The interrelationships of side-chain and main-chain conformations in proteins

Chakrabarti, Pinak; Pal, Debnath

doi:10.1016/s0079-6107(01)00005-0

Cited by 203 publications

(181 citation statements)

References 273 publications

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“…Chakrabarti and Pal estimated populations of c 1 rotamer angles as a function of backbone dihedral angles, f and y, for individual amino acids by performing a search of a set of 393 crystal structures from the PDB. [31] They report a dominant sampling of c 1 % 608 (g À side chain conformation) for y = 1708 for S and T. This rotamer angle corresponds to the ST-turn defining angle of the side chain, f e % À608, which is found in types I and II ST-turns [18] and would be consistent with what we found for the sampling of y distributions. The t side-chain conformation (c 1 % 1808), which is the least populated for S and T according to Chakrabarti and Pal, [31] would be required for a type II' ST-turn (most commonly found), of which we determined the y e angle to not be significantly populated.…”

Section: Discussionsupporting

confidence: 87%

Amino Acids with Hydrogen‐Bonding Side Chains have an Intrinsic Tendency to Sample Various Turn Conformations in Aqueous Solution

Hagarman

Mathieu

Toal

et al. 2011

Chemistry A European J

160

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Local structure in unfolded proteins, especially turn segments, has been suggested to initiate the hierarchical protein-folding process. To determine the intrinsic propensity to form such turn structures, amide I' band profiles of the Raman, IR, and vibrational circular dichroism (VCD) spectra, and several structure-sensitive NMR J-coupling constants, have been measured for a series of GxG (x=D, N, T, C) peptides, in which the central x residues are abundant in various turn motifs in folded proteins. In addition, we revisited earlier measured GSG experimental data. To check whether this relatively high propensity for these residues to sample turns reflects an intrinsic propensity, the experimental data were analyzed in terms of conformational distributions that can be described as a superposition of two-dimensional Gaussian distributions associated with different so-called mesostates. The analysis reveals that the investigated residues sample dihedral angles similar to those found in the corner residues of various turns, namely, type I/I', II/II', and IV β-turns. Aspartic acid (D) was found to predominantly sample regions attributed to turns, including distributions at the upper border of the upper-right quadrant of the Ramachandran plot, which bear some resemblance to asx-turns observed in proteins. This conformation enables hydrogen bonding between the side-chain carboxylate and the C-terminal amide group. Altogether, the study shows that the high propensity for T, S, C, N, and D to be located in turn motifs reflects, to a substantial degree, an intrinsic property and supports the role of these residues as initiation sites for hierarchical folding processes that can lead to compact structures in the unfolded state of peptides and proteins.

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Section: Discussionsupporting

confidence: 87%

Amino Acids with Hydrogen‐Bonding Side Chains have an Intrinsic Tendency to Sample Various Turn Conformations in Aqueous Solution

Hagarman

Mathieu

Toal

et al. 2011

Chemistry A European J

160

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“…Proline is frequently found in turns and loop structures of proteins and, together with glycine residues, is predicted to affect chain compaction early in folding (39). Also, the side chain of proline can wrap around to form a covalent interaction with the backbone, restricting its flexibility and limiting the conformation of neighboring residues (40). Therefore, proline has a unique role in determining local conformation and movement freedom in the folded protein, functioning as a molecular switch in the regulation of a number of cellular processes (39,41,42).…”

Section: Discussionmentioning

confidence: 99%

Dissecting the Metal Selectivity of MerR Monovalent Metal Ion Sensors in Salmonella

et al. 2013

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Two homologous transcription factors, CueR and GolS, that belong to the MerR metalloregulatory family are responsible for Salmonella Cu and Au sensing and resistance, respectively. They share similarities not only in their sequences, but also in their target transcription binding sites. While CueR responds similarly to Au, Ag, or Cu to induce the expression of its target genes, GolS shows higher activation by Au than by Ag or Cu. We showed that the ability of GolS to distinguish Au from Cu resides in the metal-binding loop motif. Here, we identify the amino acids within the motif that determine in vivo metal selectivity. We show that residues at positions 113 and 118 within the metal-binding loop are the main contributors to metal selectivity. The presence of a Pro residue at position 113 favors the detection of Cu, while the presence of Pro at position 118 disfavors it. Our results highlight the molecular bases that allow these regulators to coordinate the correct metal ion directing the response to a particular metal injury.T ransition metal homeostasis influences many fundamental aspects of bacterial cell physiology and pathogenesis (1-3). The intracellular concentration of essential metals or the presence of harmful elements is monitored by a set of transcriptional regulators that modulate the expression of factors that rapidly restore metal homeostasis (4, 5). A large class of these metalloregulators belongs to the MerR family, a group of proteins that share similarity at the N-terminal DNA-binding domain (6-9). According to the current model, dimeric metal-sensing MerR regulators control gene transcription via a DNA distortion mechanism. Both the apo-and the metal-bound regulator recognize and interact with their target operators (a dyad-symmetric DNA sequence at the promoter region of their target genes). Binding of the metal ion at the C-terminal inductor-binding site would provoke an allosteric change at the N-terminal DNA binding region of the protein, which in turn transduces changes in the promoter structure resulting in transcription activation of the expression of genes coding mostly for efflux or detoxification systems (10-12).Most of the metal ion sensors of the MerR family are poorly selective because they cannot distinguish between cognate metals with similar physicochemical properties, including charge and coordination chemistry. For example, the Cu sensor CueR can discriminate between metal ions with ϩ1 and ϩ2 charges, but it cannot distinguish between monovalent metal ions of group 1B-i.e., Cu(I), Ag(I), and Au(I) (13). Structural studies indicate that CueR has only two coordinating ligands, the S-atoms of the conserved C112 and C120 residues which are appropriate for the interaction with the ϩ1 metal ion in a linear array but not to coordinate metal ions with a ϩ2 charge, which requires higher number of ligands (14). The recent identification of two Au-selective MerR sensors, first in the bacterial pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) and then in Cupriavidus met...

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“…Asx-turns have three residues, i(asx), i + 1, and i + 2, so the residue numbering differs from that of homologous ␤-turns, such that i + 1 of asx-turns corresponds to i + 2 of ␤-turns. Several authors (Tainer et al 1982;Rees et al 1983;Richardson and Richardson 1989;Eswar and Ramakrishnan 1999;Wan and Milner-White 1999a;Chakrabarti and Pal 2001) discuss the asx-turn and others (Presta and Rose 1988;Richardson and Richardson 1988;Bordo and Argos 1994;Doig et al 1997;Aurora and Rose 1998;Pal et al 2003) show it is common at the N terminus of ␣-helices.…”

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confidence: 99%

Mimicry by asx‐ and ST‐turns of the four main types of β‐turn in proteins

et al. 2004

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Hydrogen-bonded ␤-turns in proteins occur in four categories: type I (the most common), type II, type II', and type I'. Asx-turns resemble ␤-turns, in that both have an NH . . . OC hydrogen bond forming a ring of 10 atoms. Serine and threonine side chains also commonly form hydrogen-bonded turns, here called ST-turns. Asx-turns and ST-turns can be categorized into four classes, based on side chain rotamers and the conformation of the central turn residue, which are geometrically equivalent to the four types of ␤-turns. We propose asx-and ST-turns be named using the type I, II, I', and II' ␤-turn nomenclature. Using this, the frequency of occurrence of both asx-and ST-turns is: type II' > type I > type II > type I', whereas for ␤-turns it is type I > type II > type I' > type II'. Almost all type II asx-turns occur as a recently described three residue feature named an asx-nest.

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The interrelationships of side-chain and main-chain conformations in proteins

Cited by 203 publications

References 273 publications

Amino Acids with Hydrogen‐Bonding Side Chains have an Intrinsic Tendency to Sample Various Turn Conformations in Aqueous Solution

Amino Acids with Hydrogen‐Bonding Side Chains have an Intrinsic Tendency to Sample Various Turn Conformations in Aqueous Solution

Dissecting the Metal Selectivity of MerR Monovalent Metal Ion Sensors in Salmonella

Mimicry by asx‐ and ST‐turns of the four main types of β‐turn in proteins

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