated ab initio methods at the CCSD(T)/CBS level, calculated as E + (E(CCSD(T))-E(MP2))(Small Basis). Bidentate complexes show very strong interactions in the range from -10.79 up to -7.15 and -8.20 up to -6.14 kcal mol(-1) for the DFT-D and CCSD(T)/CBS level, respectively. These values were compared with the sum of interaction energies of the appropriate monodentate carbohydrate-naphthalene complexes. The comparison reveals that the bidentate complex interaction energy is higher (interaction is weaker) than the sum of monodentate complex interaction energies. Bidentate complex interaction energy corresponds to 2/3 of the sum of the appropriate monodentate complex interaction energies (averaging over all modeled carbohydrate complexes). The observed interaction energies were also compared with the sum of interaction energies of the corresponding previously published carbohydrate-benzene complexes. Also in this case the interaction energy of the bidentate complex was higher (i.e. weaker interaction) than the sum of interaction energies of the corresponding benzene complexes. However, the obtained difference is lower than before, while the bidentate complex interaction energy corresponds to 4/5 of the sum of interaction energy of the benzene complexes, averaged over all structures. The mentioned comparison might aid protein engineering efforts where amino acid residues phenylalanine or tyrosine are to be replaced by a tryptophan and can help to predict the changes in the interactions. The observed results also show that DFT-D correctly describes the CH-π interaction energy and their additive properties in comparison to CCSD(T)/CBS calculated interaction energies. Thus, the DFT-D approach might be used for calculation of larger complexes of biological interest, where dispersion interaction plays an important role.
Collapse
Affiliation(s)
- Stanislav Kozmon
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | | | | | | |
Collapse
|
36
|
Nishio M. The CH/π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates. Phys Chem Chem Phys 2011; 13:13873-900. [PMID: 21611676 DOI: 10.1039/c1cp20404a] [Citation(s) in RCA: 624] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm.
Collapse
Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338 Minamioya, Machida-shi, Tokyo, 194-0031, Japan.
| |
Collapse
|
37
|
Cocinero EJ, Çarçabal P, Vaden TD, Davis BG, Simons JP. Exploring Carbohydrate−Peptide Interactions in the Gas Phase: Structure and Selectivity in Complexes of Pyranosides with N-Acetylphenylalanine Methylamide. J Am Chem Soc 2011; 133:4548-57. [DOI: 10.1021/ja109664k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emilio J. Cocinero
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Pierre Çarçabal
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Timothy D. Vaden
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Benjamin G. Davis
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - John P. Simons
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| |
Collapse
|
38
|
Kumari M, Balaji PV, Sunoj RB. Quantification of binding affinities of essential sugars with a tryptophan analogue and the ubiquitous role of C-H···π interactions. Phys Chem Chem Phys 2011; 13:6517-30. [PMID: 21369604 DOI: 10.1039/c0cp02559c] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of noncovalent interactions in carbohydrate recognition by aromatic amino acids has long been reported. To develop a molecular understanding of noncovalent interactions in the recognition process, we have examined a series of binary complexes between 3-methylindole (3-MeIn) and sugars. In particular, the geometries and binding affinities of 3-MeIn with α/β-D-glucose, β-D-galactose, α-D-mannose and α/β-L-fucose are obtained using the MP2(full)/6-31G(d,p) and the M06/TZV2D//MP2/6-31G(d,p) level of theories. The conventional hydrogen bonding such as N-H···O and C-H···O as well as nonconventional O-H···π and C-H···π type of interactions is, in general, identified as responsible for the moderately strong interaction energies. Large variations in the position-orientations of 3-MeIn with respect to saccharide are noticed, within the same sugar family, as well as across different sugar series. Furthermore, complexes with large differences in their geometries are recognized as capable of exhibiting very similar interaction energies, underscoring the significance of exhaustive conformation sampling, as carried out in the present study. These observations are readily attributed to the differences in the efficiency of the type of interactions enlisted above. The highest and lowest interaction energies, upon inclusion of 50% BSSE correction, are found to be -16.02 and -6.22 kcal mol(-1), respectively, for α-D-glucose (1a) and α-L-fucose (5j). While more number of prominent conventional hydrogen bonding contacts remains as a characteristic feature of the strongly bound complexes, the lower end of the interaction energy spectrum is dominated by multiple C-H···π interactions. The complexes exhibiting as many as four C-H···π contacts are identified in the case of α/β-D-glucose, β-D-galactose, and α/β-L-fucose with an interaction energy hovering around -8 kcal mol(-1). The presence of effective C-H···π interactions is found to be dependent on the saccharide configuration as well as the area of the apolar patch constituted by the C-H groups. The study offers a comprehensive set of binary complexes, across different saccharides, which serves as an illustration of the significance and ubiquitous nature of C-H···π interactions in carbohydrate binding in saccharide-protein complexes.
Collapse
Affiliation(s)
- Manju Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | | |
Collapse
|
39
|
Hillier IH, Pandian S, Percy JM, Vincent MA. Mapping the potential energy surfaces for ring-closing metathesis reactions of prototypical dienes by electronic structure calculations. Dalton Trans 2011; 40:1061-72. [DOI: 10.1039/c0dt01314e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
40
|
An evaluation of the GLYCAM06 and MM3 force fields, and the PM3-D* molecular orbital method for modelling prototype carbohydrate–aromatic interactions. J Mol Graph Model 2010; 29:321-5. [DOI: 10.1016/j.jmgm.2010.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 07/09/2010] [Indexed: 11/23/2022]
|
41
|
Taylor CJ, Nix MGD, Dessent CEH. Noncovalent Interactions in the Gas-Phase Conformers of Anionic Iduronate (methyl 2-O-sulfo-α-L-iduronate): Variation of Subconformer versus Ring Conformer Energetics for a Prototypical Anionic Monosaccharide Studied Using Computational Methods. J Phys Chem A 2010; 114:11153-60. [DOI: 10.1021/jp102657t] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
| | - Michael G. D. Nix
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
| | | |
Collapse
|
42
|
Frank M, Schloissnig S. Bioinformatics and molecular modeling in glycobiology. Cell Mol Life Sci 2010; 67:2749-72. [PMID: 20364395 PMCID: PMC2912727 DOI: 10.1007/s00018-010-0352-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 03/08/2010] [Accepted: 03/11/2010] [Indexed: 12/11/2022]
Abstract
The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein-carbohydrate interaction are reviewed.
Collapse
Affiliation(s)
- Martin Frank
- Molecular Structure Analysis Core Facility-W160, Deutsches Krebsforschungszentrum (German Cancer Research Centre), 69120 Heidelberg, Germany.
| | | |
Collapse
|
43
|
Rutledge LR, Wetmore SD. The assessment of density functionals for DNA–protein stacked and T-shaped complexes. CAN J CHEM 2010. [DOI: 10.1139/v10-046] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The present work uses 129 nucleobase – amino acid CCSD(T)/CBS stacking and T-shaped interaction energies as reference data to test the ability of various density functionals with double-zeta quality basis sets, as well as some semi-empirical and molecular mechanics methods, to accurately describe noncovalent DNA–protein π–π and π+–π interactions. The goal of this work is to identify methods that can be used in hybrid approaches (QM/MM, ONIOM) for large-scale modeling of enzymatic systems involving active-site (substrate) π–π contacts. Our results indicate that AMBER is a more appropriate choice for the lower-level method in hybrid techniques than popular semi-empirical methods (AM1, PM3), and suggest that AMBER accurately describes the π–π interactions found throughout DNA–protein complexes. The M06–2X and PBE-D density functionals were found to provide very promising descriptions of the 129 nucleobase – amino acid interaction energies, which suggests that these may be the most suitable methods for describing high-level regions. Therefore, M06–2X and PBE-D with both the 6–31G(d) and 6–31+G(d,p) basis sets were further examined through potential-energy surface scans to better understand how these techniques describe DNA–protein π–π interactions in both minimum and nonminimum regions of the potential-energy surfaces, which is critical information when modeling enzymatic reaction pathways. Our results suggest that studies of stacked nucleobase – amino acid systems should implement the PBE-D/6–31+G(d,p) method. However, if T-shaped contacts are involved and (or) smaller basis sets must be considered due to limitations in computational resources, then M06–2X/6–31G(d) provides an overall excellent description of both nucleobase – amino acid stacking and T-shaped interactions for a range of DNA–protein π–π and π+–π interactions.
Collapse
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| |
Collapse
|
44
|
Assary RS, Redfern PC, Hammond JR, Greeley J, Curtiss LA. Computational Studies of the Thermochemistry for Conversion of Glucose to Levulinic Acid. J Phys Chem B 2010; 114:9002-9. [DOI: 10.1021/jp101418f] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajeev S. Assary
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, and Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208
| | - Paul C. Redfern
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, and Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208
| | - Jeff R. Hammond
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, and Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208
| | - Jeffrey Greeley
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, and Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208
| | - Larry A. Curtiss
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, and Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208
| |
Collapse
|
45
|
Jacquemin D, Perpète EA, Ciofini I, Adamo C, Valero R, Zhao Y, Truhlar DG. On the Performances of the M06 Family of Density Functionals for Electronic Excitation Energies. J Chem Theory Comput 2010; 6:2071-85. [DOI: 10.1021/ct100119e] [Citation(s) in RCA: 339] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Denis Jacquemin
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Eric A. Perpète
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Ilaria Ciofini
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Carlo Adamo
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Rosendo Valero
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Yan Zhao
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Donald G. Truhlar
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| |
Collapse
|
46
|
Ravinder P, Subramanian V. Substitution Effects of Diborane on the Interaction with Borazine (Inorganic Benzene). J Phys Chem A 2010; 114:5565-72. [DOI: 10.1021/jp910717j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- P. Ravinder
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| |
Collapse
|
47
|
Clayden J, Hennecke U, Vincent MA, Hillier IH, Helliwell M. The origin of the conformational preference of N,N′-diaryl-N,N′-dimethyl ureas. Phys Chem Chem Phys 2010; 12:15056-64. [DOI: 10.1039/c0cp00571a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
48
|
Raju RK, Hillier IH, Burton NA, Vincent MA, Doudou S, Bryce RA. The effects of perfluorination on carbohydrate–π interactions: computational studies of the interaction of benzene and hexafluorobenzene with fucose and cyclodextrin. Phys Chem Chem Phys 2010; 12:7959-67. [DOI: 10.1039/c002058c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
49
|
Raju RK, Burton NA, Hillier IH. Modelling the binding of HIV-reverse transcriptase and nevirapine: an assessment of quantum mechanical and force field approaches and predictions of the effect of mutations on binding. Phys Chem Chem Phys 2010; 12:7117-25. [DOI: 10.1039/c001384f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
50
|
Assessment of approximate quantum chemical methods for calculating the interaction energy of nucleic acid bases with graphene and carbon nanotubes. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2009.11.068] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|