Three Types of Induced Tryptophan Optical Activity Compared in Model Dipeptides: Theory and Experiment

The tryptophan (Trp) aromatic residue in chiral matrices often exhibits a large optical activity and thus provides valuable structural information. However, it can also obscure spectral contributions from other peptide parts. To better understand the induced chirality, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA) spectra of Trp‐containing cyclic dipeptides c‐(Trp‐X) (where X=Gly, Ala, Trp, Leu, nLeu, and Pro) are analyzed on the basis of experimental spectra and density functional theory (DFT) computations. The results provide valuable insight into the molecular conformational and spectroscopic behavior of Trp. Whereas the ECD is dominated by Trp π–π* transitions, VCD is dominated by the amide modes, well separated from minor Trp contributions. The ROA signal is the most complex. However, an ROA marker band at 1554 cm^?1 indicates the local χ₂ angle value in this residue, in accordance with previous theoretical predictions. The spectra and computations also indicate that the peptide ring is nonplanar, with a shallow potential so that the nonplanarity is primarily induced by the side chains. Dispersion‐corrected DFT calculations provide better results than plain DFT, but comparison with experiment suggests that they overestimate the stability of the folded conformers. Molecular dynamics simulations and NMR results also confirm a limited accuracy of the dispersion‐DFT model in nonaqueous solvents. Combination of chiral spectroscopies with theoretical analysis thus significantly enhances the information that can be obtained from the induced chirality of the Trp aromatic residue.     

The Route from the Folded to the Amyloid State: Exploring the Potential Energy Surface of a Drug-Like Miniprotein

The amyloid formation of the folded segment of a variant of Exenatide (a marketed drug for type-2 diabetes mellitus) was studied by electronic circular dichroism (ECD) and NMR spectroscopy. We found that the optimum temperature for E5 protein amyloidosis coincides with body temperature and requires well below physiological salt concentration. Decomposition of the ECD spectra and its barycentric representation on the folded-unfolded-amyloid potential energy surface allowed us to monitor the full range of molecular transformation of amyloidogenesis. We identified points of no return (e.g.; T=37 °C, pH 4.1, c_E5=250 μm , c_NaCl=50 mm , t>4–6 h) that will inevitably gravitate into the amyloid state. The strong B-type far ultraviolet (FUV)-ECD spectra and an unexpectedly strong near ultraviolet (NUV)-ECD signal (Θ_{≈275–285 nm}) indicate that the amyloid phase of E5 is built from monomers of quasi-elongated backbone structure (φ≈−145°, ψ≈+145°) with strong interstrand Tyr↔Trp interaction. Misfolded intermediates and the buildup of “toxic” early-stage oligomers leading to self-association were identified and monitored as a function of time. Results indicate that the amyloid transition is triggered by subtle misfolding of the α-helix, exposing aromatic and hydrophobic side chains that may provide the first centers for an intermolecular reorganization. These initial clusters provide the spatial closeness and sufficient time for a transition to the β-structured amyloid nucleus, thus the process follows a nucleated growth mechanism.     

Multiple Decay Mechanisms and 2D‐UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine‐Uracil Monophosphate

The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D‐UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine ¹L_a state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine ¹L_b and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter‐base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long‐lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the ¹L_b, S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D‐UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm^?1 in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D‐UV spectroscopy to disentangle the photophysics of multichromophoric systems.     

Oxo transfer reaction: Dioxido and monooxidovanadium(V) complexes

A dioxidovanadium(V) complex of type [(L_ONOH^?)(VO₂)] (1) was isolated where L_ONOH₂ is a tridentate ONO donor benzhydrazide ligand. 1 undergoes an oxo transfer reaction with triphenylphosphine in presence of 8-hydroxyquinoline (HQ) and affords a monooxidovanadium(V) complex of type [(L_ONO^2?)(VO)(Q^?)] (2). 1 and 2 were substantiated by elemental analyses, ESI-mass, IR, ¹H NMR, ⁵¹V NMR and UV–vis spectra. The molecular geometries of 1 and 2 were authenticated by single crystal X?ray crystallography. UV–vis absorption spectra of 1 and 2 display bands respectively at 325 and 320 nm due to oxido → vanadium(V) charge transfer transitions. 1 exhibit an irreversible cathodic peak at ?0.44 V whereas 2 displays a reversible cathodic wave at ?0.60 V in cyclic voltammogram due to the VO³⁺/VO²⁺ redox couple.     

Magnetic circular dichroism studies 23. 1. Magnetic circular dichroism spectra of indole alkaloids

The magnetic circular dichroism spectra of a number of indole alkaloids show two B-terms of opposite sign in the 250–330 nm wavelength region associated with the ¹L_b and ¹L_a electronic transitions, the long wavelength, ¹L^b, band being of positive sign, whereas both bands strongly overlap in absorption. Various substituents in different positions of the indole ring cause a red shift of both bands and a broadening of the long wavelength B-term. The sign pattern, howver, remains unchanged in all examples thus far investigated. Dihydroindole and oxindole, on the other hand, exhibit MCD. bands with the opposite sign sequence as compared to the indole chromophore. This observation allows identification of the indole chromophore in alkaloids from the sign pattern of the MCD. bands.     

Structural Insights into the Trp‐Cage Folding Intermediate Formation

The 20 residue long Trp‐cage is the smallest protein known, and thus has been the subject of several in vitro and in silico folding studies. Here, we report the multistate folding scenario of the miniprotein in atomic detail. We detected and characterized different intermediate states by temperature dependent NMR measurements of the ¹⁵N and ¹³C/¹⁵N labeled protein, both at neutral and acidic pH values. We developed a deconvolution technique to characterize the invisible—fully folded, unfolded and intermediate—fast exchanging states. Using nonlinear fitting methods we can obtain both the thermodynamic parameters (ΔH^F–I, T_m^F–I, ΔC_p^F–I and ΔH^I–U, T_m^I–U, ΔC_p^I–U) and the NMR chemical shifts of the conformers of the multistate unfolding process. During the unfolding of Trp‐cage distinct intermediates evolve: a fast‐exchanging intermediate is present under neutral conditions, whereas a slow‐exchanging intermediate‐pair emerges at acidic pH. The fast‐exchanging intermediate has a native‐like structure with a short α‐helix in the G¹¹–G¹⁵ segment, whereas the slow‐exchanging intermediate‐pair presents elevated dynamics, with no detectable native‐like residue contacts in which the G¹¹? P¹² peptide bond has either cis or trans conformation. Heteronuclear relaxation studies combined with MD simulations revealed the source of backbone mobility and the nature of structural rearrangements during these transitions. The ability to detect structural and dynamic information about folding intermediates in vitro provides an excellent opportunity to gain new insights into the energetic aspects of the energy landscape of protein folding. Our new experimental data offer exceptional testing ground for further computational simulations.     

Direct Observation of the Reversible Two‐State Unfolding and Refolding of an α/β Protein by Single‐Molecule Atomic Force Microscopy

Directly observing protein folding in real time using atomic force microscopy (AFM) is challenging. Here the use of AFM to directly monitor the folding of an α/β protein, NuG2, by using low‐drift AFM cantilevers is demonstrated. At slow pulling speeds (<50 nm s^?1), the refolding of NuG2 can be clearly observed. Lowering the pulling speed reduces the difference between the unfolding and refolding forces, bringing the non‐equilibrium unfolding–refolding reactions towards equilibrium. At very low pulling speeds (ca. 2 nm s^?1), unfolding and refolding were observed to occur in near equilibrium. Based on the Crooks fluctuation theorem, we then measured the equilibrium free energy change between folded and unfolded states of NuG2. The improved long‐term stability of AFM achieved using gold‐free cantilevers allows folding–unfolding reactions of α/β proteins to be directly monitored near equilibrium, opening the avenue towards probing the folding reactions of other mechanically important α/β and all‐β elastomeric proteins.     

BLUF Hydrogen network dynamics and UV/Vis spectra: A combined molecular dynamics and quantum chemical study

Blue light sensing using flavin (BLUF) protein photoreceptor domains change their hydrogen bond network after photoexcitation. To explore this phenomenon, BLUF domains from R. sphaeroides were simulated using Amber99 molecular dynamics (MD). Five starting configurations were considered, to study different BLUF proteins (AppA/BlrB), Trp conformations (“W_in”/“W_out”), structure determination (X‐ray/NMR), and finally, His protonation states. We found dependencies of the hydrogen bonds on almost all parameters. Our data show an especially strong correlation of the Trp position and hydrogen bonds involving Gln63. The latter is in some contradiction to earlier results (Obanayama et al., Photochem. Photobiol. 2008, 84 10031010). Possible origins and implications are discussed. Our calculations support conjectures that Gln63 is more flexible with Trp104 in W_in position. Using snapshots from MD and time‐dependent density functional theory, UV/vis spectra for the chromophore were determined, which account for molecular motion of the protein under ambient conditions. In accord with experiment, it is found that the UV/vis spectra of BLUF bound flavin are red‐shifted and thermally broadened for all calculated π → π* transitions, relative to gas phase flavin at T = 0 K. However, differences in the spectra between the various BLUF configurations cannot be resolved with the present approach. © 2012 Wiley Periodicals, Inc.     

Synthesis,Characterization and SOD Activities of IP-copper（Ⅱ）-L-amino Acid Complexes

Four new ternary complexes： [Cu（IP）（L-Val）（H2O）]ClO4·1.5H2O（1）, [Cu（IP）（L-Leu）（H2O）]ClO4（2）, [Cu（IP）（L-Tyr）（H2O）]ClO4·H2O（3） and [Cu（IP）（L-Trp）（H2O）]ClO4·1.5H2O（4） have been synthesized and character/zed by elementa/analysis, molar conductivity, infrared absorption spectroscopy, electronic absorption spectroscopy and cyclic voltammetry, where IP=imidazo[4,5-f][1,10] phenanthroline, L-Val=L-valinate, L-Leu=L-leucinate, L-Tyr=L-tyrosinate and L-Trp=L-tryptophanate. Complex 3 was structurally characterized by X-ray diffraction method, which crystallizes in orthorhornbic space group P21212 in a unit cell of dimensions a=3.0567（4） nm, b=0.74079（9） nm, c= 1.06198（13） nm, V=2.4047（5） nm^3, Z=4,μ=0.1084 cm^-1. The SOD-like activities of catalytic disrnutation of superoxide anions （O2^-· ） by the complexes were determined by means of modified nitroblue tetrazolium （NBT） photoreduction. The IC50 values of complexes 1, 2, 3 and 4 are 0.072, 0.147, 0.429 and 0.264 μmol·L^-1, respectively     

Bridge‐Localized HOMO‐Binding Character of Divinylanthracene‐Bridged Dinuclear Ruthenium Carbonyl Complexes: Spectroscopic,Spectroelectrochemical, and Computational Studies

The electronic properties of four divinylanthracene‐bridged diruthenium carbonyl complexes [{RuCl(CO)(PMe₃)₃}₂(μ? CH?CHArCH?CH)] (Ar=9,10‐anthracene ( 1 ), 1,5‐anthracene ( 2 ), 2,6‐anthracene ( 3 ), 1,8‐anthracene ( 4 )) obtained by molecular spectroscopic methods (IR, UV/Vis/near‐IR, and EPR spectroscopy) and DFT calculations are reported. IR spectroelectrochemical studies have revealed that these complexes are first oxidized at the noninnocent bridging ligand, which is in line with the very small ν(C?O) wavenumber shift that accompanies this process and also supported by DFT calculations. Because of poor conjugation in complex 1 , except oxidized 1⁺ , the electronic absorption spectra of complexes 2⁺ , 3⁺ , and 4⁺ all display the characteristic near‐IR band envelopes that have been deconvoluted into three Gaussian sub‐bands. Two of the sub‐bands belong mainly to metal‐to‐ligand charge‐transfer (MLCT) transitions according to results from time‐dependent DFT calculations. EPR spectroscopy of chemically generated 1⁺ – 4⁺ proves largely ligand‐centered spin density, again in accordance with IR spectra and DFT calculations results.     

Darstellung und spektroskopische Charakterisierung der Nona-halogenodiiridate(III), [Ir2X9]3−, X = Cl,Br

Preparation and Spectroscopic Characterization of Nonahalogenodiiridates(III), [Ir₂X₉]^3?, X = Cl, Br The pure nonahalogenodiiridates(III), A₃[Ir₂X₉] (A = K, Cs, tetraalkylammonium; X = Cl, Br) have been prepared. They are formed from the monomer hexahalogenoiridates(III) which are bridged to confacial bioctahedral complexes by ligand abstraction in less polar organic solvents. The IR and Raman spectra exhibit bands in three characteristic regions; at high wavenumbers stretching vibrations with terminal ligands ν(Ir?Cl_t): 360?300, ν(Ir?Br_t): 250?220; in a middle region with bridging ligands ν(Ir?Cl_b): 290?235, ν(Ir?Br_b): 205?190 cm^?1; the deformation bands are observed at distinct lower frequencies. The distance between ν(Ir?X_t) and ν(Ir?X_b) increases with decreasing size of the cations. The electronic spectra measured at thin films of the pure complex salts at 10 K show some intensive charge transfer transitions in the UV and one or two weak d? d bands in the visible region.     

Detection of the reduced forms of radical adducts on the ESR trace using HPLC‐electrochemical detector‐ultraviolet absorption detector‐electron spin resonance‐MS

To detect and identify the electron spin resonance (ESR) silent forms of the α‐(4‐pyridyl‐1‐oxide)‐N‐tert‐butylnitrone (4‐POBN) radical adducts, an electrochemical detector (ECD) was employed as a reactor in the HPLC‐ECD‐UV absorption detector‐ESR‐MS (HPLC‐ECD‐UV‐ESR‐MS). The ECD was employed to regenerate the radical forms from the reduced forms. The reduced forms of the 4‐POBN/pentyl radical adducts were analyzed using the HPLC‐ECD‐UV‐ESR‐MS. On addition of the ECD applied potential of +0.3 V, a peak appeared on the ESR trace of the HPLC‐ECD‐UV‐ESR‐MS analyses, indicating that the radical forms are regenerated from the reduced forms. The HPLC‐ECD‐UV‐ESR‐MS analyses were also performed for the reaction mixtures of phenylhydrazine with CuCl₂. Two peaks (peaks I and II) were detected on the UV trace (300 nm) of the HPLC‐ECD‐UV‐ESR‐MS. The mass spectra showed that the peak I and peak II compounds are radical and reduced forms of the 4‐POBN/phenyl radical adducts under the ECD applied potential of 0.0 V. Peak I was only detected on the ESR trace under the ECD applied potential of 0.0 V. In addition to peak I, peak II appeared on the ESR trace under the ECD applied potential of +0.3 V, indicating that the reduced forms are oxidized to the corresponding radical forms.     

UV Raman markers for structural analysis of aromatic side chains in proteins

UV Raman spectroscopy is a powerful tool for investigating the structures and interactions of the aromatic side chains of Phe, Tyr, Trp, and His in proteins. This is because Raman bands of aromatic ring vibrations are selectively enhanced with UV excitation, and intensities and wavenumbers of Raman bands sensitively reflect structures and interactions. Interpretation of protein Raman spectra is greatly assisted by using empirical correlations between spectra and structure. Many Raman bands of aromatic side chains have been proposed to be useful as markers of structures and interactions on the basis of empirical correlations. This article reviews the usefulness and limitations of the Raman markers for protonation/deprotonation, conformation, metal coordination, environmental polarity, hydrogen bonding, hydrophobic interaction, and cation-π interaction of the aromatic side chains. The utility of Raman markers is demonstrated through an application to the structural analysis of a membrane-bound proton channel protein.     

Synthesis,spectroscopic, thermal analyses,biological activity and molecular docking studies on mixed ligand complexes derived from Schiff base ligands and 2,6‐pyridine dicarboxylic acid

Two novel Schiff base ligands (L^a and L^b) were prepared from the condensation of quinoline 2‐aldehyde with 2‐aminopyridine (ligand L^a) and from the condensation of oxamide with furfural (ligand L^b). Mixed ligand complexes of the type M⁺²L^a/b L^c were prepared, where (L^a and L^b) the primary ligands and L^c was 2,6‐pyridinedicarboxylic acid as secondary ligand. Metal ions used were Fe(II), Co(II), Ni(II) and Zn(II) for mixed ligands L^a L^c and Fe(II), Co(II), Ni(II), Cu(II), Hg(II) and Zn(II) for L^bL^c mixed ligands. L^a and L^b Schiff base ligands were both characterized using elemental analyses, molar conductance, IR, ¹H and ¹³C NMR. Mass spectra for L^b, [Zn(L^a)L^cCl]Cl and [Cu(L^b)L^cCl]Cl were also studied. ESR spectrum of the [Cu(L^b) L^cCl]Cl complex was also recorded The metal complexes were synthesized and characterized using elemental analyses, spectroscopic (IR, ¹H NMR, UV‐visible, diffused reflectance), molar conductance, magnetic moment and thermal studies. The IR and ¹H NMR spectral data revealed that 2,6‐pyridinedicarboxalic acid ligand coordinated to the metal ions via pyridyl N and carboxylate O without proton displacement. In addition, the IR data showed that L^a and L^b ligands behaved as neutral bidentate ligands with N₂ donation sites (quinoline N and azomethine N for L^a and two azomethine N for L^b). Based on spectroscopic studies, an octahedral geometry was proposed for the complexes. The thermal stability and degradation of the metal complexes were investigated by thermogravimetric analysis. The binding modes and affinities of L^a, L^b and Zn(II) complexes towards receptors of crystal structure of E. coli (PDB ID: 3 t88) and mutant oxidoreductase of breast cancer (PDB ID: 3 hb5) receptors were also studied. The antimicrobial activity against two species of Gram positive, Gram negative bacteria and fungi were tested for the Schiff base ligands, 2,6‐pyridinedicarboxylic acid and the mixed ligand complexes and revealed that the synthesized mixed ligand complexes exhibited higher antimicrobial activity than their free Schiff base ligands.     

1H NMR,IR and UV/VIS Spectroscopic Studies of Some Schiff Bases Derived from 2‐Aminobenzothiazole and 2‐Amino‐3‐Hydroxypyridine

By condensing 2‐aminobenzothiazole with 2‐hydroxy‐1‐naphthaldehyde, 2‐hydroxybenzaldehyde, 4‐methoxybenzaldehyde, 4‐hydroxybenzal‐dehyde, benzaldehyde and 4‐dimethylaminobenzaldehyde, and five Schiff bases Ia‐Ie are prepared. Also, two Schiff bases IIa and IIb are prepared by condensation of 2‐amino‐3‐hydroxypyridine with 2‐hydroxy‐1‐naphthaldehyde and 2‐hydroxybenzaldehyde. The ¹H NMR, IR and UV/Vis spectra of these seven Schiff bases are investigated. The signals of the ¹H NMR spectra as well as the important bands in the IR spectra are considered and discussed in relation to molecular structure. The UV/Vis absorption bands in ethanol are assigned to the corresponding electronic transitions and the electronic absorption spectra of Schiff bases Ib and IIb are studied in organic solvents of different polarities. The UV/Vis absorption spectra of 2‐amino‐3‐hydroxypyridine Schiff bases IIa and IIb are investigated in buffer solutions of different pH values containing 5% (v/v) methanol, and the results are utilized for the determination of pK_a and ΔG^* of the ionization of the phenolic OH‐groups. The fluorescence spectra of IIa and IIb are studied in organic solvents of different polarities. The obtained spectral results are confirmed by some molecular calculations using the atom super position and electron delocalization molecular orbital theory for the Schiff base IIb.     

A pair of humulane sesquiterpenoid enantiomers from Syringa pinnatifolia

Two humulane-type sesquiterpenoids, namely (+)-alashanoid I (1a) and (–)-alashanoid I (1b), were isolated as a pair of enantiomers from the peeled stems of Syringa pinnatifolia. Their structures were elucidated by extensive spectroscopic data (1?D and 2?D NMR, UV, and IR), and the absolute configurations were resolved by X-ray diffraction and experimental and calculated ECD data analysis.     

Preparation of Novel Arrays Silver Nanoparticles Modified Polyrutin Coat‐Paraffin‐Impregnated Graphite Electrode for Tyrosine and Tryptophan's Oxidation

A novel array silver nanoparticles and Rutin complex film modified paraffin‐impregnated graphite electrode was proposed in this work (denoted as Ag/Rutin/WGE). The characteristics were investigated by the field emission scanning electron microscopy (FE‐SEM), infrared spectra (IR), UV‐visible (UV), X‐ray photoelectron spectroscopy (XPS) and electrochemical techniques. Silver ions were gradually chelated by polyrutin film at 4′‐oxo‐5′‐OH and 5‐OH‐4‐oxo sites accompanying adsorption, then. Silver nanoparticles were highly‐dispersed electrodeposited on polyrutin film. The electrochemical behaviors of tyrosine (Tyr) and tryptophan (Trp) were studied by cyclic voltammetry (CV) and differential pulse voltammetry (DPV) techniques. The Ag/Rutin/WGE electrode shows overlapping catalysis for the oxidation of Tyr and Trp. The linear response of Tyr and Trp were 0.3–10.0 and 0.7–70.0 μM with detection limit of 0.07 and 0.1 μM in a signal‐to‐noise ratio of 3.     

Comparative sensibility of S1 ←S0 and S2 ←S0 indole electronic transitions to environment perturbations. The positions of the 0—0 bands in polar media

The modifications under environmental perturbations of the well separated two first electronic systems of carbazole are used to demonstrate the possibility of including solute-ether complexes in polyethylene films. The application of this technique to indole allows to differentiate the overlapping ¹L_a and ¹L_b transitions in the spectrum of hydrogen bonded indole. The ground state interactions of indole, 5-methoxyindole and 3-methylindole in several well defined environment conditions (hydrogen bond in a polar cage, hydrogen bond in a nonpolar cage) are investigated through UV absorption spectroscopy between 293 and 88 K. A strong red shift of the ¹L_a bands under the hydrogen bonding occurs with all the indoles investigated. The comparative analysis of the spectra in three types of environment, allows to give the accurate location of the first bands for the two overlapping vibronic systems of these molecules in polar media. Particularly, it is unambiguously shown that the first ¹L_a band and the first ¹L_b band of indole in alcohols are superposed at 288 nm. These results offer reliable new bases for the study of the emission properties of indole and its derivatives.     

A localized specific interaction alters the unfolding pathways of structural homologues

Reductive unfolding studies of proteins are designed to provide information about intramolecular interactions that govern the formation (and stabilization) of the native state and about folding/unfolding pathways. By mutating Tyr92 to G, A, or L in the model protein, bovine pancreatic ribonuclease A, and through analysis of temperature factors and molecular dynamics simulations of the crystal structures of these mutants, it is demonstrated that the markedly different reductive unfolding rates and pathways of ribonuclease A and its structural homologue onconase can be attributed to a single, localized, ring-stacking interaction between Tyr92 and Pro93 in the bovine variant. The fortuitous location of this specific stabilizing interaction in a disulfide-bond-containing loop region of ribonuclease A results in the localized modulation of protein dynamics that, in turn, enhances the susceptibility of the disulfide bond to reduction leading to an alteration in the reductive unfolding behavior of the homologues. These results have important implications for folding studies involving topological determinants to obtain folding/unfolding rates and pathways, for protein structure-function prediction through fold recognition, and for predicting proteolytic cleavage sites.     

Closed loop folding units from structural alignments: Experimental foldons revisited

Nonoverlapping closed loops of around 25–35 amino acids formed via nonlocal interactions at the loop ends have been proposed as an important unit of protein structure. This hypothesis is significant as such short loops can fold quickly and so would not be bound by the Leventhal paradox, giving insight into the possible nature of the funnel in protein folding. Previously, these closed loops have been identified either by sequence analysis (conservation and autocorrelation) or studies of the geometry of individual proteins. Given the potential significance of the closed loop hypothesis, we have explored a new strategy for determining closed loops from the insertions identified by the structural alignment of proteins sharing the same overall fold. We determined the locations of the closed loops in 37 pairs of proteins and obtained excellent agreement with previously published closed loops. The relevance of NMR structures to closed loop determination is briefly discussed. For cytochrome c, cytochrome b₅₆₂ and triosephophate isomerase, independent folding units have been determined on the basis of hydrogen exchange experiments and misincorporation proton‐alkyl exchange experiments. The correspondence between these experimentally derived foldons and the theoretically derived closed loops indicates that the closed loop hypothesis may provide a useful framework for analyzing such experimental data. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010