Conformational Interconversion Research Articles

Electronically rich N-substituted tetrahydroisoquinoline 3-carboxylic acid esters: concise synthesis and conformational studies

Recent work in our laboratory has shown that the highly substituted, electronically rich 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (THIQ3CA) scaffold is a key building block for a novel class of promising anticoagulants.10 The synthesis of THIQ3CA analogs, especially containing specific, electronically rich substituents, has been a challenge and essentially no efficient methods have been reported in the literature. We describe three complementary, glycine donor-based strategies for high yielding synthesis of highly substituted, electronically rich THIQ3CA esters. Three glycine donors studied herein include hydantoin 1, (±)-Boc-α-phosphonoglycine trimethyl ester 2, and (±)-Z-α-phosphonoglycine trimethyl ester 3. Although the synthesis of THIQ3CA analogs could be achieved using either of the three, an optimal, high yielding approach for the desired THIQ3CA esters was best achieved using 3 in three mild, efficient steps. Using this approach, a focused library of advanced N-arylacyl, N-arylalkyl, and bis-THIQ3CA analogs was synthesized. Variable temperature and solvent-dependent NMR chemical shift studies indicated the presence of two major conformational rotamers in 3:1 proportion for N-arylacyl–THIQ3CA analogs, which were separated by a high kinetic barrier of ∼17 kcal/mol. In contrast, N-arylalkyl and bis-THIQ3CA variants displayed no rotamerism, which implicates restricted rotation around the amide bond as the origin for high-barrier conformational interconversion. This phenomenon is of major significance because structure-based drug design typically utilizes only one conformation. Overall, the work presents fundamental studies on the synthesis and conformational properties of highly substituted, electronically rich THIQ3CA analogs.

Synthesis of novel enantiomerically pure tetra-carbohydrazide cyclophane macrocycles

A total of twelve novel enantiomerically pure tetra-carbohydrazide cyclophane macrocycles have been synthesised in quantitative yields by reacting chiral (4R,5R)- and (4S,5S)-1,3-dioxolane-4,5-dicarbohydrazides with aromatic bis-aldehydes in a [2 + 2]-cyclocondensation reaction. The compounds show a dynamic behaviour in solution, which has been rationalized in terms of an unprecedented conformational interconversion between two conformers one stabilised by intramolecular hydrogen bonding and π-π stacking interactions.

Insights in the (un)structural organization of Bacillus pasteurii UreG, an intrinsically disordered GTPase enzyme

In the past, enzymatic activity has always been expected to be dependent on overall protein rigidity, necessary for substrate recognition and optimal orientation. However, increasing evidence is now accumulating, revealing that some proteins characterized by intrinsic disorder are actually able to perform catalysis. Among them, the only known natural intrinsically disordered enzyme is UreG, a GTPase that, in plants and bacteria, is involved in the protein interaction network leading to Ni(2+) ions delivery into the active site of urease. In this paper, we report a detailed analysis of the unfolding behaviour of UreG from Bacillus pasteurii (BpUreG), following its thermal and chemical denaturation with a combination of fluorescence spectroscopy, calorimetry, CD and NMR. The results demonstrate that BpUreG exists as an ensemble of inter-converting conformations, whose degrees of secondary structure depend on temperature and denaturant concentration. In particular, three major types of conformational ensembles with different degrees of residual structure were identified, with major structural characteristics resembling those of a molten globule (low temperature, absence of denaturant), pre-molten globule (high temperature, absence or presence of denaturant) and random coil (low temperature, presence of denaturant). Transitions among these ensembles of conformational states occur non-cooperatively although reversibly, with a gradual loss or acquisition of residual structure depending on the conditions. A possible role of disorder in the biological function of UreG is envisaged and discussed.

Reaction Mechanism in Crystalline Solids: Kinetics and Conformational Dynamics of the Norrish Type II Biradicals from α-Adamantyl-p-Methoxyacetophenone

In an effort to determine the details of the solid-state reaction mechanism and diastereoselectivity in the Norrish type II and Yang cyclization of crystalline α-adamantyl-p-methoxyacetophenone, we determined its solid-state quantum yields and transient kinetics using nanocrystalline suspensions. The transient spectroscopy measurements were complemented with solid-state NMR spectroscopy spin-lattice relaxation experiments using isotopically labeled samples and with the analysis of variable-temperature anisotropic displacement parameters from single-crystal X-ray diffraction to determine the rate of interconversion of biradical conformers by rotation of the globular adamantyl group. Our experimental findings include a solid-state quantum yield for reaction that is 3 times greater than that in solution, a Norrish type II hydrogen-transfer reaction that is about 8 times faster in crystals than in solution, and a biradical decay that occurs on the same time scale as conformational exchange, which helps to explain the diastereoselectivity observed in the solid state.

Unwinding Initiation by the Viral RNA Helicase NPH-II

Viral RNA helicases of the NS3/NPH-II group unwind RNA duplexes by processive, directional translocation on one of the duplex strands. The translocation is preceded by a poorly understood unwinding initiation phase. For NPH-II from vaccinia virus, unwinding initiation is rate limiting for the overall unwinding reaction. To develop a mechanistic understanding of the unwinding initiation, we studied kinetic and thermodynamic aspects of this reaction phase for NPH-II in vitro, using biochemical and single molecule fluorescence approaches. Our data show that NPH-II functions as a monomer and that different stages of the ATP hydrolysis cycle dictate distinct binding preferences of NPH-II for duplex versus single-stranded RNA. We further find that the NPH-II–RNA complex does not adopt a single conformation but rather at least two distinct conformations in each of the analyzed stages of ATP hydrolysis. These conformations interconvert with rate constants that depend on the stage of the ATP hydrolysis cycle. Our data establish a basic mechanistic framework for unwinding initiation by NPH-II and suggest that the various stages of the ATP hydrolysis cycle do not induce single, stage-specific conformations in the NPH-II–RNA complex but primarily control transitions between multiple states.

Theoretical study of the conformational energy hypersurface of cyclotrisarcosyl

Abstract The multidimensional Conformational Potential Energy Hypersurface (PEHS) of cyclotrisarcosyl was comprehensively investigated at the DFT (B3LYP/6-31G(d), B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p)), levels of theory. The equilibrium structures, their relative stability, and the Transition State (TS) structures involved in the conformational interconversion pathways were analyzed. Aug-cc-pVTZ//B3LYP/6-311++G(d,p) and MP2/6-31G(d)//B3LYP/6-311++G(d,p) single point calculations predict a symmetric cis-cis-cis crown conformation as the energetically preferred form for this compound, which is in agreement with the experimental data. The conformational interconversion between the global minimum and the twist form requires 20.88 kcal mol-1 at the MP2/6-31G(d)//B3LYP/6-311++G(d,p) level of theory. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of this cyclic tripeptide, describing the conformations as well as the conformational interconversion processes in this hypersurface. In addition, a comparative analysis between the conformational behaviors of cyclotrisarcosyl with that previously reported for cyclotriglycine was carried out

ChemInform Abstract: Chemistry and Structural Biology of DNA Damage and Biological Consequences

AbstractReview: 387 refs.

Solution Structure of the State 1 Conformer of GTP-bound H-Ras Protein and Distinct Dynamic Properties between the State 1 and State 2 Conformers

Ras small GTPases undergo dynamic equilibrium of two interconverting conformations, state 1 and state 2, in the GTP-bound forms, where state 2 is recognized by effectors, whereas physiological functions of state 1 have been unknown. Limited information, such as static crystal structures and (31)P NMR spectra, was available for the study of the conformational dynamics. Here we determine the solution structure and dynamics of state 1 by multidimensional heteronuclear NMR analysis of an H-RasT35S mutant in complex with guanosine 5'-(β, γ-imido)triphosphate (GppNHp). The state 1 structure shows that the switch I loop fluctuates extensively compared with that in state 2 or H-Ras-GDP. Also, backbone (1)H,(15)N signals for state 2 are identified, and their dynamics are studied by utilizing a complex with c-Raf-1. Furthermore, the signals for almost all the residues of H-Ras·GppNHp are identified by measurement at low temperature, and the signals for multiple residues are found split into two peaks corresponding to the signals for state 1 and state 2. Intriguingly, these residues are located not only in the switch regions and their neighbors but also in the rigidly structured regions, suggesting that global structural rearrangements occur during the state interconversion. The backbone dynamics of each state show that the switch loops in state 1 are dynamically mobile on the picosecond to nanosecond time scale, and these mobilities are significantly reduced in state 2. These results suggest that multiconformations existing in state 1 are mostly deselected upon the transition toward state 2 induced by the effector binding.

Multistep conformational interconversion mechanism of cyclododecane. A simple and fast analysis using potential energy curves

AbstractAn ab initio and Density Functional Theory (DFT) study of the conformational properties of cyclododecane was carried out. The energetically preferred equilibrium structures, their relative stability, and some of the transition state (TS) structures involved in the conformational interconversion pathways were analyzed from RHF/6‐31G(d), B3LYP/6‐31G(d,p) and B3LYP/6311++G(d,p) calculations. Aug‐cc‐pVDZ//B3LYP/6311++G(d,p) single point calculations predict that the multistep conformational interconversion mechanism requires 11.07 kcal/mol, which is in agreement with the available experimental data. These results allow us to form a concise idea about the internal intricacies of the preferred forms of cyclododecane, describing the conformations as well as the conformational interconversion processes in the conformational potential energy hypersurface. Our results indicated that performing an exhaustive analysis of the potential energy curves connecting the most representative conformations is a valid alternate tool to determine the principal conformational interconversion paths for cyclododecane. This methodology represents a satisfactory first approximation for the conformational analysis of medium‐ and large‐size flexible cyclic compounds. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

Structural Dynamics of Free Proteins in Diffraction

Among the macromolecular patterns of biological significance, right-handed α-helices are perhaps the most abundant structural motifs. Here, guided by experimental findings, we discuss both ultrafast initial steps and longer-time-scale structural dynamics of helix-coil transitions induced by a range of temperature jumps in large, isolated macromolecular ensembles of an α-helical protein segment thymosin β(9) (Tβ(9)), and elucidate the comprehensive picture of (un)folding. In continuation of an earlier theoretical work from this laboratory that utilized a simplistic structure-scrambling algorithm combined with a variety of self-avoidance thresholds to approximately model helix-coil transitions in Tβ(9), in the present contribution we focus on the actual dynamics of unfolding as obtained from massively distributed ensemble-convergent MD simulations which provide an unprecedented scope of information on the nature of transient macromolecular structures, and with atomic-scale spatiotemporal resolution. In addition to the use of radial distribution functions of ultrafast electron diffraction (UED) simulations in gaining an insight into the elementary steps of conformational interconversions, we also investigate the structural dynamics of the protein via the native (α-helical) hydrogen bonding contact metric which is an intuitive coarse graining approach. Importantly, the decay of α-helical motifs and the (globular) conformational annealing in Tβ(9) occur consecutively or competitively, depending on the magnitude of temperature jump.

Kinetics of Conformational Sampling in Ubiquitin

Molecular recognition plays a central role in many biological processes. For enzymatic reactions and slow protein–protein recognition events, turn-over rates and on-rates in the millisecond-to-second time scale have been connected to internal protein dynamics detected with atomic resolution by NMR spectroscopy, and in particular conformational sampling could be established as a mechanism for enzyme–substrate and protein–protein recognition. Recent theoretical studies indicate that faster rates of conformational interconversion in the microsecond time scale might limit on-rates for protein–protein recognition. However experimental proofs were lacking so far, mainly because such rates could not be determined accurately enough and kinetic experiments in the microsecond time range are difficult to perform. Nevertheless, for proteins and TAR-RNA, recent studies based on residual dipolar couplings (RDCs) and other NMR spectroscopy techniques have detected substantial internal dynamics in a time window from the rotational correlation time tc (one-digit nanoseconds) to approximately 50 ms, called the supra-tc window in the following. However, the exact rates of internal dynamics within this four orders of magnitude wide time window could not be determined. Supra-tc dynamics in ubiquitin [9] and TAR-RNA could be connected to the conformational sampling required for molecular recognition. While the amplitudes of motions have been indirectly detected by RDCs and characterized in great detail, it has so far been impossible to directly observe these motions and to determine the exact rate of these supra-tc motions. In contrast, conformational sampling in enzymes occurs on a time scale that is 100 to 1000 times slower than supra-tc dynamics and therefore NMR relaxation dispersion (RD) techniques have been able to establish the functional link to enzyme kinetics with atomic resolution at physiological conditions. 5] However, for technical reasons, RD is not sensitive to motion faster than approximately 50 ms (RD window) and therefore does not access motion in the supra-tc window at room temperature. Here we determine the rate of interconversion between conformers of free ubiquitin by a combination of NMR RD experiments in super-cooled solution and dielectric relaxation spectroscopy (DR). Furthermore, we corroborate the motional amplitudes in the RDC-derived ensembles quantitatively with the observed amplitudes of RD and DR. The methods utilized herein can be used to directly study protein dynamics in a time range that was previously inaccessible. Significant motional amplitude in the supra-tc window has been observed using RDC measurements, and was connected to the conformational sampling for a protein in the ground

Mapping the Landscape of RNA Dynamics with NMR Spectroscopy

Among the three major classes of biomacromolecules (DNA, RNA, and proteins) RNA's pronounced dynamics are the most explicitly linked to its wide variety of functions, which include catalysis and the regulation of transcription, translation, and splicing. These functions are mediated by a range of RNA biomachinery, including such varied examples as macromolecular noncoding RNAs, microRNAs, small interfering RNAs, riboswitch RNAs, and RNA thermometers. In each case, the functional dynamics of an interconversion is characterized by an associated rate constant. In this Account, we provide an introduction to NMR spectroscopic characterization of the landscape of RNA dynamics. We introduce strategies for measuring NMR parameters at various time scales as well as the underlying models for describing the corresponding rate constants. RNA exhibits significant dynamic motion, which can be modulated by (i) intermolecular interactions, including specific and nonspecific binding of ions (such as Mg(2+) and tertiary amines), (ii) metabolites in riboswitches or RNA aptamers, and (iii) macromolecular interactions within ribonucleic protein particles, including the ribosome and the spliceosome. Our understanding of the nature of these dynamic changes in RNA targets is now being incorporated into RNA-specific approaches in the design of RNA inhibitors. Interactions of RNA with proteins, other RNAs, or small molecules often occur through binding mechanisms that follow an induced fit mechanism or a conformational selection mechanism, in which one of several populated RNA conformations is selected through ligand binding. The extent of functional dynamics, including the kinetic formation of a specific RNA tertiary fold, is dependent on the messenger RNA (mRNA) chain length. Thus, during de novo synthesis of mRNA, both in prokaryotes and eukaryotes, nascent mRNA of various lengths will adopt different secondary and tertiary structures. The speed of transcription has a critical influence on the functional dynamics of the RNA being synthesized. In addition to modulating the local dynamics of a conformational RNA ensemble, a given RNA sequence may adopt more than one global, three-dimensional structure. RNA modification is one way to select among these alternative structures, which are often characterized by nearly equal stability, but with high energy barriers for conformational interconversion. The refolding of different secondary and tertiary structures has been found to be a major regulatory mechanism for transcription and translation. These conformational transitions can be characterized with NMR spectroscopy, for any given RNA sequence, in response to external stimuli.

Chemistry and structural biology of DNA damage and biological consequences.

The formation of adducts by the reaction of chemicals with DNA is a critical step for the initiation of carcinogenesis. The structural analysis of various DNA adducts reveals that conformational and chemical rearrangements and interconversions are a common theme. Conformational changes are modulated both by the nature of adduct and the base sequences neighboring the lesion sites. Equilibria between conformational states may modulate both DNA repair and error-prone replication past these adducts. Likewise, chemical rearrangements of initially formed DNA adducts are also modulated both by the nature of adducts and the base sequences neighboring the lesion sites. In this review, we focus on DNA damage caused by a number of environmental and endogenous agents, and biological consequences.

Ab Initio and DFT Studies of Conformational Properties of Heteroatom Containing Ketene Analogues and Their Comparison with the Related Cyclic Analogues

Minimum‐energy and transition state geometries of 3‐thioxoprop‐2‐enethial, 3‐thioxoacrylaldehyde, 3‐oxoprop‐2‐enethial, 3‐selenoxoprop‐2‐enethial, 3‐thioxoprop‐2‐eneselenal, 3‐selenoxoprop‐2‐eneselenal, 3‐oxoacrylaldehyde, 3‐selenoxoacrylaldehyde and 3‐oxoprop‐2‐eneselenal were calculated using HF, B3LYP and MP2 levels of theory and 6‐31+G* basis set by rotation around the related ‐C‐C‐ single bonds. In all of the above mentioned molecules, the s‐trans conformation was obtained as the most stable conformer with the 180° dihedral angle, apart from 3‐oxoprop‐2‐enethial and 3‐thioxoprop‐2‐eneselenal which their s-cis conformers were appeared more stability than related to s-trans forms. Their perpendicular geometries, with torsional angles approximately 90°, were as transition state for conformational interconversion between the two global minima forms. Cyclic structures all of the above mentioned molecules were unstable than their linear forms.

NMR Study of Conformational Exchange and Double-Well Proton Potential in Intramolecular Hydrogen Bonds in Monoanions of Succinic Acid and Derivatives

We present a (1)H, (2)H, and (13)C NMR study of the monoanions of succinic (1), meso- and rac-dimethylsuccinic (2, 3), and methylsuccinic (4) acids (with tetraalkylammonium as the counterion) dissolved in CDF(3)/CDF(2)Cl at 300-120 K. In all four monoanions, the carboxylic groups are linked by a short intramolecular OHO hydrogen bond revealed by the bridging-proton chemical shift of about 20 ppm. We show that the flexibility of the carbon skeleton allows for two gauche isomers in monoanions 1, 2, and 4, interconverting through experimental energy barriers of 10-15 kcal/mol (the process itself and the energy barrier are also reproduced in MP2/6-311++G** calculations). In 3, one of the gauche forms is absent because of the steric repulsion of the methyl groups. In all four monoanions, the bridging proton is located in a double-well potential and subject, at least to some extent, to proton tautomerism, for which we estimate the two proton positions to be separated by ca. 0.2 Å. In 1 and 3, the proton potential is symmetric. In 2, slowing the conformational interconversion introduces an asymmetry to the proton potential, an effect that might be strong enough even to synchronize the proton tautomerism with the interconversion of the two gauche forms. In 4, the asymmetry of the proton potential is due to the asymmetric substitution. The intramolecular H-bond is likely to remain intact during the interconversion of the gauche forms in 1, 3, and 4, whereas the situation in 2 is less clear.

Ab Initio Study of Conformational Properties of Heteroatom-Containing 1,2-Bisketene Analogues

Minimum-energy and transition-state geometries of 4-oxobuta-1,3-diene-1-thione, buta-1,3-diene-1,4-dithione, 4-selenoxobuta-1,3-diene-1-thione, 4-selenoxobuta-1,3-diene-1-one, and buta-1,3-diene-1,4-diselenone were calculated using HF, B3LYP, and MP2 levels of theory and 6–31 + G* basis set by rotation around the related ‒C‒C‒ single bonds. In all of the above-mentioned molecules, the s-trans conformation was obtained as the most stable conformer with the 180° dihedral angle. In buta-1,3-diene-1,4-dithione, 4-selenoxobuta-1,3-diene-1-thione, and buta-1,3-diene-1,4-diselenone, the s-cis form of these compounds corresponded to the other energy-minimum geometry. Their skew geometries, with torsional angles approximately 100°, were a transition state for conformational interconversion between the two global minima forms. In 4-oxobuta-1,3-diene-1-thione and 4-selenoxobuta-1,3-diene-1-one, geometries with the C˭C‒C˭C dihedral angles about 51 and 43° (respectively) were attributed to the second energy-minimum geometry. Transition-state structures from both molecules were found in the torsional angles at about 0 and 100°. Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file. GRAPHICAL ABSTRACT

Three-component conformational equilibria of some flexible pyrrolidin-2-(thi)ones in solution by NMR data ( δC, δH, and nJHH) and their DFT predictions: a confrontation of different approaches

Three standard gas-phase B3LYP/6-31G( d) methods of the analysis of δ C, δ H, and J HH NMR data for solutions initially used for the title γ-lactams 1a– c led to conflicting findings on fractional populations ηs of their fast interconverting conformers A– C, which were also inconsistent with energy data. In order to find the source(s) of these discrepancies, several additional DFT computations were carried out at the double- and triple-zeta theory level with simultaneous modeling of the solutions in explicit solvents with the COSMO or IEF-PCM technique. The WC04/WP04 functionals and IGLO-II (or IGLO-III) basis set were applied for predicting δ C/ δ H, and J HH data, respectively. The limits of efficiency and accuracy of a few current NMR-oriented computational protocols were determined by their specific use to the main forms of 1a– c treated as test cases. Thus, an unreliability of the modified Karplus-type equation for this purpose was shown. In turn, only the use of DFT-D3 corrections for the attractive van der Waals dispersion interactions (London forces) not present in conventional DFT, to Gibbs free energies (Δ G) estimated for the forms A– C of 1a– c in solution, yielded energetics and so populations ( η Gs) compatible within ±15% (only ±2%, for 1a) with the best results found by considering the 1H NMR data. These η Hs were found by a linear regression of GIAO-predicted δ H sets reproducing experiment in the best way ( r 2>0.9996, for 1a and 1b, r 2=0.9970, for 1c with strongly degenerated δ Hs). As for η Js, they permitted only for evaluations of the ratios ( A+ B)/ C, excepting sufficiently differentiated J HHs ( 1b in acetone). In contrast, an application of δ Cs for assessing η Cs was unsuccessful. Selected findings were finally compared with the DP4-probability results ( η DP4s) and fairly good agreement was found. The greatest divergence in ηs exists for the C S bond-containing object 1b, what suggests a large effect of the intramolecular London forces on its structure and properties. The present results should be useful guidelines for NMR studies on the other multi-conformer systems in rapid equilibrium between more than two energetically feasible forms.

Mouse FKBP23 mediates conformer-specific functions of BiP by catalyzing Pro117cis/trans isomerization

FK506-binding proteins (FKBPs) are cellular receptors for the immunosuppressant FK506 and rapamycin. They belong to the ubiquitous peptidyl-prolyl cis/trans isomerases (PPIases) family, which can catalyze the cis/trans isomerization of peptidyl-prolyl bond in peptides and proteins. In previous work, we revealed that mouse FKBP23 binds immunoglobulin binding protein (BiP), the major heat shock protein (Hsp) 70 chaperone in the ER, and the binding is interrelated with [Ca2+]. Furthermore, the binding can suppress the ATPase activity of BiP through the PPIase activity of FKBP23. In this work, FKBP23 is demonstrated to mediate functions of BiP by catalyzing the Pro117cis/trans conformational interconversion in the ATPase domain of BiP. This result may provide new understanding to the novel role of PPIase as a molecular switch.

Prolyl cis/trans isomerase signalling pathways in cancer

It is an emerging view that in many cases cell signalling relies on slow conformational interconversions of the backbone of key proteins as exemplified by the prolyl cis/trans isomerization, and that prolyl cis/trans isomerases (PPIases), such as cyclophilins, FK506-binding proteins and the parvulin-like Pin1, serve to integrate temporally and spatially protein conformers with signalling events. The causal relationship between prolyl cis/trans isomerization catalysis, malignant transformation and tumour progression is not yet fully understood because of the pleiotropic biochemical effects characterizing these enzymes. However, recent studies on the role of cyclophilins and Pin1 indicate that PPIases utilize isomerization catalysis on client proteins under physiological and pathophysiological conditions. This knowledge could offer new cancer intervention strategies based on the development of isoenzyme-specific, tissue-specific and organelle-specific PPIase inhibitors.

Critical Roles of Interactions among Switch I-preceding Residues and between Switch II and Its Neighboring α-Helix in Conformational Dynamics of the GTP-bound Ras Family Small GTPases

GTP-bound forms of Ras family small GTPases exhibit dynamic equilibrium between two interconverting conformations, "inactive" state 1 and "active" state 2. A great variation exists in their state distribution; H-Ras mainly adopts state 2, whereas M-Ras predominantly adopts state 1. Our previous studies based on comparison of crystal structures representing state 1 and state 2 revealed the importance of the hydrogen-bonding interactions of two flexible effector-interacting regions, switch I and switch II, with the γ-phosphate of GTP in establishing state 2 conformation. However, failure to obtain both state structures from a single protein hampered further analysis of state transition mechanisms. Here, we succeed in solving two crystal structures corresponding to state 1 and state 2 from a single Ras polypeptide, M-RasD41E, carrying an H-Ras-type substitution in residue 41, immediately preceding switch I, in complex with guanosine 5'-(β,γ-imido)triphosphate. Comparison among the two structures and other state 1 and state 2 structures of H-Ras/M-Ras reveal two new structural features playing critical roles in state dynamics; interaction of residues 31/41 (H-Ras/M-Ras) with residues 29/39 and 30/40, which induces a conformational change of switch I favoring its interaction with the γ-phosphate, and the hydrogen-bonding interaction of switch II with its neighboring α-helix, α3-helix, which induces a conformational change of switch II favoring its interaction with the γ-phosphate. The importance of the latter interaction is proved by mutational analyses of the residues involved in hydrogen bonding. These results define the two novel functional regions playing critical roles during state transition.