Binding Pockets and Pathways for Dioxygen through the KijD3 N‐Oxygenase in Complex with Flavin Mononucleotide Cofactor and a 3‐Aminoglucose Substrate: Predictions from Molecular Dynamics Simulations

In this work, two protein systems, Kij3D? FMN? AKM? O₂ and Kij3D? FMN? O₂, made of KijD3 N‐oxygenase, flavin mononucleotide (FMN) cofactor, dTDP‐3‐amino‐2,3,6‐trideoxy‐4‐keto‐3‐methyl‐D ‐glucose (AKM) substrate, and dioxygen (O₂), have been assembled by adding a molecule of O₂, and removing (or not) AKM, to crystal data for the Kij3D? FMN? AKM complex. Egress of AKM and O₂ from these systems was then investigated by applying a tiny external random force, in turn, to their center of mass in the course of molecular dynamics in explicit H₂O. It turned out that the wide AKM channel, even when emptied, does not constitute the main route for O₂ egress. Other routes appear to be also viable, while various binding pockets (BPs) outside the active center are prone to trap O₂. By reversing the reasoning, these can also be considered as routes for uptake of O₂ by the protein, before or after AKM uptake, while BPs may serve as reservoirs of O₂. This shows that the small molecule O₂ is capable of permeating the protein by exploiting all nearby interstices that are created on thermal fluctuations of the protein, rather than having necessarily to look for farther, permanent channels.     

On Dioxygen and Substrate Access to Soluble Methane Monooxygenases: An all‐Atom Molecular Dynamics Investigation in Water Solution

In a preliminary exploration of the dummy model for diiron proteins, random‐acceleration molecular dynamics (RAMD) revealed that a pure four‐helix bundle structure, like hemerythrin, constitutes an efficient cage for dioxygen (O₂), which can only leave from defined, albeit very broad, gates. However, this well ordered structure does not constitute an archetype on which to compare O₂ permeation of other diiron proteins, like the complex of soluble methane monooxygenase hydroxylase with the regulatory protein (sMMOH‐MMOB). The reason is that with this complex, unlike hemerythrin, the four helices of the four‐helix bundle are heavily bent, and RAMD showed that most traps for O₂ lie outside them. It was also observed that, in spite of a nearly identical van der Waals radius for O₂ and the natural substrate CH₄, the latter behaves under RAMD as a bulkier molecule than O₂, requiring a higher external force to be brought out of sMMOH‐MMOB along trajectories of viable length. All that determined with sMMOH‐MMOB multiple gates and multiple pathways to each of them through several binding pockets, for both O₂ and CH₄. Of the two equally preferred pathways for O₂, at right angle with one another, one proved to be in accordance with the Xe‐atom mapping for sMMOH. In contrast, none of the pathways identified for CH₄ proved to be in accordance with such mapping, CH₄ looking for more open avenues instead.     

On Dioxygen Permeation through a Dehydrogenase‐Pyrroloquinoline Quinone Complex. A Molecular‐Dynamics Investigation

In this work, an all atom model of the quinoprotein dehydrogenase PqqC in complex with the PQQ (=4,5‐dihydro‐4,5‐dioxo‐1H‐pyrrolo[2,3‐f]quinoline‐2,7,9‐tricarboxylic acid) cofactor and dioxygen (O₂), solvated with TIP3 water in periodic boxes, was subjected to random‐acceleration molecular dynamics (RAMD). It was found that O₂ leaves the active binding pocket, in front of PQQ, to get to the solvent, as easily as with a variety of other O₂‐activating enzymes, O₂ carriers, and gas‐sensing proteins. The shortest pathway, orthogonal to the center of the mean plane of PQQ, was largely preferred by O₂ over pathways slightly deviating from this line. These observations challenge the interpretation of an impermeable active binding pocket of PqqC‐PQQ, as drawn from both X‐ray diffraction data of the crystal at low temperature and physiological experimentation.     

On the Quest of Dioxygen by Monomeric Sarcosine Oxidase. A Molecular Dynamics Investigation

It is reported here on random acceleration molecular dynamics (RAMD) simulations with the 2GF3 bacterial monomeric sarcosine oxidase (MSOX), O₂, and furoic acid in place of sarcosine, solvated by TIP3 H₂O in a periodic box. An external tiny force, acting randomly on O₂, accelerated its relocation, from the center of activation between residue K265 and the si face of the flavin ring of the flavin adenine dinucleotide cofactor, to the surrounding solvent. Only three of the four O₂ gates previously described for this system along a composite method technique were identified, while two more major O₂ gates were found. The RAMD simulations also revealed that the same gate can be reached by O₂ along different pathways, often involving traps for O₂. Both the residence time of O₂ in the traps, and the total trajectory time for O₂ getting to the solvent, could be evaluated. The new quick pathways discovered here suggest that O₂ exploits all nearby interstices created by the thermal fluctuations of the protein, not having necessarily to look for the permanent large channel used for uptake of the FADH cofactor. To this regard, MSOX resembles closely KijD3 N‐oxygenase. These observations solicit experimental substantiation, in a long term aim at discovering whether gates and pathways for the small gaseous ligands inside the proteins are under Darwinian functional evolution or merely stochastic control operates.     

Unveiling the Pathways of Dioxygen Through the C2 Component of the Environmentally Relevant Monooxygenase p‐Hydroxyphenylacetate Hydroxylase from Acinetobacter baumannii: A Molecular Dynamics Investigation

In this work, models of the homotetrameric C2 component of the monooxygenase p‐hydroxyphenylacetate hydroxylase from Acinetobacter baumannii, in complex with dioxygen (O₂) and, or not, the substrate p‐hydroxyphenylacetate (HPA) were built. Both models proved to be amenable to random‐acceleration molecular dynamics (RAMD) simulations, whereby a tiny randomly oriented external force, acting on O₂ at the active site in front of flavin mononucleotide (FMNH^?), accelerated displacement of O₂ toward the bulk solvent. This allowed us to carry out a sufficiently large number of RAMD simulations to be of statistical significance. The two systems behaved very similarly under RAMD, except for O₂ leaving the active site more easily in the absence of HPA, but then finding similar obstacles in getting to the gate as when the active site was sheltered by HPA. This challenges previous conclusions that HPA can only reach the active center after that the C4aOOH derivative of FMNH^? is formed, requiring uptake of O₂ at the active site before HPA. According to these RAMD simulations, O₂ could well get to FMNH^? also in the presence of the substrate at the active site.     

On the Permeation by Dioxygen of Urate Oxidase from Aspergillus flavus in Complex with Xanthine Anion: Dioxygen Pathways and a Portrait of the Enzyme Cavities from Molecular Dynamics Simulations in Water Solution

This work describes molecular dynamics (MD) simulations in aqueous media for the complex of the homotetrameric urate oxidase (UOX) from Aspergillus flavus with xanthine anion ( 5 ) in the presence of dioxygen (O₂). After 196.6 ns of trajectory from unrestrained MD, a O₂ molecule was observed leaving the bulk solvent to penetrate the enzyme between two subunits, A/C. From here, the same O₂ molecule was observed migrating, across subunit C, to the hydrophobic cavity that shares residue V227 with the active site. The latter was finally attained, after 378.3 ns of trajectory, with O₂ at a bonding distance from 5 . The reverse same O₂ pathway, from 5 to the bulk solvent, was observed as preferred pathway under random acceleration MD (RAMD), where an external, randomly oriented force was acting on O₂. Both MD and RAMD simulations revealed several cavities populated by O₂ during its migration from the bulk solvent to the active site or backwards. Paying attention to the last hydrophobic cavity that apparently serves as O₂ reservoir for the active site, it was noticed that its volume undergoes ample fluctuations during the MD simulation, as expected from the thermal motion of a flexible protein, independently from the particular subunit and no matter whether the cavity is filled or not by O₂.     

On the Pathways of Biologically Relevant Diatomic Gases through Proteins. Dioxygen and Heme Oxygenase from the Perspective of Molecular Dynamics

This work deals with dioxygen (O₂) binding sites and pathways through inducible human heme oxygenase (HO‐1). The experimentally known distal binding site 1, and sites 2–3 above it, could be reproduced by means of non‐deterministic random‐acceleration molecular‐dynamics (RAMD) simulations. In addition, RAMD revealed the proximal binding site 5, a deeply‐seated binding site 4, which lies behind heme, as well as a few gates communicating with the external medium. In getting from site 1 to the main gate, which lies on the protein front opposed to site 4, O₂ follows chiefly the shortest direct pathway. Less frequently, O₂ visits intermediate sites 2, 4, or 5 along longer pathways. A similarity between HO‐1, myoglobin, and cytoglobin in using, for diatomic gas delivery, the direct shortest pathway from the heme center to the surrounding medium, is emphasized. Otherwise, comparing other proteins and diatomic gases, each system reveals its peculiarities as to sites, gates, and pathways. Thus, relating these properties to the physiological functions of the proteins remains in general a challenge for future studies.     

Binding Pockets and Permeation Channels for Dioxygen through Cofactorless 3‐Hydroxy‐2‐methylquinolin‐4‐one 2,4‐Dioxygenase in Association with Its Natural Substrate, 3‐Hydroxy‐2‐methylquinolin‐4(1H)‐one. A Perspective from Molecular Dynamics Simulations

This work describes an investigation of pathways and binging pockets (BPs) for dioxygen (O₂) through the cofactorless oxygenase 3‐hydroxy‐2‐methylquinolin‐4‐one 2,4‐dioxygenase in complex with its natural substrate, 3‐hydroxy‐2‐methylquinolin‐4(1H)‐one, in aqueous solution. The investigation tool was random‐acceleration molecular dynamics (RAMD), whereby a tiny, randomly oriented external force is applied to O₂ in order to accelerate its movements. In doing that, care was taken that the external force only continues, if O₂ moves along a direction for a given period of time, otherwise the force changed direction randomly. Gates for expulsion of O₂ from the protein, which can also be taken as gates for O₂ uptake, were found throughout almost the whole external surface of the protein, alongside a variety of BPs for O₂. The most exploited gates and BPs were not found to correspond to the single gate and BP proposed previously from the examination of the static model from X‐ray diffraction analysis of this system. Therefore, experimental investigations of this system that go beyond the static model are urgently needed.     

On Dioxygen Permeation of MaL Laccase from the Thermophilic Fungus Melanocarpus albomyces: An all‐Atom Molecular Dynamics Investigation

In this article, biased molecular dynamics (MD) simulations of O₂ egress from the active center of MaL laccase toward the bulk solvent were described. Parameterization of the set of four Cu(II) ions, in the framework of CHARMM‐36 FF, was carried out on a recent dummy‐atom model that takes into account the Jahn–Teller effect. By carrying out a number of statistically relevant MD simulations, under a tiny randomly oriented external force applied to the molecule O₂, three preferred gates for O₂ egress from the enzyme and a few intermediate binding pockets (BPs) for O₂ were visible; all the gates and pockets were located on two of the three domains. This wide distribution of preferred gates notwithstanding the molecule O₂ was seen to follow specific pathways, exploiting consistently the interstices created by the enzyme thermal fluctuations. These are features that can be imagined to have evolved to make MaL laccase extremely efficient as catalysts in various reactions that require O₂.     

On the Pathways for CO Egress from Carboxy Human Cytoglobin. A Molecular‐Dynamics Investigation

This work discloses two bona fide gates through which the CO ligand can leave the distal cavity of carboxy human cytoglobin, reaching the solvent. The investigation was based on molecular dynamics, aided by a minimal randomly‐oriented force applied to the ligand. The shortest pathway progresses toward the main gate, H81‐R84, in the open state, with the H81 imidazole moiety turned toward the solvent. A longer pathway develops toward the diametrically opposed W31‐W151 gate. In between, CO may be entrapped into binding cavities, either along the path toward the gates, or in a cul‐de‐sac, from which CO may even be incapable to escape. This behavior contrasts with carboxy myoglobin, where the corresponding H64 gate, when opened, is the sole used by CO to get to the solvent. These observations, which could hold also for other small ligands of biological interest, such as O₂, NO, and NO$\rm{{_{3}^{-}}}$ , provide an answer to a neglected aspect of the mysterious six‐coordinated globins.     

Molecular Dynamics Simulation of Dioxygen Pathways through Mini Singlet Oxygen Generator (miniSOG), a Genetically Encoded Marker and Killer Protein

In this work, molecular dynamics (MD) simulations of the permeation of proteins by small gases of biological significance have been extended from gas carrier, sensor, and enzymatic proteins to genetically encoded tags and killer proteins. To this end, miniSOG was taken as an example of current high interest, using a biased form of MD, called random‐acceleration MD. Various egress gates and binding pockets for dioxygen, as an indistinguishable mimic of singlet dioxygen, were found on both above and below the isoalloxazine plane of the flavin mononucleotide cofactor in miniSOG. Of such gates and binding pockets, those lying within two opposite cones, coaxial with a line normal to the isoalloxazine plane, and with the vertex at the center of such a plane are those most visited by the escaping gas molecule. Out of residues most capable of quenching ¹O₂, Y30, lying near the base of one such a cone, and H85, near the base of the opposite cone, are held to be most responsible for the reduced quantum yield of ¹O₂ with folded miniSOG with respect to free flavin mononucleotide in solution.     

On 3LEZ,a Deep‐Sea Halophilic Protein with in vitro Class‐A β‐Lactamase Activity: Molecular‐Dynamics,Docking, and Reactivity Simulations

This work shows that a deep‐sea protein, 3LEZ, with known in vitro β‐lactamase activity, proved stable, substantially in the conformation detected by X‐ray diffraction of the crystal, when subjected to molecular‐dynamics (MD) simulations under conditions compatible with shallow seas. Docking simulations showed that the β‐lactamase active site S85 of 3LEZ (S70 in Ambler numbering) is the preferential binding pocket for not only β‐lactam antibiotics and inhibitors, but, surprisingly, also for a wide variety of other biologically active compounds in various chemical classes, including marine metabolites. In line with the in vitro β‐lactamase activity, a) affinities on docking β‐lactam antibiotics and inhibitors onto 3LEZ were found to roughly parallel published K_m and K_i values, obtained from Michaelis? Menten kinetics under room conditions, and b) DFT calculations agreed with experiments that the irreversible reaction of the β‐lactamase inhibitor clavulanic acid with the whole S85 catalytic center of 3LEZ is spontaneous. These observations must be viewed in the light that a) the compounds in other chemical classes showed comparable affinities, and, in some cases, even higher than β‐lactams, for the S85 active site, b) K_m and K_i data are not available at the high hydrostatic pressure of the deep sea, where 3LEZ is believed to have evolved, c) an inverse order of affinities for the β‐lactams, with respect to both experimentation and simulations at room conditions, was observed from comparative docking simulations with 3LEZ derived from MD under high hydrostatic pressure. Although MD requires a general assessment for high hydrostatic pressure before c) above is given the same weight as all other observations, this work questions the conclusion that the in vitro determined β‐lactamase activity represents the ecological role of 3LEZ.     

Gates and Binding Pockets for Nitric Oxide with Cytochrome c′, According to Molecular Dynamics

Random‐acceleration molecular‐dynamics (RAMD) simulations with models of homodimeric 6‐ligated distal‐NO and 5‐ligated proximal‐NO cytochrome c′ complexes, in TIP3 H₂O, showed two distinct, non‐intercommunicating worlds. In the framework of a long cavity formed by four protein helices with heme at one extremity, NO was observed to follow different pathways with the two complexes to reach the solvent. With the 6‐ligated complex, NO was observed to progress by exploiting protein internal channels created by thermal fluctuations, and be temporarily trapped into binding pockets before reaching the preferred gate at the heme end of the cavity. In contrast, with the 5‐ligated complex, NO was observed to surface the solvent‐exposed helix 7, up to a gate at the other extremity of the protein, only occasionally finding an earlier, direct way out toward the solvent. That only bulk NO gets involved in forming the 5‐ligated proximal‐NO complex is in agreement with previous experimental observations, while the occurrence of binding pockets suggests that also reservoir NO might play a role with the distal‐NO complex.     

New Vistas on the Recruiting of Ferrous Iron and Dioxygen by Ferritins: A Case Study of the Escherichia coli 24‐mer Ferritin by All‐Atom Molecular Dynamics in Aqueous Medium

It is shown here that Fe²⁺ and O₂ ligands are displaced from the ferroxidase center of the C1 four‐helix bundle of E. coli 24‐mer ferritin under molecular dynamics (MD) aided by a randomly oriented external force applied to the ligand. Under these conditions, ligand egress toward the external aqueous medium occurs preferentially from the same four‐helix bundle, in the case of O₂, or other bundle, in the case of Fe². Viewing ligand egress from the protein as the microscopic reverse of ligand influx into the protein under unbiased MD, these findings challenge current views that preferential gates for recruitment of Fe²⁺ are 3‐fold channels with human ferritin, or the short path from the ferroxidase center to H93 with bacterial ferritins.     

Restoring Histone Deacetylase Activity by Waste Product Release. A View from Molecular Mechanics Simulations with Mammalian HDAC8

HDAC8 is a Zn^II‐based, single‐peptide mammalian histone deacetylase that is localized mainly in the cytoskeleton of smooth muscle cells, thus regulating muscle contractility. HDACs are also widely involved in cellular processes, ranging from cell differentiation to proliferation, senescence, and apoptosis; in particular, protecting a telomerase activator from ubiquitin‐mediated degradation. How HDACs can eliminate the hydrolytic reaction products, in order that the process of deacetylation of the acetyllysine moiety of histones can take place again, has long been debated in the scientific literature, without reaching any firm conclusion, however. This question is the subject of the present work, carried out along a theoretical line that is capable of describing the whole pathway followed by the acetate product (ACT). A model was built here on the crystal data for the Y306F‐mutated HDAC8 complex with a diacetylated peptide of the p53‐tumor‐suppressor class. That was followed by manually hydrolyzing the acetylated moiety bound to Zn^II and discharging the monoacetylated peptide product (MAP). The latter was replaced by a H₂O molecule bound to Zn^II, while ACT was left free in the reaction cage. This Zn^II cluster was DFT‐parameterized for the ff99SB force field without any further bias. As the result of random‐acceleration molecular dynamics (RAMD) simulations, egress of ACT from the reaction cage toward the aqueous environment can follow three pathways. Two of them utilize the channel for peptide (or histone) uptake and are preferred, if ACT leaves the reaction center before MAP (or the deacetylated histone). The third pathway, developing along the internal channel, is available to ACT even if MAP is still in place.     

Uptake of Organohalide Pollutants,and Release of Partially Dehalogenated Products,by NpRdhA,a ‘Base‐Off’ Cob(II)alamin‐Dependent Reductive Dehalogenase from a Deep Sea Bacterium. A Molecular Dynamics Investigation

This work shows that, during MD aided by external tiny random forces, 3‐bromo‐4‐hydroxybenzoic acid (LHB), the product of reductive dehalogenation of 3,5‐dibromo‐4‐hydroxybenzoic acid (LBB) by the corrin‐based marine enzyme NpRdhA, is expelled along mainly the wide channel that connects the corrin to the external medium. In accordance, unbiased MD showed that LBB migrates relatively rapidly from the external medium to the inside of the channel, finally getting to the corrin active center of NpRdhA. The LBB pose, with bromide head and carboxylate tail nearly equidistant from the corrin Co ion, does not fit the results of previous automatic docking. Either the experimental structure of the NpRdhA‐LBB complex, or a quantum‐mechanical study of LBB at the corrin active site, are therefore urged.     

On the Dynamical Behavior of the Cysteine Dioxygenase‐l‐Cysteine Complex in the Presence of Free Dioxygen and l‐Cysteine

In this work, viable models of cysteine dioxygenase (CDO) and its complex with l ‐cysteine dianion were built for the first time, under strict adherence to the crystal structure from X‐ray diffraction studies, for all atom molecular dynamics (MD). Based on the CHARMM36 FF, the active site, featuring an octahedral dummy Fe(II) model, allowed us observing water exchange, which would have escaped attention with the more popular bonded models. Free dioxygen (O₂) and l ‐cysteine, added at the active site, could be observed being expelled toward the solvating medium under Random Accelerated Molecular Dynamics (RAMD) along major and minor pathways. Correspondingly, free dioxygen (O₂), added to the solvating medium, could be observed to follow the same above pathways in getting to the active site under unbiased MD. For the bulky l ‐cysteine, 600 ns of trajectory were insufficient for protein penetration, and the molecule was stuck at the protein borders. These models pave the way to free energy studies of ligand associations, devised to better clarify how this cardinal enzyme behaves in human metabolism.     

Molecular modeling reveals binding interface of γ‐tubulin with GCP4 and interactions with noscapinoids

The initiation of microtubule assembly within cells is guided by a cone shaped multi‐protein complex, γ‐tubulin ring complex (γTuRC) containing γ‐tubulin and atleast five other γ‐tubulin‐complex proteins (GCPs), i.e., GCP2, GCP3, GCP4, GCP5, and GCP6. The rim of γTuRC is a ring of γ‐tubulin molecules that interacts, via one of its longitudinal interfaces, with GCP2, GCP3, or GCP4 and, via other interface, with α/β?tubulin dimers recruited for the microtubule lattice formation. These interactions however, are not well understood in the absence of crystal structure of functional reconstitution of γTuRC subunits. In this study, we elucidate the atomic interactions between γ‐tubulin and GCP4 through computational techniques. We simulated two complexes of γ‐tubulin‐GCP4 complex (we called dimer1 and dimer2) for 25 ns to obtain a stable complex and calculated the ensemble average of binding free energies of ?158.82 and ?170.19 kcal/mol for dimer1 and ?79.53 and ?101.50 kcal/mol for dimer2 using MM‐PBSA and MM‐GBSA methods, respectively. These highly favourable binding free energy values points to very robust interactions between GCP4 and γ‐tubulin. From the results of the free‐energy decomposition and the computational alanine scanning calculation, we identified the amino acids crucial for the interaction of γ‐tubulin with GCP4, called hotspots. Furthermore, in the endeavour to identify chemical leads that might interact at the interface of γ‐tubulin‐GCP4 complex; we found a class of compounds based on the plant alkaloid, noscapine that binds with high affinity in a cavity close to γ‐tubulin‐GCP4 interface compared with previously reported compounds. All noscapinoids displayed stable interaction throughout the simulation, however, most robust interaction was observed for bromo‐noscapine followed by noscapine and amino‐noscapine. This offers a novel chemical scaffold for γ‐tubulin binding drugs near γ‐tubulin‐GCP4 interface. Proteins 2015; 83:827–843. © 2015 Wiley Periodicals, Inc.     

PASylation Enhances the Stability,Potency, and Plasma Half‐Life of Interferon α‐2a: A Molecular Dynamics Simulation

In this study, the effectiveness of PASylation in enhancing the potency and plasma half‐life of pharmaceutical proteins has been accredited as an alternative technique to the conventional methods such as PEGylation. Proline, alanine, and serine (PAS) chain has shown some advantages including biodegradability improvement and plasma half‐life enhancement while lacking immunogenicity or toxicity. Although some experimental studies have been performed to find the mechanism behind PASylation, the detailed mechanism of PAS effects on the pharmaceutical proteins has remained obscure, especially at the molecular level. In this study, the interaction of interferon α‐2a (IFN) and PAS chain is investigated using molecular dynamics simulation method. Several important parameters including secondary structure, root‐mean‐square distance, and solvent accessible surface area to investigate the stability, bioavailability, and bioactivity of the PASylated protein are studied. The results demonstrate that IFN conformation is not affected critically through PASylation while it results in improvement of the protein stability and bioactivity. Therefore, PASylation can be considered as a proper biological alternative technique to increase the plasma half‐life of the biopharmaceutical proteins through enlarging apparent volume. The proposed simulation represents a computational approach that would provide a basis for the study of PASylated pharmaceutical proteins for different future applications.     

Understanding How H‐NOX (Heme Nitric Oxide/Oxygen) Domain Works Needs First Clarifying How Diatomic Gases Are Relocated Inside This Sensing Protein. A Molecular‐Mechanics Approach

H‐NOX (Heme Nitric Oxide/Oxygen) domain has widespread occurrence, either standalone or associated with functional proteins, sending signals for functions that span from modulating vasodilation and neurotransmission with humans to competition and symbiosis with bacteria. Understanding how H‐NOX works, and possibly intervening on degeneration for health purposes, needs first clarifying how diatomic gases are relocated through this protein in relation to the deeply buried heme. To this end, a biased form of molecular dynamics, i.e., Random Accelaration Molecular Dynamics (RAMD), is used by applying a randomly oriented tiny force to heme‐dissociated CO of Nostoc sp. H‐NOX, while changing randomly the direction of the force, if CO travels less than specified for the evaluated block. The result is that a large area of the protein, comprising amino acids from serine 44 to leucine 67 along two adjacent helices, offers a broad portal to CO from the surrounding medium to the deeply buried heme. Most traffic is concentrated through a channel lined by tyrosine 49, valine 52, and leucine 67. This modifies the picture drawn from mapping Xe cavities on pressurizing Nostoc sp. H‐NOX with Xe gas. What is the main pathway with Xe‐cavity mapping becomes a minor pathway with RAMD, and vice versa. The reason is that the fluctuating protein under MD creates clefts for CO slipping through, as it is expected to occur in nature.