1
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Kumar M, Rathore RS. Disallowed spots in protein structures. Biochim Biophys Acta Gen Subj 2023; 1867:130493. [PMID: 37865175 DOI: 10.1016/j.bbagen.2023.130493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 10/23/2023]
Abstract
Ramachandran (ϕ, ψ) steric map was introduced in 1963 to describe available conformation space for protein structures. Subsequently, residues were observed in high-energy disallowed regions of the map. To unequivocally identify the locations of disallowed conformations of residues, we got 36 noise-free protein structures (resolution ≤1 Å, Rwork/Rfree ≤ 0.10). These stringent criteria were applied to rule out data or model errors or any crystallographic disorders. No disallowed conformation was found in the dataset. Further, we also examined disallowed conformations in a larger dataset (resolution ≤1.5 Å, devoid of any model errors, or disorders). The observed locations of disallowed residues are referred as disallowed spots. These spots include short loops of 3-5 residues, and locations where residues participate in disulfide bonding or intramolecular interactions or inter-molecular interactions with neighboring water, metals or ligands. Conformational sampling revealed that short loops in between secondary structures hardly have any opportunity to relieve from conformational strain. Residues involved in interactions, which provide energetic compensation for high-energy conformational states, were relieved from strain once the causative interaction was removed. The present study aims to identify disallowed spots in the native state of proteins, wherein residues are forced to be trapped in high-energy disallowed conformations. Moreover, it was also observed that pre-Pro, Ser, Asp, trans-Pro, Val, Asn & Gly have higher tendency to occur in disallowed conformation, which could be attributed to factors such as conformational restrictions, residue propensity of secondary structures and compensating sidechain and mainchain interactions, stabilizing turn-mimics.
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Affiliation(s)
- Mayank Kumar
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar 824236, India
| | - R S Rathore
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar 824236, India.
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2
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Brown SM, Mayer-Bacon C, Freeland S. Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It. Life (Basel) 2023; 13:2281. [PMID: 38137883 PMCID: PMC10744825 DOI: 10.3390/life13122281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.
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3
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Biondi B, Formaggio F, Toniolo C, Peggion C, Crisma M. Isolated α-turns in peptides: a selected literature survey. J Pept Sci 2023:e3476. [PMID: 36603599 DOI: 10.1002/psc.3476] [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: 10/28/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
The results of classifying into various types the 68 examples of isolated α-turns in the X-ray diffraction crystal structures of peptides documented in the literature are presented and discussed in this review article. α-Turns characterized by the trans disposition of all ω torsion angles are common for the backbone linear peptides investigated. In contrast, the cis arrangement of the N-terminal (ωi + 1 ) torsion angle, among those generated by the three residues internal to the α-turn, is a peculiar feature of 65% of the cyclic peptides. Among linear and cyclic peptides featuring the all-trans disposition of the ω torsion angles, only one third of the α-turns display φ,ψ values not too far from those characterizing regular α-helices. In general, our findings, taken together, suggest that a significant conformational diversity is compatible with the formation of an intramolecularly H-bonded C13 -member pseudocycle (α-turn) in linear and cyclic peptides.
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Affiliation(s)
- Barbara Biondi
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
| | - Fernando Formaggio
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Claudio Toniolo
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Cristina Peggion
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Marco Crisma
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
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4
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Roy Chowdhury S, Haldar D. A gama-turn mimetic for selective sensing of Cu(II) and combinatorial multiple logic gate. CrystEngComm 2022. [DOI: 10.1039/d2ce00462c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have designed and synthesized a gama-turn mimetic using fenamic acid and α-aminoisobutyricacid (Aib), the conformation and optoelectronic properties of which can be changed by appropriate external stimuli. From single-crystal...
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5
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Kato K, Nakayoshi T, Ishikawa Y, Kurimoto E, Oda A. Computational Analysis of the Mechanism of Nonenzymatic Peptide Bond Cleavage at the C-Terminal Side of an Asparagine Residue. ACS OMEGA 2021; 6:30078-30084. [PMID: 34778679 PMCID: PMC8582265 DOI: 10.1021/acsomega.1c04821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
The nonenzymatic peptide bond cleavage at the C-terminal side of Asn residues is a protein post-translational modification that occurs under physiological conditions. This reaction proceeds much slower than the deamidation of the Asn side chain and causes denaturation and hypofunction of proteins. The peptide bond cleavage of Asn is detected primarily in crystallins and aquaporin 0 in the eye lens. Therefore, cleavage is thought to be involved in age-related cataracts. In this study, to clarify the mechanism underlying succinimide formation for the peptide bond cleavage of the Asn residue, we performed quantum chemical calculations on the model compound Ace-Asn-Gly-Nme (Ace = acetyl and Nme = methylamino). The density functional theory with the B3LYP/6-31+G(d,p) level of theory was used to obtain optimized geometries. The results suggested that the reaction proceeds through two steps, cyclization and C-terminal fragment release, and the required proton transfers can be mediated by H2PO4 - and HCO3 - ions. The conformational change of the main chain on the N-terminal side of Asn was needed for the C-terminal fragmentation step, and a separate conformational change at the C-terminal side was required for the cyclization step. Furthermore, the calculated activation barriers of the reactions catalyzed by the H2PO4 - ion (130 kJ mol-1) and the HCO3 - ion (123 kJ mol-1) were sufficiently low for the reactions to occur under normal physiological conditions.
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Affiliation(s)
- Koichi Kato
- Faculty
of Pharmaceutical Sciences, Shonan University
of Medical Sciences, 16-48 Kamishinano, Totsuka-ku, Yokohama, Kanagawa 244-0806, Japan
- College
of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Tomoki Nakayoshi
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Graduate
School of Information Sciences, Hiroshima
City University, 3-4-1 Ozukahigasi, Asaminami-ku, Hiroshima, Hiroshima 731-3194, Japan
| | - Yoshinobu Ishikawa
- Faculty
of Pharmaceutical Sciences, Shonan University
of Medical Sciences, 16-48 Kamishinano, Totsuka-ku, Yokohama, Kanagawa 244-0806, Japan
| | - Eiji Kurimoto
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Akifumi Oda
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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6
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Mayer-Bacon C, Agboha N, Muscalli M, Freeland S. Evolution as a Guide to Designing xeno Amino Acid Alphabets. Int J Mol Sci 2021; 22:ijms22062787. [PMID: 33801827 PMCID: PMC8000707 DOI: 10.3390/ijms22062787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 02/02/2023] Open
Abstract
Here, we summarize a line of remarkably simple, theoretical research to better understand the chemical logic by which life’s standard alphabet of 20 genetically encoded amino acids evolved. The connection to the theme of this Special Issue, “Protein Structure Analysis and Prediction with Statistical Scoring Functions”, emerges from the ways in which current bioinformatics currently lacks empirical science when it comes to xenoproteins composed largely or entirely of amino acids from beyond the standard genetic code. Our intent is to present new perspectives on existing data from two different frontiers in order to suggest fresh ways in which their findings complement one another. These frontiers are origins/astrobiology research into the emergence of the standard amino acid alphabet, and empirical xenoprotein synthesis.
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Affiliation(s)
- Christopher Mayer-Bacon
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA; (C.M.-B.); (N.A.)
| | - Neyiasuo Agboha
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA; (C.M.-B.); (N.A.)
| | - Mickey Muscalli
- Individualized Study Program, University of Maryland, Baltimore County, Baltimore, MD 21250, USA;
| | - Stephen Freeland
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA; (C.M.-B.); (N.A.)
- Individualized Study Program, University of Maryland, Baltimore County, Baltimore, MD 21250, USA;
- Correspondence:
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7
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Ahmed MH, Catalano C, Portillo SC, Safo MK, Neel Scarsdale J, Kellogg GE. 3D interaction homology: The hydropathic interaction environments of even alanine are diverse and provide novel structural insight. J Struct Biol 2019; 207:183-198. [DOI: 10.1016/j.jsb.2019.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/12/2019] [Accepted: 05/17/2019] [Indexed: 01/23/2023]
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8
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Torshin IY, Batyanovskii AV, Uroshlev LA, Tumanyan VG, Volotovskii ID, Esipova NG. The Conformational Stability/Lability of Peptide Fragments in the Sequence Context of Amino Acids. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350919020180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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9
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Govindu PCV, Mohanan A, Dolle A, Gowd KH. Conformations of cysteine disulfides of peptide toxins: Advantage of differentiating forward and reverse asymmetric disulfide conformers. J Biomol Struct Dyn 2018; 37:2017-2029. [DOI: 10.1080/07391102.2018.1475257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Panchada Ch V Govindu
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, Karnataka, India
| | - Athul Mohanan
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, Karnataka, India
| | - Ashwini Dolle
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, Karnataka, India
| | - Konkallu Hanumae Gowd
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, Karnataka, India
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10
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Torshin IY, Batyanovskii AV, Uroshlev LA, Esipova NG, Tumanyan VG. Noncanonical and Strongly Disallowed Conformations of the Backbone in Polypeptide Chains of Globular Proteins. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918020240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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11
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Saravanan KM, Selvaraj S. Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins. J Biol Phys 2017; 43:265-278. [PMID: 28577238 PMCID: PMC5471173 DOI: 10.1007/s10867-017-9451-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 04/13/2017] [Indexed: 12/22/2022] Open
Abstract
In theory, a polypeptide chain can adopt a vast number of conformations, each corresponding to a set of backbone rotation angles. Many of these conformations are excluded due to steric overlaps. Ramachandran and coworkers were the first to look into this problem by plotting backbone dihedral angles in a two-dimensional plot. The conformational space in the Ramachandran map is further refined by considering the energetic contributions of various non-bonded interactions. Alternatively, the conformation adopted by a polypeptide chain may also be examined by investigating interactions between the residues. Since the Ramachandran map essentially focuses on local interactions (residues closer in sequence), out of interest, we have analyzed the dihedral angle preferences of residues that make non-local interactions (residues far away in sequence and closer in space) in the folded structures of proteins. The non-local interactions have been grouped into different types such as hydrogen bond, van der Waals interactions between hydrophobic groups, ion pairs (salt bridges), and ππ-stacking interactions. The results show the propensity of amino acid residues in proteins forming local and non-local interactions. Our results point to the vital role of different types of non-local interactions and their effect on dihedral angles in forming secondary and tertiary structural elements to adopt their native fold.
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Affiliation(s)
- Konda Mani Saravanan
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, 600 025, India
| | - Samuel Selvaraj
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, 600 025, India.
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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12
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Ponnuraj K, Saravanan KM. Dihedral angle preferences of DNA and RNA binding amino acid residues in proteins. Int J Biol Macromol 2017; 97:434-439. [PMID: 28099891 DOI: 10.1016/j.ijbiomac.2017.01.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/12/2017] [Accepted: 01/13/2017] [Indexed: 11/30/2022]
Abstract
A protein can interact with DNA or RNA molecules to perform various cellular processes. Identifying or analyzing DNA/RNA binding site amino acid residues is important to understand molecular recognition process. It is quite possible to accurately model DNA/RNA binding amino acid residues in experimental protein-DNA/RNA complex by using the electron density map whereas, locating/modeling the binding site amino acid residues in the predicted three dimensional structures of DNA/RNA binding proteins is still a difficult task. Considering the above facts, in the present work, we have carried out a comprehensive analysis of dihedral angle preferences of DNA and RNA binding site amino acid residues by using a classical Ramachandran map. We have computed backbone dihedral angles of non-DNA/RNA binding residues and used as control dataset to make a comparative study. The dihedral angle preference of DNA and RNA binding site residues of twenty amino acid type is presented. Our analysis clearly revealed that the dihedral angles (φ, ψ) of DNA/RNA binding amino acid residues prefer to occupy (-89° to -60°, -59° to -30°) bins. The results presented in this paper will help to model/locate DNA/RNA binding amino acid residues with better accuracy.
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Affiliation(s)
- Karthe Ponnuraj
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamilnadu, India
| | - Konda Mani Saravanan
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamilnadu, India.
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13
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Mazzier D, Grassi L, Moretto A, Alemán C, Formaggio F, Toniolo C, Crisma M. En route towards the peptideγ-helix: X-ray diffraction analyses and conformational energy calculations of Adm-rich short peptides. J Pept Sci 2016; 23:346-362. [DOI: 10.1002/psc.2957] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Daniela Mazzier
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Luigi Grassi
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Alessandro Moretto
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
| | - Carlos Alemán
- Departament d'Enginyeria Quimica, ETSEIB; Universitat Politècnica de Catalunya; 08028 Barcelona Spain
| | - Fernando Formaggio
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
| | - Claudio Toniolo
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
| | - Marco Crisma
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
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14
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Extension of the classical classification of β-turns. Sci Rep 2016; 6:33191. [PMID: 27627963 PMCID: PMC5024104 DOI: 10.1038/srep33191] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/22/2016] [Indexed: 11/29/2022] Open
Abstract
The functional properties of a protein primarily depend on its three-dimensional (3D) structure. These properties have classically been assigned, visualized and analysed on the basis of protein secondary structures. The β-turn is the third most important secondary structure after helices and β-strands. β-turns have been classified according to the values of the dihedral angles φ and ψ of the central residue. Conventionally, eight different types of β-turns have been defined, whereas those that cannot be defined are classified as type IV β-turns. This classification remains the most widely used. Nonetheless, the miscellaneous type IV β-turns represent 1/3rd of β-turn residues. An unsupervised specific clustering approach was designed to search for recurrent new turns in the type IV category. The classical rules of β-turn type assignment were central to the approach. The four most frequently occurring clusters defined the new β-turn types. Unexpectedly, these types, designated IV1, IV2, IV3 and IV4, represent half of the type IV β-turns and occur more frequently than many of the previously established types. These types show convincing particularities, in terms of both structures and sequences that allow for the classical β-turn classification to be extended for the first time in 25 years.
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15
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Insights into resistance mechanism of the macrolide biosensor protein MphR(A) binding to macrolide antibiotic erythromycin by molecular dynamics simulation. J Comput Aided Mol Des 2015; 29:1123-36. [DOI: 10.1007/s10822-015-9881-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/06/2015] [Indexed: 01/31/2023]
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16
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Brereton AE, Karplus PA. Native proteins trap high-energy transit conformations. SCIENCE ADVANCES 2015; 1:e1501188. [PMID: 26601321 PMCID: PMC4646835 DOI: 10.1126/sciadv.1501188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/14/2015] [Indexed: 06/05/2023]
Abstract
During protein folding and as part of some conformational changes that regulate protein function, the polypeptide chain must traverse high-energy barriers that separate the commonly adopted low-energy conformations. How distortions in peptide geometry allow these barrier-crossing transitions is a fundamental open question. One such important transition involves the movement of a non-glycine residue between the left side of the Ramachandran plot (that is, ϕ < 0°) and the right side (that is, ϕ > 0°). We report that high-energy conformations with ϕ ~ 0°, normally expected to occur only as fleeting transition states, are stably trapped in certain highly resolved native protein structures and that an analysis of these residues provides a detailed, experimentally derived map of the bond angle distortions taking place along the transition path. This unanticipated information lays to rest any uncertainty about whether such transitions are possible and how they occur, and in doing so lays a firm foundation for theoretical studies to better understand the transitions between basins that have been little studied but are integrally involved in protein folding and function. Also, the context of one such residue shows that even a designed highly stable protein can harbor substantial unfavorable interactions.
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17
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Improta R, Vitagliano L, Esposito L. The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis. Proteins 2015; 83:1973-86. [DOI: 10.1002/prot.24876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/24/2015] [Accepted: 08/03/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture e Bioimmagini; Consiglio Nazionale delle Ricerche (CNR); Napoli I-80134 Italy
| | - Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini; Consiglio Nazionale delle Ricerche (CNR); Napoli I-80134 Italy
| | - Luciana Esposito
- Istituto di Biostrutture e Bioimmagini; Consiglio Nazionale delle Ricerche (CNR); Napoli I-80134 Italy
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18
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DasGupta D, Kaushik R, Jayaram B. From Ramachandran Maps to Tertiary Structures of Proteins. J Phys Chem B 2015; 119:11136-45. [DOI: 10.1021/acs.jpcb.5b02999] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debarati DasGupta
- Department of Chemistry, ‡Supercomputing Facility for Bioinformatics & Computational Biology, and §Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India
| | - Rahul Kaushik
- Department of Chemistry, ‡Supercomputing Facility for Bioinformatics & Computational Biology, and §Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India
| | - B. Jayaram
- Department of Chemistry, ‡Supercomputing Facility for Bioinformatics & Computational Biology, and §Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India
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19
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Ahmed MH, Koparde VN, Safo MK, Neel Scarsdale J, Kellogg GE. 3d interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information-rich hydropathic interaction environments described by maps. Proteins 2015; 83:1118-36. [DOI: 10.1002/prot.24813] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/24/2015] [Accepted: 04/05/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Mostafa H. Ahmed
- Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University; Richmond VA 23298 USA
- Department of Medicinal Chemistry; Virginia Commonwealth University; Richmond VA 23298 USA
| | - Vishal N. Koparde
- Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University; Richmond VA 23298 USA
- Department of Medicinal Chemistry; Virginia Commonwealth University; Richmond VA 23298 USA
| | - Martin K. Safo
- Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University; Richmond VA 23298 USA
- Department of Medicinal Chemistry; Virginia Commonwealth University; Richmond VA 23298 USA
| | - J. Neel Scarsdale
- Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University; Richmond VA 23298 USA
- Center for the Study of Biological Complexity; Virginia Commonwealth University; Richmond VA 23298 USA
| | - Glen E. Kellogg
- Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University; Richmond VA 23298 USA
- Department of Medicinal Chemistry; Virginia Commonwealth University; Richmond VA 23298 USA
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20
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Crisma M, De Zotti M, Moretto A, Peggion C, Drouillat B, Wright K, Couty F, Toniolo C, Formaggio F. Single and multiple peptide γ-turns: literature survey and recent progress. NEW J CHEM 2015. [DOI: 10.1039/c4nj01564a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Published data on peptide isolated and repetitive γ-turns are reviewed. Advancements in our laboratories on these 3D-structures are also presented.
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Affiliation(s)
- Marco Crisma
- ICB
- Padova Unit
- CNR
- Department of Chemistry
- University of Padova
| | - Marta De Zotti
- ICB
- Padova Unit
- CNR
- Department of Chemistry
- University of Padova
| | | | | | - Bruno Drouillat
- ILV
- UMR CNRS 8180
- University of Versailles
- 78035 Versailles
- France
| | - Karen Wright
- ILV
- UMR CNRS 8180
- University of Versailles
- 78035 Versailles
- France
| | - François Couty
- ILV
- UMR CNRS 8180
- University of Versailles
- 78035 Versailles
- France
| | - Claudio Toniolo
- ICB
- Padova Unit
- CNR
- Department of Chemistry
- University of Padova
| | | |
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